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Strosahl J, Ye K, Pazdro R. Novel insights into the pleiotropic health effects of growth differentiation factor 11 gained from genome-wide association studies in population biobanks. BMC Genomics 2024; 25:837. [PMID: 39237910 PMCID: PMC11378601 DOI: 10.1186/s12864-024-10710-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/14/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND Growth differentiation factor 11 (GDF11) is a member of the transforming growth factor-β (TGF-β) superfamily that has gained considerable attention over the last decade for its observed ability to reverse age-related deterioration of multiple tissues, including the heart. Yet as many researchers have struggled to confirm the cardioprotective and anti-aging effects of GDF11, the topic has grown increasingly controversial, and the field has reached an impasse. We postulated that a clearer understanding of GDF11 could be gained by investigating its health effects at the population level. METHODS AND RESULTS We employed a comprehensive strategy to interrogate results from genome-wide association studies in population Biobanks. Interestingly, phenome-wide association studies (PheWAS) of GDF11 tissue-specific cis-eQTLs revealed associations with asthma, immune function, lung function, and thyroid phenotypes. Furthermore, PheWAS of GDF11 genetic variants confirmed these results, revealing similar associations with asthma, immune function, lung function, and thyroid health. To complement these findings, we mined results from transcriptome-wide association studies, which uncovered associations between predicted tissue-specific GDF11 expression and the same health effects identified from PheWAS analyses. CONCLUSIONS In this study, we report novel relationships between GDF11 and disease, namely asthma and hypothyroidism, in contrast to its formerly assumed role as a rejuvenating factor in basic aging and cardiovascular health. We propose that these associations are mediated through the involvement of GDF11 in inflammatory signaling pathways. Taken together, these findings provide new insights into the health effects of GDF11 at the population level and warrant future studies investigating the role of GDF11 in these specific health conditions.
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Affiliation(s)
- Jessica Strosahl
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Robert Pazdro
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA.
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2
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Turi KN, Li Y, Xu Y, Gebretsadik T, Rosas-Salazar C, Wiggins DA, McKennan C, Newcomb D, Gern JE, Hartert TV. The association of infant urinary adrenal steroids with the risk of childhood asthma development. Ann Allergy Asthma Immunol 2024; 133:159-167.e3. [PMID: 38631429 PMCID: PMC11298305 DOI: 10.1016/j.anai.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Adrenal steroids play important roles in early-life development. However, our understanding of the effects of perinatal adrenal steroids on the development of childhood asthma is incomplete. OBJECTIVE To evaluate the associations between early-life adrenal steroid levels and childhood asthma. METHODS Participants included the Infant Susceptibility to Pulmonary Infections and Asthma following Respiratory Syncytial Virus Exposure birth cohort children with untargeted urinary metabolomics data measured during early infancy (n = 264) and nasal immune mediator data measured concurrently at age 2 to 6 months (n = 76). A total of 11 adrenal steroid compounds were identified using untargeted metabolomics and 6 asthma-relevant nasal immune mediators from multiplex assays were a priori selected. Current asthma at ages 5 and 6 years was ascertained using validated questionnaires. Associations were tested using logistic and linear regression with confounders adjustment. RESULTS Pregnenetriol disulfate (adjusted odds ratio [aOR] = 0.20, 95% CI = 0.06-0.68) and 3a,21-dihydroxy-5b-pregnane-11,20-dione-21-glucuronide (aOR = 0.34, 95% CI = 0.14-0.75) were inversely associated with childhood asthma at 5 and 6 years after multiple testing adjustment. There was a significant interaction effect of pregnanediol-3-glucuronide by biological sex assigned at birth (aOR = 0.11, 95% CI = 0.02-0.51, for those with female sex) on childhood asthma. Pregnenetriol disulfate was inversely associated with granulocyte-macrophage colony-stimulating factor (β = -0.45, q-value = 0.05). 3a,21-dihydroxy-5b-pregnane-11,20-dione 21-glucuronide was inversely associated with interleukin [IL]-4 (β = -0.29, q-value = 0.02), IL-5 (β = -0.35, q-value = 0.006), IL-13 (β = -0.26, q-value = 0.02), granulocyte-macrophage colony-stimulating factor (β = -0.35, q-value = 0.006), and fibroblast growth factor-β (β = -0.24, q-value = 0.01) after multiple testing adjustment. CONCLUSION The inverse association between adrenal steroids downstream of progesterone and 17-hydroxypregnenolone and the odds of childhood asthma and nasopharyngeal type 2 immune biomarkers suggest that increased early-life adrenal steroids may suppress type 2 inflammation and protect against the development of childhood asthma.
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Affiliation(s)
- Kedir N Turi
- Department of Epidemiology and Biostatistics, Indiana University, Bloomington, Indiana.
| | - Yajing Li
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tebeb Gebretsadik
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Derek A Wiggins
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Chris McKennan
- Department of Statistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Dawn Newcomb
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin
| | - Tina V Hartert
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
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3
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Kermani NZ, Li CX, Versi A, Badi Y, Sun K, Abdel-Aziz MI, Bonatti M, Maitland-van der Zee AH, Djukanovic R, Wheelock Å, Dahlen SE, Howarth P, Guo Y, Chung KF, Adcock IM. Endotypes of severe neutrophilic and eosinophilic asthma from multi-omics integration of U-BIOPRED sputum samples. Clin Transl Med 2024; 14:e1771. [PMID: 39073027 DOI: 10.1002/ctm2.1771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Clustering approaches using single omics platforms are increasingly used to characterise molecular phenotypes of eosinophilic and neutrophilic asthma. Effective integration of multi-omics platforms should lead towards greater refinement of asthma endotypes across molecular dimensions and indicate key targets for intervention or biomarker development. OBJECTIVES To determine whether multi-omics integration of sputum leads to improved granularity of the molecular classification of severe asthma. METHODS We analyzed six -omics data blocks-microarray transcriptomics, gene set variation analysis of microarray transcriptomics, SomaSCAN proteomics assay, shotgun proteomics, 16S microbiome sequencing, and shotgun metagenomic sequencing-from induced sputum samples of 57 severe asthma patients, 15 mild-moderate asthma patients, and 13 healthy volunteers in the U-BIOPRED European cohort. We used Monti consensus clustering algorithm for aggregation of clustering results and Similarity Network Fusion to integrate the 6 multi-omics datasets of the 72 asthmatics. RESULTS Five stable omics-associated clusters were identified (OACs). OAC1 had the best lung function with the least number of severe asthmatics with sputum paucigranulocytic inflammation. OAC5 also had fewer severe asthma patients but the highest incidence of atopy and allergic rhinitis, with paucigranulocytic inflammation. OAC3 comprised only severe asthmatics with the highest sputum eosinophilia. OAC2 had the highest sputum neutrophilia followed by OAC4 with both clusters consisting of mostly severe asthma but with more ex/current smokers in OAC4. Compared to OAC4, there was higher incidence of nasal polyps, allergic rhinitis, and eczema in OAC2. OAC2 had microbial dysbiosis with abundant Moraxella catarrhalis and Haemophilus influenzae. OAC4 was associated with pathways linked to IL-22 cytokine activation, with the prediction of therapeutic response to anti-IL22 antibody therapy. CONCLUSION Multi-omics analysis of sputum in asthma has defined with greater granularity the asthma endotypes linked to neutrophilic and eosinophilic inflammation. Modelling diverse types of high-dimensional interactions will contribute to a more comprehensive understanding of complex endotypes. KEY POINTS Unsupervised clustering on sputum multi-omics of asthma subjects identified 3 out of 5 clusters with predominantly severe asthma. One severe asthma cluster was linked to type 2 inflammation and sputum eosinophilia while the other 2 clusters to sputum neutrophilia. One severe neutrophilic asthma cluster was linked to Moraxella catarrhalis and to a lesser extent Haemophilus influenzae while the second cluster to activation of IL-22.
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Affiliation(s)
- Nazanin Zounemat Kermani
- National Heart and Lung Institute, Imperial College London, London, UK
- Data Science Institute, Imperial College London, London, UK
| | - Chuan-Xing Li
- Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ali Versi
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Yusef Badi
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kai Sun
- Data Science Institute, Imperial College London, London, UK
| | - Mahmoud I Abdel-Aziz
- Department of Pulmonology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Martina Bonatti
- Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Ratko Djukanovic
- NIHR Southampton Respiratory Biomedical Research Unit and Clinical and Experimental Sciences, Southampton, UK
| | - Åsa Wheelock
- Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Institute of Environmental Medicine, Centre for Allergy Research, Karolinska Institute, Stockholm, Sweden
| | - Sven-Erik Dahlen
- Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Peter Howarth
- NIHR Southampton Respiratory Biomedical Research Unit and Clinical and Experimental Sciences, Southampton, UK
| | - Yike Guo
- Data Science Institute, Imperial College London, London, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
- Data Science Institute, Imperial College London, London, UK
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, London, UK
- Data Science Institute, Imperial College London, London, UK
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4
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Yoshimura H, Takeda Y, Shirai Y, Yamamoto M, Nakatsubo D, Amiya S, Enomoto T, Hara R, Adachi Y, Edahiro R, Yaga M, Masuhiro K, Koba T, Itoh-Takahashi M, Nakayama M, Takata S, Hosono Y, Obata S, Nishide M, Hata A, Yanagawa M, Namba S, Iwata M, Hamano M, Hirata H, Koyama S, Iwahori K, Nagatomo I, Suga Y, Miyake K, Shiroyama T, Fukushima K, Futami S, Naito Y, Kawasaki T, Mizuguchi K, Kawashima Y, Yamanishi Y, Adachi J, Nogami-Itoh M, Ueki S, Kumanogoh A. Galectin-10 in serum extracellular vesicles reflects asthma pathophysiology. J Allergy Clin Immunol 2024; 153:1268-1281. [PMID: 38551536 DOI: 10.1016/j.jaci.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 11/13/2023] [Accepted: 12/07/2023] [Indexed: 05/07/2024]
Abstract
BACKGROUND Novel biomarkers (BMs) are urgently needed for bronchial asthma (BA) with various phenotypes and endotypes. OBJECTIVE We sought to identify novel BMs reflecting tissue pathology from serum extracellular vesicles (EVs). METHODS We performed data-independent acquisition of serum EVs from 4 healthy controls, 4 noneosinophilic asthma (NEA) patients, and 4 eosinophilic asthma (EA) patients to identify novel BMs for BA. We confirmed EA-specific BMs via data-independent acquisition validation in 61 BA patients and 23 controls. To further validate these findings, we performed data-independent acquisition for 6 patients with chronic rhinosinusitis without nasal polyps and 7 patients with chronic rhinosinusitis with nasal polyps. RESULTS We identified 3032 proteins, 23 of which exhibited differential expression in EA. Ingenuity pathway analysis revealed that protein signatures from each phenotype reflected disease characteristics. Validation revealed 5 EA-specific BMs, including galectin-10 (Gal10), eosinophil peroxidase, major basic protein, eosinophil-derived neurotoxin, and arachidonate 15-lipoxygenase. The potential of Gal10 in EVs was superior to that of eosinophils in terms of diagnostic capability and detection of airway obstruction. In rhinosinusitis patients, 1752 and 8413 proteins were identified from EVs and tissues, respectively. Among 11 BMs identified in EVs and tissues from patients with chronic rhinosinusitis with nasal polyps, 5 (including Gal10 and eosinophil peroxidase) showed significant correlations between EVs and tissues. Gal10 release from EVs was implicated in eosinophil extracellular trapped cell death in vitro and in vivo. CONCLUSION Novel BMs such as Gal10 from serum EVs reflect disease pathophysiology in BA and may represent a new target for liquid biopsy approaches.
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Affiliation(s)
- Hanako Yoshimura
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
| | - Yuya Shirai
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Makoto Yamamoto
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Daisuke Nakatsubo
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Saori Amiya
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takatoshi Enomoto
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Reina Hara
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuichi Adachi
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Ryuya Edahiro
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Moto Yaga
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kentaro Masuhiro
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Taro Koba
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Miho Itoh-Takahashi
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Mana Nakayama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - So Takata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuki Hosono
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Sho Obata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Akinori Hata
- Department of Radiology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Masahiro Yanagawa
- Department of Radiology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Satoko Namba
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Momoko Hamano
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kota Iwahori
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yasuhiko Suga
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kotaro Miyake
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takayuki Shiroyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kiyoharu Fukushima
- Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, Japan
| | - Shinji Futami
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yujiro Naito
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takahiro Kawasaki
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan; Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, Japan
| | - Kenji Mizuguchi
- Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan; Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan; Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Nagoya, Aichi, Japan
| | - Jun Adachi
- Laboratory of Proteomics for Drug Discovery Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Mari Nogami-Itoh
- Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Shigeharu Ueki
- Department of General Internal Medicine and Clinical Laboratory Medicine, University Graduate School of Medicine, Hondo, Akita, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan; Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, Japan; Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Japan Agency for Medical Research and Development-Core Research for Evolutionary Medical Science and Technology (AMED-CREST), Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, Japan; Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan
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5
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Bunyavanich S, Becker PM, Altman MC, Lasky-Su J, Ober C, Zengler K, Berdyshev E, Bonneau R, Chatila T, Chatterjee N, Chung KF, Cutcliffe C, Davidson W, Dong G, Fang G, Fulkerson P, Himes BE, Liang L, Mathias RA, Ogino S, Petrosino J, Price ND, Schadt E, Schofield J, Seibold MA, Steen H, Wheatley L, Zhang H, Togias A, Hasegawa K. Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop. J Allergy Clin Immunol 2024; 153:954-968. [PMID: 38295882 PMCID: PMC10999353 DOI: 10.1016/j.jaci.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Studies of asthma and allergy are generating increasing volumes of omics data for analysis and interpretation. The National Institute of Allergy and Infectious Diseases (NIAID) assembled a workshop comprising investigators studying asthma and allergic diseases using omics approaches, omics investigators from outside the field, and NIAID medical and scientific officers to discuss the following areas in asthma and allergy research: genomics, epigenomics, transcriptomics, microbiomics, metabolomics, proteomics, lipidomics, integrative omics, systems biology, and causal inference. Current states of the art, present challenges, novel and emerging strategies, and priorities for progress were presented and discussed for each area. This workshop report summarizes the major points and conclusions from this NIAID workshop. As a group, the investigators underscored the imperatives for rigorous analytic frameworks, integration of different omics data types, cross-disciplinary interaction, strategies for overcoming current limitations, and the overarching goal to improve scientific understanding and care of asthma and allergic diseases.
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Affiliation(s)
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Jessica Lasky-Su
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | | | - Talal Chatila
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | - Wendy Davidson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Dong
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Fang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Patricia Fulkerson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Liming Liang
- Harvard T. H. Chan School of Public Health, Boston, Mass
| | | | - Shuji Ogino
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass; Harvard T. H. Chan School of Public Health, Boston, Mass; Broad Institute of MIT and Harvard, Boston, Mass
| | | | | | - Eric Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Max A Seibold
- National Jewish Health, Denver, Colo; University of Colorado School of Medicine, Aurora, Colo
| | - Hanno Steen
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lisa Wheatley
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Hongmei Zhang
- School of Public Health, University of Memphis, Memphis, Tenn
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Kohei Hasegawa
- Massachusetts General Hospital and Harvard Medical School, Boston, Mass
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6
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Serio C, Leung ASY, Eigenmann P, Lezmi G. Editorial comment on "Epigenomic and epigenetic investigations of food allergy". Pediatr Allergy Immunol 2024; 35:e14117. [PMID: 38556795 DOI: 10.1111/pai.14117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024]
Affiliation(s)
- Cristina Serio
- Scuola di Specializzazione in Pediatria, University of Bari "Aldo Moro", Bari, Italy
| | - Agnes S Y Leung
- Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, China
| | - Philippe Eigenmann
- Pediatric Allergy Unit, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Geneva, Switzerland
| | - Guillaume Lezmi
- Department of Pediatric Pulmonology and Allergy, Assistance Publique Hôpitaux de Paris, Hôpital Necker Enfants Malades and University of Paris Cité, Paris, France
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7
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Chun Y, Lee JH, Bunyavanich S. Epigenomic and epigenetic investigations of food allergy. Pediatr Allergy Immunol 2024; 35:e14065. [PMID: 38284919 PMCID: PMC10825314 DOI: 10.1111/pai.14065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024]
Abstract
As a potential link between genetic predisposition, environmental exposures, and food allergy outcomes, epigenetics has been a molecular variable of interest in ongoing efforts to understand food allergy mechanisms and outcomes. Here we review population-based investigations of epigenetic loci associated with food allergy, focusing on established clinical food allergy. We first provide an overview of epigenetic mechanisms that have been studied in cohorts with food allergy, predominantly DNA methylation but also microRNA. We then discuss investigations that have implemented epigenome-wide approaches aimed at genome-wide profiling and discovery. Such epigenome-wide studies have collectively identified differentially methylated and differentially regulated loci associated with T cell development, antigen presentation, reaction severity, and causal mediation in food allergy. We then discuss candidate-gene investigations that have honed in on Th1, Th2, T regulatory, and innate genes of a priori interest in food allergy. These studies have highlighted methylation changes in specific candidate genes as associated with T regulatory cell activity as well as differential methylation of Type 1 and Type 2 cytokine genes associated with various food allergies. Intriguingly, epigenetic loci associated with food allergy have also been explored as potential biomarkers for the clinical management of food allergy. We conclude by highlighting several priority directions for advancing population-based epigenomic and epigenetic understandings of food allergy.
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Affiliation(s)
- Yoojin Chun
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jo Hsuan Lee
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Supinda Bunyavanich
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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8
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Savin IA, Zenkova MA, Sen’kova AV. Bronchial Asthma, Airway Remodeling and Lung Fibrosis as Successive Steps of One Process. Int J Mol Sci 2023; 24:16042. [PMID: 38003234 PMCID: PMC10671561 DOI: 10.3390/ijms242216042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Bronchial asthma is a heterogeneous disease characterized by persistent respiratory system inflammation, airway hyperreactivity, and airflow obstruction. Airway remodeling, defined as changes in airway wall structure such as extensive epithelial damage, airway smooth muscle hypertrophy, collagen deposition, and subepithelial fibrosis, is a key feature of asthma. Lung fibrosis is a common occurrence in the pathogenesis of fatal and long-term asthma, and it is associated with disease severity and resistance to therapy. It can thus be regarded as an irreversible consequence of asthma-induced airway inflammation and remodeling. Asthma heterogeneity presents several diagnostic challenges, particularly in distinguishing between chronic asthma and other pulmonary diseases characterized by disruption of normal lung architecture and functions, such as chronic obstructive pulmonary disease. The search for instruments that can predict the development of irreversible structural changes in the lungs, such as chronic components of airway remodeling and fibrosis, is particularly difficult. To overcome these challenges, significant efforts are being directed toward the discovery and investigation of molecular characteristics and biomarkers capable of distinguishing between different types of asthma as well as between asthma and other pulmonary disorders with similar structural characteristics. The main features of bronchial asthma etiology, pathogenesis, and morphological characteristics as well as asthma-associated airway remodeling and lung fibrosis as successive stages of one process will be discussed in this review. The most common murine models and biomarkers of asthma progression and post-asthmatic fibrosis will also be covered. The molecular mechanisms and key cellular players of the asthmatic process described and systematized in this review are intended to help in the search for new molecular markers and promising therapeutic targets for asthma prediction and therapy.
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Affiliation(s)
| | | | - Aleksandra V. Sen’kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev Ave 8, 630090 Novosibirsk, Russia; (I.A.S.); (M.A.Z.)
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9
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Clemente-Suárez VJ, Mielgo-Ayuso J, Ramos-Campo DJ, Beltran-Velasco AI, Martínez-Guardado I, Navarro Jimenez E, Redondo-Flórez L, Yáñez-Sepúlveda R, Tornero-Aguilera JF. Basis of preventive and non-pharmacological interventions in asthma. Front Public Health 2023; 11:1172391. [PMID: 37920579 PMCID: PMC10619920 DOI: 10.3389/fpubh.2023.1172391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/18/2023] [Indexed: 11/04/2023] Open
Abstract
Asthma is one of the most common atopic disorders in all stages of life. Its etiology is likely due to a complex interaction between genetic, environmental, and lifestyle factors. Due to this, different non-pharmacological interventions can be implemented to reduce or alleviate the symptoms caused by this disease. Thus, the present narrative review aimed to analyze the preventive and non-pharmacological interventions such as physical exercise, physiotherapy, nutritional, ergonutritional, and psychological strategies in asthma treatment. To reach these aims, an extensive narrative review was conducted. The databases used were MedLine (PubMed), Cochrane (Wiley), Embase, PsychINFO, and CinAhl. Asthma is an immune-mediated inflammatory condition characterized by increased responsiveness to bronchoconstrictor stimuli. Different factors have been shown to play an important role in the pathogenesis of asthma, however, the treatments used to reduce its incidence are more controversial. Physical activity is focused on the benefits that aerobic training can provide, while physiotherapy interventions recommend breathing exercises to improve the quality of life of patients. Nutritional interventions are targeted on implement diets that prioritize the consumption of fruits and vegetables and supplementation with antioxidants. Psychological interventions have been proposed as an essential non-pharmacological tool to reduce the emotional problems associated with asthma.
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Affiliation(s)
- Vicente Javier Clemente-Suárez
- Faculty of Sports Sciences, Universidad Europea de Madrid, Madrid, Spain
- Studies Centre in Applied Combat (CESCA), Toledo, Spain
| | - Juan Mielgo-Ayuso
- Department of Health Sciences, Faculty of Health Sciences, University of Burgos, Burgos, Spain
| | - Domingo Jesús Ramos-Campo
- LFE Research Group, Department of Health and Human Performance, Faculty of Physical Activity and Sport Science-INEF, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Ismael Martínez-Guardado
- BRABE Group, Department of Psychology, Faculty of Life and Natural Sciences, Universidad Camilo José Cela, Madrid, Spain
| | | | - Laura Redondo-Flórez
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | | | - Jose Francisco Tornero-Aguilera
- Faculty of Sports Sciences, Universidad Europea de Madrid, Madrid, Spain
- Studies Centre in Applied Combat (CESCA), Toledo, Spain
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10
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Gaiteri C, Connell DR, Sultan FA, Iatrou A, Ng B, Szymanski BK, Zhang A, Tasaki S. Robust, scalable, and informative clustering for diverse biological networks. Genome Biol 2023; 24:228. [PMID: 37828545 PMCID: PMC10571258 DOI: 10.1186/s13059-023-03062-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data. However, due to foundational issues in how they are defined and detected, such clusters are not always reliable, leading to unstable conclusions. We compare popular clustering algorithms across thousands of synthetic and real biological datasets, including a new consensus clustering algorithm-SpeakEasy2: Champagne. These tests identify trends in performance, show no single method is universally optimal, and allow us to examine factors behind variation in performance. Multiple metrics indicate SpeakEasy2 generally provides robust, scalable, and informative clusters for a range of applications.
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Affiliation(s)
- Chris Gaiteri
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA.
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| | - David R Connell
- Rush University Graduate College, Rush University Medical Center, Chicago, IL, USA
| | - Faraz A Sultan
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Artemis Iatrou
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Harvard University, Belmont, MA, USA
| | - Bernard Ng
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Boleslaw K Szymanski
- Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, USA
- Network Science and Technology Center, Rensselaer Polytechnic Institute, Troy, NY, USA
- Academy of Social Sciences, Łódź, Poland
| | - Ada Zhang
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
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11
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Keet C, Sicherer SH, Bunyavanich S, Visness C, Fulkerson PC, Togias A, Davidson W, Perry S, Hamrah S, Calatroni A, Robinson K, Dunaway L, Davis CM, Anvari S, Leong-Kee SM, Hershey GK, DeFranco E, Devonshire A, Kim H, Joseph C, Davidson B, Strong NK, Tsuang AJ, Groetch M, Wang J, Dantzer J, Mudd K, Aina A, Shreffler W, Yuan Q, Simmons V, Leung DY, Hui-Beckman J, Ramos JA, Chinthrajah S, Winn V, Sindher T, Jones SM, Manning NA, Scurlock AM, Kim E, Stuebe A, Gern JE, Singh AM, Krupp J, Wood RA. The SunBEAm birth cohort: Protocol design. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2023; 2:100124. [PMID: 37771674 PMCID: PMC10509956 DOI: 10.1016/j.jacig.2023.100124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 09/30/2023]
Abstract
Background Food allergy (FA) and atopic dermatitis (AD) are common conditions that often present in the first year of life. Identification of underlying mechanisms and environmental determinants of FA and AD is essential to develop and implement effective prevention and treatment strategies. Objectives: We sought to describe the design of the Systems Biology of Early Atopy (SunBEAm) birth cohort. Methods Funded by the National Institute of Allergy and Infectious Diseases (NIAID) and administered through the Consortium for Food Allergy Research (CoFAR), SunBEAm is a US population-based, multicenter birth cohort that enrolls pregnant mothers, fathers, and their newborns and follows them to 3 years. Questionnaire and biosampling strategies were developed to apply a systems biology approach to identify environmental, immunologic, and multiomic determinants of AD, FA, and other allergic outcomes. Results Enrollment is currently underway. On the basis of an estimated FA prevalence of 6%, the enrollment goal is 2500 infants. AD is defined on the basis of questionnaire and assessment, and FA is defined by an algorithm combining history and testing. Although any FA will be recorded, we focus on the diagnosis of egg, milk, and peanut at 5 months, adding wheat, soy, cashew, hazelnut, walnut, codfish, shrimp, and sesame starting at 12 months. Sampling includes blood, hair, stool, dust, water, tape strips, skin swabs, nasal secretions, nasal swabs, saliva, urine, functional aspects of the skin, and maternal breast milk and vaginal swabs. Conclusions The SunBEAm birth cohort will provide a rich repository of data and specimens to interrogate mechanisms and determinants of early allergic outcomes, with an emphasis on FA, AD, and systems biology.
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Affiliation(s)
- Corinne Keet
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC
| | | | | | | | - Patricia C. Fulkerson
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Alkis Togias
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Wendy Davidson
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Susan Perry
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sanaz Hamrah
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | | | - Lars Dunaway
- Rho Inc, Federal Research Operations, Durham, NC
| | - Carla M. Davis
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Sara Anvari
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Susan M. Leong-Kee
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Tex
| | | | | | | | | | | | | | | | | | | | - Julie Wang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jennifer Dantzer
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Kim Mudd
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Abimbola Aina
- Department of Obstetrics and Gynecology, Johns Hopkins University School of Medicine, Baltimore, Md
| | | | - Qian Yuan
- Massachusetts General Hospital, Newton-Wellesley Hospital, Newton, Mass
| | - Virginia Simmons
- Massachusetts General Hospital, Newton-Wellesley Hospital, Newton, Mass
| | | | | | | | - Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Palo Alto, Calif
| | - Virginia Winn
- Division Maternal Fetal Medicine and Obstetrics, Stanford University, Palo Alto, Calif
| | - Tina Sindher
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Palo Alto, Calif
| | - Stacie M. Jones
- University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, Ark
| | | | - Amy M. Scurlock
- University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, Ark
| | - Edwin Kim
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC
| | - Alison Stuebe
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, NC
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wis
| | | | - Jennifer Krupp
- Maternal and Fetal Medicine, Obstetrics and Gynecology, SSM Health, Madison, Wis
| | - Robert A. Wood
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Md
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12
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Yang F, Zhao X, Liu W, Zhou B, Deng L, Chen H, Zhang Z, Zhou L. Positive rate of wheat allergens in the Chinese allergic population: a systematic review and meta-analysis. Sci Rep 2023; 13:10579. [PMID: 37386279 PMCID: PMC10310853 DOI: 10.1038/s41598-023-37648-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
In recent years, the prevalence of allergic diseases has increased significantly, causing great concern, and wheat, as one of the top 8 food allergens, is a common allergy trigger. Nevertheless, reliable estimates of the positivity rate of wheat allergens in the allergic population in China are still lacking. The systematic review and meta-analysis aims to evaluate the positive detection rate of wheat allergens in the Chinese allergic population and further provide a reference for the prevention of allergy. CNKI, CQVIP, WAN-FANG DATA, Sino Med, PubMed, Web of Science, Cochrane Library, and Embase databases were retrieved. Related research and case reports about the positive rate of wheat allergen in the Chinese allergic population published from inception to June 30, 2022, were searched, and meta-analysis was performed using Stata software. The pooled positive rate of wheat allergens and 95% confidence interval were calculated by random effect models, and the publication bias was evaluated using Egger's test. A total of 13 articles were included for the final meta-analysis, in which wheat allergen detection methods involved only serum sIgE testing and SPT assessment. The results showed that the wheat allergen positivity detection rate in Chinese allergic patients was 7.30% (95% CI 5.68-8.92%). Subgroup analysis showed that the positivity rate of wheat allergens was influenced by region, but hardly by age and assessment method. The positive rates of wheat allergy in the population with allergic diseases were 2.74% (95% CI 0.90-4.58%) and 11.47% (95% CI 7.08-15.87%) in southern and northern China, respectively. In particular, the positive rates of wheat allergens were greater than 10% in Shaanxi, Henan and Nei Mongol, all of which belong to the northern region. These results suggest that wheat allergens are an important cause of sensitization in allergic populations from northern China, and therefore attention should be paid to early prevention in high-risk populations.
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Affiliation(s)
- Fengmei Yang
- School of Public Health, Shenyang Medical College, Shenyang, 110034, China
| | - Xinyi Zhao
- School of Public Health, Shenyang Medical College, Shenyang, 110034, China
| | - Wenfeng Liu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, China
| | - Bo Zhou
- School of Public Health, Shenyang Medical College, Shenyang, 110034, China
| | - Lili Deng
- School of Public Health, Shenyang Medical College, Shenyang, 110034, China
- College of Integrated Chinese and Western Medical, Liaoning University of Traditional Chinese Medicine, Shenyang, 110033, China
| | - Hongbing Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, China
| | - Zhuo Zhang
- School of Public Health, Shenyang Medical College, Shenyang, 110034, China.
| | - Lin Zhou
- School of Public Health, Shenyang Medical College, Shenyang, 110034, China.
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13
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Hulsen T, Friedecký D, Renz H, Melis E, Vermeersch P, Fernandez-Calle P. From big data to better patient outcomes. Clin Chem Lab Med 2023; 61:580-586. [PMID: 36539928 DOI: 10.1515/cclm-2022-1096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Among medical specialties, laboratory medicine is the largest producer of structured data and must play a crucial role for the efficient and safe implementation of big data and artificial intelligence in healthcare. The area of personalized therapies and precision medicine has now arrived, with huge data sets not only used for experimental and research approaches, but also in the "real world". Analysis of real world data requires development of legal, procedural and technical infrastructure. The integration of all clinical data sets for any given patient is important and necessary in order to develop a patient-centered treatment approach. Data-driven research comes with its own challenges and solutions. The Findability, Accessibility, Interoperability, and Reusability (FAIR) Guiding Principles provide guidelines to make data findable, accessible, interoperable and reusable to the research community. Federated learning, standards and ontologies are useful to improve robustness of artificial intelligence algorithms working on big data and to increase trust in these algorithms. When dealing with big data, the univariate statistical approach changes to multivariate statistical methods significantly shifting the potential of big data. Combining multiple omics gives previously unsuspected information and provides understanding of scientific questions, an approach which is also called the systems biology approach. Big data and artificial intelligence also offer opportunities for laboratories and the In Vitro Diagnostic industry to optimize the productivity of the laboratory, the quality of laboratory results and ultimately patient outcomes, through tools such as predictive maintenance and "moving average" based on the aggregate of patient results.
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Affiliation(s)
- Tim Hulsen
- Department of Hospital Services & Informatics, Philips Research, Eindhoven, The Netherlands
| | - David Friedecký
- Department of Clinical Biochemistry, Laboratory for Inherited Metabolic Disorders, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Harald Renz
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
- Department of Clinical Immunology and Allergy, Laboratory of Immunopathology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Els Melis
- Ortho Clinical Diagnostics, Zaventem, Belgium
| | - Pieter Vermeersch
- Clinical Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
- European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Milan, Italy
| | - Pilar Fernandez-Calle
- European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Milan, Italy
- Department of Laboratory Medicine, Hospital Universitario La Paz, Madrid, Spain
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14
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Wright RJ. Advancing Exposomic Research in Prenatal Respiratory Disease Programming. Immunol Allergy Clin North Am 2023; 43:43-52. [PMID: 36411007 DOI: 10.1016/j.iac.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Disease programming reflects interactions between genes and the environment. Unlike the genome, environmental exposures and our response to exposures change over time. Starting in utero, the respiratory system and related processes develop sequentially in a carefully timed cascade, thus effects depend on both exposure dose and timing. A multitude of environmental and microbial exposures influence respiratory disease programming. Effects result from toxin-induced shifts in a host of molecular, cellular, and physiologic states and their interacting systems. Moreover, pregnant women and the developing child are not exposed to a single toxin, but to complex mixtures.
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Affiliation(s)
- Rosalind J Wright
- Department of Environmental Medicine and Public Health, New York, NY, USA; Institute for Exposomic Research, New York, NY, USA.
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15
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The Role of Systems Biology in Deciphering Asthma Heterogeneity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101562. [PMID: 36294997 PMCID: PMC9605413 DOI: 10.3390/life12101562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
Asthma is one of the most common and lifelong and chronic inflammatory diseases characterized by inflammation, bronchial hyperresponsiveness, and airway obstruction episodes. It is a heterogeneous disease of varying and overlapping phenotypes with many confounding factors playing a role in disease susceptibility and management. Such multifactorial disorders will benefit from using systems biology as a strategy to elucidate molecular insights from complex, quantitative, massive clinical, and biological data that will help to understand the underlying disease mechanism, early detection, and treatment planning. Systems biology is an approach that uses the comprehensive understanding of living systems through bioinformatics, mathematical, and computational techniques to model diverse high-throughput molecular, cellular, and the physiologic profiling of healthy and diseased populations to define biological processes. The use of systems biology has helped understand and enrich our knowledge of asthma heterogeneity and molecular basis; however, such methods have their limitations. The translational benefits of these studies are few, and it is recommended to reanalyze the different studies and omics in conjugation with one another which may help understand the reasons for this variation and help overcome the limitations of understanding the heterogeneity in asthma pathology. In this review, we aim to show the different factors that play a role in asthma heterogeneity and how systems biology may aid in understanding and deciphering the molecular basis of asthma.
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16
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Radzikowska U, Baerenfaller K, Cornejo‐Garcia JA, Karaaslan C, Barletta E, Sarac BE, Zhakparov D, Villaseñor A, Eguiluz‐Gracia I, Mayorga C, Sokolowska M, Barbas C, Barber D, Ollert M, Chivato T, Agache I, Escribese MM. Omics technologies in allergy and asthma research: An EAACI position paper. Allergy 2022; 77:2888-2908. [PMID: 35713644 PMCID: PMC9796060 DOI: 10.1111/all.15412] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
Abstract
Allergic diseases and asthma are heterogenous chronic inflammatory conditions with several distinct complex endotypes. Both environmental and genetic factors can influence the development and progression of allergy. Complex pathogenetic pathways observed in allergic disorders present a challenge in patient management and successful targeted treatment strategies. The increasing availability of high-throughput omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics allows studying biochemical systems and pathophysiological processes underlying allergic responses. Additionally, omics techniques present clinical applicability by functional identification and validation of biomarkers. Therefore, finding molecules or patterns characteristic for distinct immune-inflammatory endotypes, can subsequently influence its development, progression, and treatment. There is a great potential to further increase the effectiveness of single omics approaches by integrating them with other omics, and nonomics data. Systems biology aims to simultaneously and longitudinally understand multiple layers of a complex and multifactorial disease, such as allergy, or asthma by integrating several, separated data sets and generating a complete molecular profile of the condition. With the use of sophisticated biostatistics and machine learning techniques, these approaches provide in-depth insight into individual biological systems and will allow efficient and customized healthcare approaches, called precision medicine. In this EAACI Position Paper, the Task Force "Omics technologies in allergic research" broadly reviewed current advances and applicability of omics techniques in allergic diseases and asthma research, with a focus on methodology and data analysis, aiming to provide researchers (basic and clinical) with a desk reference in the field. The potential of omics strategies in understanding disease pathophysiology and key tools to reach unmet needs in allergy precision medicine, such as successful patients' stratification, accurate disease prognosis, and prediction of treatment efficacy and successful prevention measures are highlighted.
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Affiliation(s)
- Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - José Antonio Cornejo‐Garcia
- Research LaboratoryIBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMAMálagaSpain
| | - Cagatay Karaaslan
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Elena Barletta
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Basak Ezgi Sarac
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Alma Villaseñor
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain,Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Ibon Eguiluz‐Gracia
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain
| | - Cristobalina Mayorga
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain,Andalusian Centre for Nanomedicine and Biotechnology – BIONANDMálagaSpain
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain
| | - Domingo Barber
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Markus Ollert
- Department of Infection and ImmunityLuxembourg Institute of HealthyEsch‐sur‐AlzetteLuxembourg,Department of Dermatology and Allergy CenterOdense Research Center for AnaphylaxisOdense University Hospital, University of Southern DenmarkOdenseDenmark
| | - Tomas Chivato
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain,Department of Clinic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | | | - Maria M. Escribese
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
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17
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Current Limitations and Recent Advances in the Management of Asthma. Dis Mon 2022:101483. [DOI: 10.1016/j.disamonth.2022.101483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Xie Q, Xue W. IgE-Mediated food allergy: Current diagnostic modalities and novel biomarkers with robust potential. Crit Rev Food Sci Nutr 2022; 63:10148-10172. [PMID: 35587740 DOI: 10.1080/10408398.2022.2075312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Food allergy (FA) is a serious public health issue afflicting millions of people globally, with an estimated prevalence ranging from 1-10%. Management of FA is challenging due to overly restrictive diets and the lack of diagnostic approaches with high accuracy and prediction. Although measurement of serum-specific antibodies combined with patient medical history and skin prick test is a useful diagnostic tool, it is still an imprecise predictor of clinical reactivity with a high false-positive rate. The double-blind placebo-controlled food challenge represents the gold standard for FA diagnosis; however, it requires large healthcare and involves the risk of acute onset of allergic reactions. Improvement in our understanding of the molecular mechanism underlying allergic disease pathology, development of omics-based methods, and advances in bioinformatics have boosted the generation of a number of robust diagnostic biomarkers of FA. In this review, we discuss how traditional diagnostic modalities guide appropriate diagnosis and management of FA in clinical practice, as well as uncover the potential of the latest biomarkers for the diagnosis, monitoring, and prediction of FA. We also raise perspectives for precise and targeted medical intervention to fill the gap in the diagnosis of FA.
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Affiliation(s)
- Qiang Xie
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R. China
| | - Wentong Xue
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R. China
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19
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Zhou R, Zhang L, Zhang K, Zhou P. Difference of egg ovalbumin sensitization between egg and duck eggs in BALB/c mice. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-021-03943-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Kang M, Ko E, Mersha TB. A roadmap for multi-omics data integration using deep learning. Brief Bioinform 2022; 23:bbab454. [PMID: 34791014 PMCID: PMC8769688 DOI: 10.1093/bib/bbab454] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 12/18/2022] Open
Abstract
High-throughput next-generation sequencing now makes it possible to generate a vast amount of multi-omics data for various applications. These data have revolutionized biomedical research by providing a more comprehensive understanding of the biological systems and molecular mechanisms of disease development. Recently, deep learning (DL) algorithms have become one of the most promising methods in multi-omics data analysis, due to their predictive performance and capability of capturing nonlinear and hierarchical features. While integrating and translating multi-omics data into useful functional insights remain the biggest bottleneck, there is a clear trend towards incorporating multi-omics analysis in biomedical research to help explain the complex relationships between molecular layers. Multi-omics data have a role to improve prevention, early detection and prediction; monitor progression; interpret patterns and endotyping; and design personalized treatments. In this review, we outline a roadmap of multi-omics integration using DL and offer a practical perspective into the advantages, challenges and barriers to the implementation of DL in multi-omics data.
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Affiliation(s)
- Mingon Kang
- Department of Computer Science at the University of Nevada, Las Vegas, NV, USA
| | - Euiseong Ko
- Department of Computer Science at the University of Nevada, Las Vegas, NV, USA
| | - Tesfaye B Mersha
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
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21
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Abstract
PURPOSE OF REVIEW Asthma is the most common chronic disease of childhood. Investigations of the lower and upper airway microbiomes have significantly progressed over recent years, and their roles in pediatric asthma are becoming increasingly clear. RECENT FINDINGS Early studies identified the existence of upper and lower airway microbiomes, including imbalances in both associated with pediatric asthma. The infant airway microbiome may offer predictive value for the development of asthma in later childhood, and it may also be influenced by external factors such as respiratory viral illness. The airway microbiome has also been associated with the clinical course of asthma, including rates of exacerbation and level of control. Advances in -omics sciences have enabled improved identification of the airway microbiome's relationships with host response and function in children with asthma. Investigations are now moving toward the application of the above findings to explore risk modification and treatment options. SUMMARY The airway microbiome provides an intriguing window into pediatric asthma, offering insights into asthma diagnosis, clinical course, and perhaps treatment. Further investigation is needed to solidify these associations and translate research findings into clinical practice.
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Affiliation(s)
- Rhia Shah
- Division of Pulmonary Medicine, Department of Pediatrics,
Icahn School of Medicine at Mount Sinai, New York, NY
| | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of
Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, NY
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22
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Gao S, Wang J, Zhang Q, Shu J, Li C, Li H, Lin J. Cytokine antibody array-based analysis of IL-37 treatment effects in asthma. Aging (Albany NY) 2021; 13:21729-21742. [PMID: 34516405 PMCID: PMC8457575 DOI: 10.18632/aging.203515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/08/2021] [Indexed: 01/16/2023]
Abstract
Asthma is driven by group 2 innate lymphoid cells, antigen-specific CD4+ T helper type 2 cells and their cytokines such as interleukin (IL)-4, IL-5, IL-13. IL-37 is decreased in asthma and negatively related to Th2 cytokines and other pro-inflammatory cytokines. Our study showed that IL-37 level in asthmatic peripheral blood mononuclear cells was lower than in healthy. Further, IL-37 was negatively correlated with exhaled nitric oxide, asthma control test score, atopy and rhinitis history in asthmatics. Then an OVA-induced asthma mice model treated with rhIL-37 was established. An antibody array was employed to uncover altered cytokines induced by IL-37 in mice lung tissue. 20 proteins differentially expressed after rhIL-37 treatment and five of them were validated in asthmatic peripheral blood mononuclear cells. Consistent with cytokine antibody array, CCL3, CCL4, CCL5 decreased after IL-37 administration. While CXCL9 and CXCL13 were no change. We concluded that IL-37 reduce asthmatic symptoms by inhibit pro-inflammatory cytokine such as CCL3, CCL4, CCL5.
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Affiliation(s)
- Shengnan Gao
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100730, China.,Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 10029, China
| | - Jingru Wang
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing 10029, China
| | - Qing Zhang
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100730, China.,Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 10029, China
| | - Jun Shu
- Institute of Clinical Medicine Science, China-Japan Friendship Hospital, Beijing 10029, China
| | - Chunxiao Li
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing 10029, China
| | - Hongwen Li
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing 10029, China
| | - Jiangtao Lin
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100730, China.,Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 10029, China
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23
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Alvarez-Perea A, Dimov V, Popescu FD, Zubeldia JM. The applications of eHealth technologies in the management of asthma and allergic diseases. Clin Transl Allergy 2021; 11:e12061. [PMID: 34504682 PMCID: PMC8420996 DOI: 10.1002/clt2.12061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 01/14/2023] Open
Abstract
Portable devices, such as smartphones and mobile Internet access have become ubiquitous in the last decades. The term 'eHealth' stands for electronic health. The tools included in the eHealth concept utilize phones, computers and the Internet and related applications to improve the health care industry. Implementation of eHealth technologies has been documented for the management of different chronic diseases, including asthma and allergic conditions. Clinicians and patients have gained opportunity to communicate in new ways, which could be used cost-effectively to improve disease control and quality of life of those affected. Additionally, these innovations bring new opportunities to academic researchers. For example, eHealth has allowed researchers to compile data points that were previously unavailable or difficult to access, and analyse them using novel tools, collectively described as 'big data'. The role of eHealth become more important since early 2020, due to the physical distancing rules and the restrictions on mobility that have been applied worldwide as a response to the coronavirus disease 2019 pandemic. In this review, we summarize the most recent developments in various eHealth platforms and their relevance to the speciality of allergy and immunology, from the point of view of three major stakeholders: clinicians, patients and researchers.
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Affiliation(s)
- Alberto Alvarez-Perea
- Allergy Service Hospital General Universitario Gregorio Marañón Madrid Spain.,Gregorio Marañón Health Research Institute Madrid Spain
| | - Ves Dimov
- Cleveland Clinic Florida FAU Charles E. Schmidt College of Medicine Weston Florida USA
| | - Florin-Dan Popescu
- Department of Allergology 'Nicolae Malaxa' Clinical Hospital 'Carol Davila' University of Medicine and Pharmacy Bucharest Romania
| | - José Manuel Zubeldia
- Allergy Service Hospital General Universitario Gregorio Marañón Madrid Spain.,Gregorio Marañón Health Research Institute Madrid Spain.,Biomedical Research Network on Rare Diseases (CIBERER)-U761 Madrid Spain
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24
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Yang Y, Li X, Yang Y, Shoaie S, Zhang C, Ji B, Wei Y. Advances in the Relationships Between Cow's Milk Protein Allergy and Gut Microbiota in Infants. Front Microbiol 2021; 12:716667. [PMID: 34484158 PMCID: PMC8415629 DOI: 10.3389/fmicb.2021.716667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Cow's milk protein allergy (CMPA) is an immune response to cow's milk proteins, which is one of the most common food allergies in infants and young children. It is estimated that 2-3% of infants and young children have CMPA. The diet, gut microbiota, and their interactions are believed to be involved in the alterations of mucosal immune tolerance, which might lead to the development of CMPA and other food allergies. In this review, the potential molecular mechanisms of CMPA, including omics technologies used for analyzing microbiota, impacts of early microbial exposures on CMPA development, and microbiota-host interactions, are summarized. The probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and other modulation strategies for gut microbiota and the potential application of microbiota-based design of diets for the CMPA treatment are also discussed. This review not only summarizes the current studies about the interactions of CMPA with gut microbiota but also gives insights into the possible CMPA treatment strategies by modulating gut microbiota, which might help in improving the life quality of CMPA patients in the future.
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Affiliation(s)
- Yudie Yang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xiaoqi Li
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Ying Yang
- Jing’an District Central Hospital of Shanghai, Jing’an Branch, Huashan Hospital, Fudan University, Shanghai, China
| | - Saeed Shoaie
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Faculty of Dentistry, Oral and Craniofacial Sciences, Centre for Host-Microbiome Interactions, King’s College London, London, United Kingdom
| | - Cheng Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Yongjun Wei
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
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25
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Adam-Bonci TI, Bonci EA, Pârvu AE, Herdean AI, Moț A, Taulescu M, Ungur A, Pop RM, Bocșan C, Irimie A. Vitamin D Supplementation: Oxidative Stress Modulation in a Mouse Model of Ovalbumin-Induced Acute Asthmatic Airway Inflammation. Int J Mol Sci 2021; 22:7089. [PMID: 34209324 PMCID: PMC8268667 DOI: 10.3390/ijms22137089] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 01/15/2023] Open
Abstract
Asthma oxidative stress disturbances seem to enable supplementary proinflammatory pathways, thus contributing to disease development and severity. The current study analyzed the impact of two types of oral vitamin D (VD) supplementation regimens on the redox balance using a murine model of acute ovalbumin-induced (OVA-induced) asthmatic inflammation. The experimental prevention group received a long-term daily dose of 50 µg/kg (total dose of 1300 µg/kg), whereas the rescue group underwent a short-term daily dose of 100 µg/kg (total dose of 400 µg/kg). The following oxidative stress parameters were analyzed in serum, bronchoalveolar lavage fluid (BALF) and lung tissue homogenate (LTH): total oxidative status, total antioxidant response, oxidative stress index, malondialdehyde and total thiols. Results showed that VD significantly reduced oxidative forces and increased the antioxidant capacity in the serum and LTH of treated mice. There was no statistically significant difference between the two types of VD supplementation. VD also exhibited an anti-inflammatory effect in all treated mice, reducing nitric oxide formation in serum and the expression of nuclear factor kappa B p65 in the lung. In conclusion, VD supplementation seems to exhibit a protective role in oxidative stress processes related to OVA-induced acute airway inflammation.
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Affiliation(s)
- Teodora-Irina Adam-Bonci
- Department of Pathophysiology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (T.-I.A.-B.); (A.-E.P.)
| | - Eduard-Alexandru Bonci
- Department of Oncological Surgery and Gynecologic Oncology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400015 Cluj-Napoca, Romania;
| | - Alina-Elena Pârvu
- Department of Pathophysiology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (T.-I.A.-B.); (A.-E.P.)
| | - Andrei-Ioan Herdean
- Department of Anatomy and Embryology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania;
| | - Augustin Moț
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, “Babeș-Bolyai” University, 400028 Cluj-Napoca, Romania;
| | - Marian Taulescu
- Department of Pathology, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (M.T.); (A.U.)
- Synevovet Laboratory, 81 Pache Protopopescu, 021408 Bucharest, Romania
| | - Andrei Ungur
- Department of Pathology, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (M.T.); (A.U.)
| | - Raluca-Maria Pop
- Department of Pharmacology, Toxicology and Clinical Pharmacology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (R.-M.P.); (C.B.)
| | - Corina Bocșan
- Department of Pharmacology, Toxicology and Clinical Pharmacology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (R.-M.P.); (C.B.)
| | - Alexandru Irimie
- Department of Oncological Surgery and Gynecologic Oncology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400015 Cluj-Napoca, Romania;
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26
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Evaluation of Sensitivity and Specificity of Interleukins 25 and 33 in Diagnosis of Pediatric Asthma. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The roles of interleukin 25 (a member of the interleukin 17 family) and interleukin 33 (a member of the interleukin 1 family) in asthma and airway hyperresponsiveness are yet to be fully understood. The aim of this study was to investigate the roles of IL- 25 and IL- 33 in the diagnosis of pediatric asthma and their association with severity and treatment of the disease. This was a case-control study comprising 74 children with asthma as the patient group and 75 healthy children as the control group. The age of the participants ranged from 1 to 15 years. Levels of IL- 25 and IL- 33 in the serum were measured using ELISA kits. The highest positive predictive values (88.9%) occurred in IL- 25 with sensitivity and specificity of about 97.3% and 88.0% respectively, while the sensitivity and specificity of IL- 33 were about 51.4% and 66.0% respectively, with a positive predictive value of about (60.3%). The present study thus found that IL- 25 had higher diagnostic sensitivity and specificity values than IL- 33 in children with asthma. In addition, both interleukins were found to have a statistical significance regarding treatment of the disease in children.
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27
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Carstensen S, Benediktus E, Litzenburger T, Hohlfeld JM, Müller M. Basophil activation test: Assay precision and BI 1002494 SYK inhibition in healthy and mild asthmatics. Cytometry A 2021; 101:86-94. [PMID: 33797185 DOI: 10.1002/cyto.a.24338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/09/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Application of basophil activation test (BAT) in clinical trials requires assay validity. Whether assay variability differs between healthy and asthmatic subjects is mostly unknown. This study compares basophil stimulation using blood from healthy and asthmatic subjects with or without inhibition of spleen tyrosine kinase (SYK). METHODS Whole blood of healthy and mild asthmatic subjects was stimulated with anti-dinitrophenyl (DNP) IgE/DNP bovine serum albumin and anti-IgE. Basophil activation was detected by CD63 and CD203c expression. CD63 expression levels were compared with serum IgE levels. Three operators repeated experiments with three subjects each from both groups at 3 days to observe assay precision. The effect of the SYK inhibitor BI 1002494 was assessed in BAT for both healthy and asthmatic subjects. RESULTS BAT was reproducible in both groups. Acceptance criteria of <25% CV were mostly fulfilled. Stimulation with anti-DNP (p < 0.001, r = -0.80) but not anti-IgE (p = 0.74, r = 0.05) was related to serum IgE with levels > 200 IU/ml limiting anti-DNP stimulation. BI 1002494 IC50 values were 497 nM and 1080 nM in healthy and 287 nM and 683 nM in asthmatics for anti-DNP and anti-IgE stimulation, respectively. CONCLUSION BAT, performed with blood from healthy or asthmatic subjects, is a robust test for the measurement of a physiological response in clinical trials. Blood from asthmatic donors with serum IgE > 200 IU/ml is less feasible when using anti-DNP stimulation. SYK inhibition was not affected by disease status.
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Affiliation(s)
- Saskia Carstensen
- Department of Biomarker Analysis and Development, Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
| | - Ewald Benediktus
- Department of Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Tobias Litzenburger
- Department of Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jens M Hohlfeld
- Division of Airway Research, Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany.,Member of the German Center for Lung Research, Hannover, Germany.,Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Meike Müller
- Department of Biomarker Analysis and Development, Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
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28
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Tyler SR, Chun Y, Ribeiro VM, Grishina G, Grishin A, Hoffman GE, Do AN, Bunyavanich S. Merged Affinity Network Association Clustering: Joint multi-omic/clinical clustering to identify disease endotypes. Cell Rep 2021; 35:108975. [PMID: 33852839 PMCID: PMC8195153 DOI: 10.1016/j.celrep.2021.108975] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/25/2021] [Accepted: 03/18/2021] [Indexed: 12/21/2022] Open
Abstract
Although clinical and laboratory data have long been used to guide medical practice, this information is rarely integrated with multi-omic data to identify endotypes. We present Merged Affinity Network Association Clustering (MANAclust), a coding-free, automated pipeline enabling integration of categorical and numeric data spanning clinical and multi-omic profiles for unsupervised clustering to identify disease subsets. Using simulations and real-world data from The Cancer Genome Atlas, we demonstrate that MANAclust’s feature selection algorithms are accurate and outperform competitors. We also apply MANAclust to a clinically and multi-omically phenotyped asthma cohort. MANAclust identifies clinically and molecularly distinct clusters, including heterogeneous groups of “healthy controls” and viral and allergy-driven subsets of asthmatic subjects. We also find that subjects with similar clinical presentations have disparate molecular profiles, highlighting the need for additional testing to uncover asthma endotypes. This work facilitates data-driven personalized medicine through integration of clinical parameters with multi-omics. MANAclust is freely available at https://bitbucket.org/scottyler892/manaclust/src/master/. Clinical data commonly used in medical practice are underutilized in multi-omic analyses to identify disease endotypes. Tyler et al. present a python package called Merged Affinity Network Association Clustering (MANAclust) that automatically processes and integrates categorical and numeric data types, facilitating the inclusion of clinical data in multi-omic endotyping efforts.
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Affiliation(s)
- Scott R Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Victoria M Ribeiro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anh N Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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29
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Next Generation Exome Sequencing of Pediatric Asthma Identifies Rare and Novel Variants in Candidate Genes. DISEASE MARKERS 2021; 2021:8884229. [PMID: 33628342 PMCID: PMC7888305 DOI: 10.1155/2021/8884229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/21/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022]
Abstract
Multiple genes have been implicated to have a role in asthma predisposition by association studies. Pediatric patients often manifest a more extensive form of this disease and a particularly severe disease course. It is likely that genetic predisposition could play a more substantial role in this group. This study is aimed at identifying the spectrum of rare and novel variation in known pediatric asthma susceptibility genes using whole exome sequencing analysis in nine individual cases of childhood onset allergic asthma. DNA samples from the nine children with a history of bronchial asthma diagnosis underwent whole exome sequencing on Ion Proton. For each patient, the entire complement of rare variation within strongly associated candidate genes was catalogued. The analysis showed 21 variants in the subjects, 13 had been previously identified, and 8 were novel. Also, among of which, nineteen were nonsynonymous and 2 were nonsense. With regard to the novel variants, the 2 nonsynonymous variants in the PRKG1 gene (PRKG1: p.C519W and PRKG1: p.G520W) were presented in 4 cases, and a nonsynonymous variant in the MAVS gene (MAVS: p.A45V) was identified in 3 cases. The variants we found in this study will enrich the variant spectrum and build up the database in the Saudi population. Novel eight variants were identified in the study which provides more evidence in the genetic susceptibility in asthma among Saudi children, providing a genetic screening map for the molecular genetic determinants of allergic disease in Saudi children, with the goal of reducing the impact of chronic diseases on the health and the economy. We believe that the advanced specified statistical filtration/annotation programs used in this study succeeded to release such results in a preliminary study, exploring the genetic map of that disease in Saudi children.
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30
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Irizar H, Kanchan K, Mathias RA, Bunyavanich S. Advancing Food Allergy Through Omics Sciences. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2021; 9:119-129. [PMID: 32777389 PMCID: PMC7855623 DOI: 10.1016/j.jaip.2020.07.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Since the publication of the first draft of the human genome, there has been an explosion of new technologies with increasing power to interrogate the totality of biological molecules (eg, DNA, RNA, proteins, metabolites) and their modifications (eg, DNA methylation, histone modifications). These technologies, collectively called omics, have been widely applied in the last 2 decades to study biological systems to gain deeper insight into mechanisms driving the physiology and pathophysiology of human health and disease. Because of its complex, multifactorial nature, food allergy is especially well suited to be investigated using omics approaches. In this rostrum, we review how omic technologies have been applied to explore diverse aspects of food allergy, including adaptive and innate immune processes in food-allergic responses, the role of the microbiome in food allergy risk, metabolic changes in the gut and blood associated with food allergy, and the identification of biomarkers and potential therapeutic targets for the condition. We discuss the strengths and limitations of the studies performed thus far and the need to adopt systems biology approaches that integrate data from multiple omics to fully leverage the potential of these technologies to advance food allergy research and care.
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Affiliation(s)
- Haritz Irizar
- Division of Psychiatry, University College London, London, United Kingdom; Department of Genetics & Genomic Sciences and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kanika Kanchan
- Department of Medicine, Johns Hopkins University, Baltimore, Md
| | | | - Supinda Bunyavanich
- Department of Genetics & Genomic Sciences and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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31
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Krayem I, Lipoldová M. Role of host genetics and cytokines in Leishmania infection. Cytokine 2020; 147:155244. [PMID: 33059974 DOI: 10.1016/j.cyto.2020.155244] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/20/2020] [Accepted: 08/08/2020] [Indexed: 12/29/2022]
Abstract
Cytokines and chemokines are important regulators of innate and specific responses in leishmaniasis, a disease that currently affects 12 million people. We overviewed the current information about influences of genetically engineered mouse models of cytokine and chemokine on leishmaniasis. We found that genetic background of the host, parasite species and sub-strain, as well as experimental design often modify effects of genetically engineered cytokine genes. Next we analyzed genes and QTLs (quantitative trait loci) that control response to Leishmania species in mouse in order to establish relationship between genetic control of cytokine expression and organ pathology. These studies revealed a network-like complexity of the combined effects of the multiple functionally diverse QTLs and their individual specificity. Genetic control of organ pathology and systemic immune response overlap only partially. Some QTLs control both organ pathology and systemic immune response, but the effects of genes and loci with the strongest impact on disease are cytokine-independent, whereas several loci modify cytokines levels in serum without influencing organ pathology. Understanding this genetic control might be important in development of vaccines designed to stimulate certain cytokine spectrum.
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Affiliation(s)
- Imtissal Krayem
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Marie Lipoldová
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; Department of Natural Sciences, Faculty of Biomedical Engineering, Czech Technical University in Prague, Sítná 3105, 272 01 Kladno, Czech Republic.
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32
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Adachi T, Kainuma K, Asano K, Amagai M, Arai H, Ishii KJ, Ito K, Uchio E, Ebisawa M, Okano M, Kabashima K, Kondo K, Konno S, Saeki H, Sonobe M, Nagao M, Hizawa N, Fukushima A, Fujieda S, Matsumoto K, Morita H, Yamamoto K, Yoshimoto A, Tamari M. Strategic Outlook toward 2030: Japan's research for allergy and immunology - Secondary publication. Allergol Int 2020; 69:561-570. [PMID: 32600925 DOI: 10.1016/j.alit.2020.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/09/2020] [Indexed: 12/17/2022] Open
Abstract
Strategic Outlook toward 2030: Japan's Research for Allergy and Immunology (Strategy 2030) is the national research strategy based on Japan's Basic Law on Measures Against Allergic Diseases, a first of its kind worldwide. This strategy was established by a multi-disciplinary committee consisting of administrators of the Ministry of Health, Labour and Welfare of Japan, young and senior experts from various research societies and associations, and representatives of patient and public groups. Whereas the issues of transition, integration, and international collaboration have yet to be solved in this research realm in Japan, identification of unmet needs, digitization of information and transparent procedures, and strategic planning for complex problems (a process dubbed MIERUKA by the Toyota Way) are crucial to share and tackle the same vision and goals. The committee developed three specific actions focusing on preemptive treatment, interdisciplinarity and internationality, and life stage. The real success of Strategy 2030 is made by the spontaneous contributions of doctors, dentists, veterinarians, and other medical professionals; basic and clinical research scientists, research supporters, and pharmaceutical/medical device companies; manufacturers of food, healthcare, and home appliances; and patients, their families, and the public. The hope is to establish a stable society in which people can live long, healthy lives, as free as possible from allergic and immunological diseases, at each individual life stage. This article is based on a Japanese review first reported in Arerugi, introduces the developmental process and details of Strategy 2030.
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Affiliation(s)
- Takeya Adachi
- Japan Agency for Medical Research and Development (AMED), Tokyo, Japan; International Human Frontier Science Program Organization (HFSPO), Strasbourg, France; CNRS UPR 3572, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, Strasbourg, France.
| | - Keigo Kainuma
- Institute for Clinical Research, National Hospital Organization, Mie National Hospital, Mie, Japan
| | - Koichiro Asano
- Division of Pulmonary Medicine, Department of Medicine, Tokai University, School of Medicine, Kanagawa, Japan
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Hiroyuki Arai
- Pharmaceuticals and Medical Devices Agency (PMDA), Tokyo, Japan
| | - Ken J Ishii
- Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Komei Ito
- Department of Allergy, Aichi Children's Health and Medical Center, Aichi, Japan
| | - Eiichi Uchio
- Department of Ophthalmology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Motohiro Ebisawa
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization, Sagamihara National Hospital, Kanagawa, Japan
| | - Mitsuhiro Okano
- Department of Otorhinolaryngology, International University of Health and Welfare School of Medicine, Chiba, Japan
| | - Kenji Kabashima
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Kondo
- Department of Otolaryngology and Head and Neck Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Hidehisa Saeki
- Department of Cutaneous and Mucosal Pathophysiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Mariko Sonobe
- Japanese Mother's Society for Allergy Care (JMSAC), Kanagawa, Japan
| | - Mizuho Nagao
- Institute for Clinical Research, National Hospital Organization, Mie National Hospital, Mie, Japan
| | - Nobuyuki Hizawa
- Division of Respiratory Medicine, Institute of Clinical Medicine, University of Tsukuba, Ibaraki, Japan
| | | | - Shigeharu Fujieda
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, University of Fukui, Fukui, Japan
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hideaki Morita
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Yamamoto
- Center for Integrative Medical Sciences, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | | | - Mayumi Tamari
- Division of Molecular Genetics, The Jikei University School of Medicine, Research Center for Medical Science, Tokyo, Japan.
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Scichilone N, Barnes PJ, Battaglia S, Benfante A, Brown R, Canonica GW, Caramori G, Cazzola M, Centanni S, Cianferoni A, Corsico A, De Carlo G, Di Marco F, Gaga M, Hawrylowicz C, Heffler E, Matera MG, Matucci A, Paggiaro P, Papi A, Popov T, Rogliani P, Santus P, Solidoro P, Togias A, Boulet LP. The Hidden Burden of Severe Asthma: From Patient Perspective to New Opportunities for Clinicians. J Clin Med 2020; 9:jcm9082397. [PMID: 32727032 PMCID: PMC7463666 DOI: 10.3390/jcm9082397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
Severe asthma is an important topic in respiratory diseases, due to its high impact on morbidity and mortality as well as on health-care resources. The many challenges that still exist in the management of the most difficult-to-treat forms of the disease, and the acknowledgement of the existence of unexplored areas in the pathophysiological mechanisms and the therapeutic targets represent an opportunity to gather experts in the field with the immediate goals to summarize current understanding about the natural history of severe asthma and to identify gaps in knowledge and research opportunities, with the aim to contribute to improved medical care and health outcomes. This article is a consensus document from the “International Course on Severe Asthma” that took place in Palermo, Italy, on May 10–11, 2019. Emerging topics in severe asthma were addressed and discussed among experts, with special focus on patient’s needs and research opportunities, with the aim to highlight the unanswered questions in the diagnostic process and therapeutic approach.
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Affiliation(s)
- Nicola Scichilone
- Division of Respiratory Diseases, Department of Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Piazza delle Cliniche 2, 90143 Palermo, Italy; (S.B.); (A.B.)
- Correspondence: ; Tel.: +39-091-655-2146
| | - Peter John Barnes
- Airway Disease Section, National Heart & Lung Institute, Imperial College London, Dovehouse Street, London SW3 6LY, UK;
| | - Salvatore Battaglia
- Division of Respiratory Diseases, Department of Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Piazza delle Cliniche 2, 90143 Palermo, Italy; (S.B.); (A.B.)
| | - Alida Benfante
- Division of Respiratory Diseases, Department of Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Piazza delle Cliniche 2, 90143 Palermo, Italy; (S.B.); (A.B.)
| | - Robert Brown
- Department of Anesthesiology and Critical Care Medicine, Medicine, Department of Medicine, Division of Pulmonary Medicine, Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21287, USA;
| | - Giorgio Walter Canonica
- Personalised Medicine Clinic Asthma & Allergy, Humanitas University, Department of Biomedical Sciences, IRCCS Humanitas Research Hospital, Rozzano, 20089 Milan, Italy; (G.W.C.); (E.H.)
| | - Gaetano Caramori
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, 98122 Messina, Italy;
| | - Mario Cazzola
- Unit of Respiratory Medicine, Dept. Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (M.C.); (P.R.)
| | - Stefano Centanni
- Respiratory Unit, ASST Santi Paolo e Carlo, San Paolo Hospital, Department of Health Sciences, University of Milan, 20142 Milan, Italy;
| | - Antonella Cianferoni
- Pediatrics Department, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Angelo Corsico
- Division of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation and Department of Internal Medicine and Therapeutics – University of Pavia, 27100 Pavia, Italy;
| | - Giuseppe De Carlo
- The European Federation of Allergy and Airways Diseases Patients Associations (EFA), 1000 Brussels, Belgium;
| | - Fabiano Di Marco
- Respiratory Unit, ASST - Papa Giovanni XXIII Hospital, Bergamo, University of Milan, 24127 Milan, Italy;
| | - Mina Gaga
- 7th Respiratory Medicine Dept, Asthma Cen, Athens Chest Hospital, 11527 Athens, Greece;
| | - Catherine Hawrylowicz
- Division of Asthma, Allergy and Lung Biology, King’s College London, Guy’s Hospital, London SE1 9RT, UK;
| | - Enrico Heffler
- Personalised Medicine Clinic Asthma & Allergy, Humanitas University, Department of Biomedical Sciences, IRCCS Humanitas Research Hospital, Rozzano, 20089 Milan, Italy; (G.W.C.); (E.H.)
| | - Maria Gabriella Matera
- Unit of Pharmacology, Dept. Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Andrea Matucci
- Immunoallergology Unit, Careggi University Hospital, 50139 Florence, Italy;
| | - Pierluigi Paggiaro
- Department of Surgery, Medicine, Molecular Biology and Critical Care, University of Pisa, 56126 Pisa, Italy;
| | - Alberto Papi
- Research Center on Asthma and COPD, Dept of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Todor Popov
- Clinic of Occupational Diseases, University Hospital Sv. Ivan Rilski, 1431 Sofia, Bulgaria;
| | - Paola Rogliani
- Unit of Respiratory Medicine, Dept. Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (M.C.); (P.R.)
| | - Pierachille Santus
- Division of Respiratory Diseases, Department of Biomedical and Clinical Sciences (DIBIC), Università degli Studi di Milano, Ospedale L. Sacco, ASST Fatebenefratelli-Sacco, 20157 Milan, Italy;
| | - Paolo Solidoro
- Pneumology Unit U, Cardiovascular and Thoracic Department, AOU Città della Salute e della Scienza di Torino, University of Turin, 10126 Turin, Italy;
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, MD 20814, USA;
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Di Costanzo M, Carucci L, Berni Canani R, Biasucci G. Gut Microbiome Modulation for Preventing and Treating Pediatric Food Allergies. Int J Mol Sci 2020; 21:ijms21155275. [PMID: 32722378 PMCID: PMC7432728 DOI: 10.3390/ijms21155275] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
The increasing prevalence and severity of pediatric food allergies (FA) demands innovative preventive and therapeutic strategies. Emerging evidence suggests a pivotal role for the gut microbiome in modulating susceptibility to FA. Studies have demonstrated that alteration of gut microbiome could precede FA, and that particular microbial community structures early in life could influence also the disease course. The identification of gut microbiome features in pediatric FA patients is driving new prevention and treatment approaches. This review is focused on the potential role of the gut microbiome as a target for FA prevention and treatment.
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Affiliation(s)
- Margherita Di Costanzo
- Department of Pediatrics and Neonatology, Guglielmo da Saliceto Hospital, 29121 Piacenza, Italy;
- Department of Translational Medical Science-Pediatric Section, University “Federico II”, 80131 Naples, Italy; (L.C.); (R.B.C.)
- ImmunoNutritionLab-CEINGE Advanced Biotechnologies, University “Federico II”, 80131 Naples, Italy
- Correspondence:
| | - Laura Carucci
- Department of Translational Medical Science-Pediatric Section, University “Federico II”, 80131 Naples, Italy; (L.C.); (R.B.C.)
- ImmunoNutritionLab-CEINGE Advanced Biotechnologies, University “Federico II”, 80131 Naples, Italy
| | - Roberto Berni Canani
- Department of Translational Medical Science-Pediatric Section, University “Federico II”, 80131 Naples, Italy; (L.C.); (R.B.C.)
- ImmunoNutritionLab-CEINGE Advanced Biotechnologies, University “Federico II”, 80131 Naples, Italy
- Task Force on Microbiome Studies, University of Naples “Federico II”, 80131 Naples, Italy
- European Laboratory for the Investigation of Food-Induced Diseases, University of Naples “Federico II”, 80131 Naples, Italy
| | - Giacomo Biasucci
- Department of Pediatrics and Neonatology, Guglielmo da Saliceto Hospital, 29121 Piacenza, Italy;
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Korb E, Bağcıoğlu M, Garner-Spitzer E, Wiedermann U, Ehling-Schulz M, Schabussova I. Machine Learning-Empowered FTIR Spectroscopy Serum Analysis Stratifies Healthy, Allergic, and SIT-Treated Mice and Humans. Biomolecules 2020; 10:biom10071058. [PMID: 32708591 PMCID: PMC7408032 DOI: 10.3390/biom10071058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/17/2022] Open
Abstract
The unabated global increase of allergic patients leads to an unmet need for rapid and inexpensive tools for the diagnosis of allergies and for monitoring the outcome of allergen-specific immunotherapy (SIT). In this proof-of-concept study, we investigated the potential of Fourier-Transform Infrared (FTIR) spectroscopy, a high-resolution and cost-efficient biophotonic method with high throughput capacities, to detect characteristic alterations in serum samples of healthy, allergic, and SIT-treated mice and humans. To this end, we used experimental models of ovalbumin (OVA)-induced allergic airway inflammation and allergen-specific tolerance induction in BALB/c mice. Serum collected before and at the end of the experiment was subjected to FTIR spectroscopy. As shown by our study, FTIR spectroscopy, combined with deep learning, can discriminate serum from healthy, allergic, and tolerized mice, which correlated with immunological data. Furthermore, to test the suitability of this biophotonic method for clinical diagnostics, serum samples from human patients were analyzed by FTIR spectroscopy. In line with the results from the mouse models, machine learning-assisted FTIR spectroscopy allowed to discriminate sera obtained from healthy, allergic, and SIT-treated humans, thereby demonstrating its potential for rapid diagnosis of allergy and clinical therapeutic monitoring of allergic patients.
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Affiliation(s)
- Elke Korb
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria; (E.K.); (E.G.-S.); (U.W.)
| | - Murat Bağcıoğlu
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Erika Garner-Spitzer
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria; (E.K.); (E.G.-S.); (U.W.)
| | - Ursula Wiedermann
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria; (E.K.); (E.G.-S.); (U.W.)
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, 1210 Vienna, Austria;
- Correspondence: (M.E.-S.); (I.S.); Tel.: +43-1-25077-2460 (M.E.-S.); +43-1-40160-38250 (I.S.)
| | - Irma Schabussova
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria; (E.K.); (E.G.-S.); (U.W.)
- Correspondence: (M.E.-S.); (I.S.); Tel.: +43-1-25077-2460 (M.E.-S.); +43-1-40160-38250 (I.S.)
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36
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Novel Comprehensive Bioinformatics Approaches to Determine the Molecular Genetic Susceptibility Profile of Moderate and Severe Asthma. Int J Mol Sci 2020; 21:ijms21114022. [PMID: 32512817 PMCID: PMC7312607 DOI: 10.3390/ijms21114022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/25/2022] Open
Abstract
Background: Asthma is a chronic inflammatory condition linked to hyperresponsiveness in the airways. There is currently no cure available for asthma, and therapy choices are limited. Asthma is the result of the interplay between genes and the environment. The exact molecular genetic mechanism of asthma remains elusive. Aims: The aim of this study is to provide a comprehensive, detailed molecular etiology profile for the molecular factors that regulate the severity of asthma and pathogenicity using integrative bioinformatics tools. Methods: The GSE43696 omnibus gene expression dataset, which contains 50 moderate cases, 38 severe cases, and 20 healthy controls, was used to investigate differentially expressed genes (DEGs), susceptible chromosomal loci, gene networks, pathways, gene ontologies, and protein–protein interactions (PPIs) using an intensive bioinformatics pipeline. Results: The PPI network analysis yielded DEGs that contribute to interactions that differ from moderate-to-severe asthma. The combined interaction scores resulted in higher interactions for the genes STAT3, AGO2, COL1A1, CLCN6, and KSR for moderate asthma and JAK2, INSR, ERBB2, NR3C1, and PTK6 for severe asthma. Enrichment analysis (EA) demonstrated differential enrichment between moderate and severe asthma phenotypes; the ion transport regulation pathway was significantly enhanced in severe asthma phenotypes compared to that in moderate asthma phenotypes and involved PER2, GCR, IRS-2, KCNK7, KCNK6, NOX1, and SCN7A. The most enriched common pathway in both moderate and severe asthma is the development of the glucocorticoid receptor (GR) signaling pathway followed by glucocorticoid-mediated inhibition of proinflammatory and proconstrictory signaling in the airway of smooth muscle cell pathways. Gene sets were shared between severe and moderate asthma at 16 chromosome locations, including 17p13.1, 16p11.2, 17q21.31, 1p36, and 19q13.2, while 60 and 48 chromosomal locations were unique for both moderate and severe asthma, respectively. Phylogenetic analysis for DEGs showed that several genes have been intersected in phases of asthma in the same cluster of genes. This could indicate that several asthma-associated genes have a common ancestor and could be linked to the same biological function or gene family, implying the importance of these genes in the pathogenesis of asthma. Conclusion: New genetic risk factors for the development of moderate-to-severe asthma were identified in this study, and these could provide a better understanding of the molecular pathology of asthma and might provide a platform for the treatment of asthma.
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37
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Leveraging -omics for asthma endotyping. J Allergy Clin Immunol 2020; 144:13-23. [PMID: 31277743 DOI: 10.1016/j.jaci.2019.05.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/13/2022]
Abstract
Asthma is a highly heterogeneous disease, often manifesting with wheeze, dyspnea, chest tightness, and cough as prominent symptoms. The eliciting factors, natural history, underlying molecular biology, and clinical management of asthma vary highly among affected subjects. Because of this variation, many efforts have gone into subtyping asthma. Endotypes are subtypes of disease based on distinct pathophysiologic mechanisms. Endotypes can be clinically useful because they organize our mechanistic understanding of heterogeneous diseases and can direct treatment toward modalities that are likely to be the most effective. Asthma endotyping can be shaped by clinical features, laboratory parameters, and/or -omics approaches. We discuss the application of -omics approaches, including transcriptomics, epigenomics, microbiomics, metabolomics, and proteomics, to asthma endotyping. -Omics approaches have provided supporting evidence for many existing endotyping paradigms and also suggested novel ways to conceptualize asthma endotypes. Although endotypes based on single -omics approaches are relatively common, their integrated multi-omics application to asthma endotyping has been more limited thus far. We discuss paths forward to integrate multi-omics with clinical features and laboratory parameters to achieve the goal of precise asthma endotypes.
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38
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Shi HY, Pan C, Ma TT, Chen YL, Yan WJ, Liu JG, Cao MD, Huang HD, Wang DY, Wang XY, Wei JF. Clinical Efficacy Evaluation of 1-Year Subcutaneous Immunotherapy for Artemisia sieversiana Pollen Allergic Rhinitis by Serum Metabolomics. Front Pharmacol 2020; 11:305. [PMID: 32256368 PMCID: PMC7093654 DOI: 10.3389/fphar.2020.00305] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
Subcutaneous immunotherapy is the only treatment that improves the natural progression of allergic rhinitis and maintains long-term outcomes after discontinuation of the drug. Metabolomics is increasingly applied in the study of allergic diseases, including allergic rhinitis. However, little is known about the discovery of metabolites that can evaluate clinical efficacy and possible mechanisms of Artemisia sieversiana pollen subcutaneous immunotherapy. Thirty-three patients with Artemisia sieversiana pollen allergic rhinitis significantly improved after 1-year subcutaneous immunotherapy treatment, while ten patients were ineffective. Pre- and post-treatment serum samples from these patients were analyzed by metabolomics based on the combined detection of liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. As a result, L-Tyrosine can be a potential biomarker because of its opposite trend in effective patients and ineffective patients. And mechanism of immunotherapy may be closely related to NO and nitric oxide synthase. The discovery of potential biomarkers and metabolic pathways has contributed to the in-depth study of mechanisms of subcutaneous immunotherapy treatment of Artemisia sieversiana pollen allergic rhinitis.
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Affiliation(s)
- Hai-Yun Shi
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chen Pan
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ting-Ting Ma
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yan-Lei Chen
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Wei-Jun Yan
- Duolun People’s Hospital, Inner Mongolia, China
| | | | - Meng-Da Cao
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Dong Huang
- Department of Nephrology, Beijing Friendship Hospital, Faculty of Kidney Diseases, Capital Medical University, Beijing, China
| | - De-Yun Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xue-Yan Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Ji-Fu Wei
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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39
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Abstract
Food allergies are a growing public health concern affecting approximately 8% of children and 10% of adults in the United States. Several immunotherapy approaches are under active investigation, including oral immunotherapy, epicutaneous immunotherapy, and sublingual immunotherapy. Each of these approaches uses a similar strategy of administering small, increasing amounts of allergen to the allergic subject. Immunologic studies have described changes in the T-cell compartment, serum and salivary immunoglobulin profile, and mast cell and basophil degranulation status in response to allergens. This review highlights the immunologic changes induced by food allergen-specific immunotherapy and discusses future directions in this field.
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Affiliation(s)
- Johanna M Smeekens
- UNC Department of Pediatrics, UNC Food Allergy Initiative, UNC Chapel Hill, 116 Manning Drive, Mary Ellen Jones Building, Room 3004, Chapel Hill, NC 27599, USA.
| | - Michael D Kulis
- UNC Department of Pediatrics, UNC Food Allergy Initiative, UNC Chapel Hill, 116 Manning Drive, Mary Ellen Jones Building, Room 3004, Chapel Hill, NC 27599, USA
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40
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Tang HHF, Sly PD, Holt PG, Holt KE, Inouye M. Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges. Eur Respir J 2020; 55:13993003.00844-2019. [PMID: 31619470 DOI: 10.1183/13993003.00844-2019] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022]
Abstract
Asthma is a common condition caused by immune and respiratory dysfunction, and it is often linked to allergy. A systems perspective may prove helpful in unravelling the complexity of asthma and allergy. Our aim is to give an overview of systems biology approaches used in allergy and asthma research. Specifically, we describe recent "omic"-level findings, and examine how these findings have been systematically integrated to generate further insight.Current research suggests that allergy is driven by genetic and epigenetic factors, in concert with environmental factors such as microbiome and diet, leading to early-life disturbance in immunological development and disruption of balance within key immuno-inflammatory pathways. Variation in inherited susceptibility and exposures causes heterogeneity in manifestations of asthma and other allergic diseases. Machine learning approaches are being used to explore this heterogeneity, and to probe the pathophysiological patterns or "endotypes" that correlate with subphenotypes of asthma and allergy. Mathematical models are being built based on genomic, transcriptomic and proteomic data to predict or discriminate disease phenotypes, and to describe the biomolecular networks behind asthma.The use of systems biology in allergy and asthma research is rapidly growing, and has so far yielded fruitful results. However, the scale and multidisciplinary nature of this research means that it is accompanied by new challenges. Ultimately, it is hoped that systems medicine, with its integration of omics data into clinical practice, can pave the way to more precise, personalised and effective management of asthma.
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Affiliation(s)
- Howard H F Tang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia .,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Peter D Sly
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Patrick G Holt
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Kathryn E Holt
- Dept of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia.,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Alan Turing Institute, London, UK
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Krewski D, Andersen ME, Tyshenko MG, Krishnan K, Hartung T, Boekelheide K, Wambaugh JF, Jones D, Whelan M, Thomas R, Yauk C, Barton-Maclaren T, Cote I. Toxicity testing in the 21st century: progress in the past decade and future perspectives. Arch Toxicol 2019; 94:1-58. [DOI: 10.1007/s00204-019-02613-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
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Bunyavanich S, Berin MC. Food allergy and the microbiome: Current understandings and future directions. J Allergy Clin Immunol 2019; 144:1468-1477. [PMID: 31812181 PMCID: PMC6905201 DOI: 10.1016/j.jaci.2019.10.019] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Growing evidence points to an important role for the commensal microbiota in susceptibility to food allergy. Epidemiologic studies demonstrate associations between exposures known to modify the microbiome and risk of food allergy. Direct profiling of the gut microbiome in human cohort studies has demonstrated that individuals with food allergy have distinct gut microbiomes compared to healthy control subjects, and dysbiosis precedes the development of food allergy. Mechanistic studies in mouse models of food allergy have confirmed that the composition of the intestinal microbiota can imprint susceptibility or resistance to food allergy on the host and have identified a unique population of microbially responsive RORγt-positive FOXp3-positive regulatory T cells as critical for the maintenance of tolerance to foods. Armed with this new understanding of the role of the microbiota in food allergy and tolerance, therapeutics aimed at modifying the gastrointestinal microbiota are in development. In this article we review key milestones in the development of our current understanding of how the gastrointestinal microbiota contributes to food allergy and discuss our vision for the future of the field.
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Affiliation(s)
- Supinda Bunyavanich
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - M Cecilia Berin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY; PRIISM Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY.
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Al-Zayadneh EM, Alnawaiseh NA, Altarawneh AH, Aldmour IH, Albataineh EM, Al-Shagahin H, Alharazneh A, Alzayadneh E. Sensitization to inhaled allergens in asthmatic children in southern Jordan: a cross-sectional study. Multidiscip Respir Med 2019; 14:37. [PMID: 31719980 PMCID: PMC6839227 DOI: 10.1186/s40248-019-0199-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sensitization to inhaled allergens in children with bronchial asthma significantly affects asthma pathogenesis, severity and persistence into late childhood and adulthood. The present study determined the prevalence of sensitization to inhaled allergens in children with bronchial asthma and wheezing episodes in order to investigate the effect of positive sensitization on the severity and control of asthma symptoms and to screen for other associated allergic conditions. METHODS A cross-sectional study was conducted, including children between 6 months and 14 years of age attending the chest clinic of Al-Karak, south of Jordan, between November 2013 and February 2016. Skin prick tests (SPTs) using 11 standardized allergen extracts were conducted in 277 children. The severity of asthma was determined based on the Global Initiative for Asthma (GINA) assessment and the Childhood Asthma Control Test (C-ACT) in addition to the history of use of systemic steroids and hospital admissions within the past 12 months. RESULTS Sixty-seven percent of children with bronchial asthma reported sensitization to one or more of the inhaled allergens. The most common allergens were olive pollens (18%), cat fur (13.5%), and Dermatophagoides pteronyssinus (11.9%). There was a significant increase in allergen sensitization with age (p < 0.001). The most common concomitant allergic condition among children was allergic rhinitis (71.5%); however, allergic conjunctivitis was the only allergic condition that correlated with the skin test reactivity (p = 0.01). A family history of bronchial asthma was confirmed in 40.4% of children. Children with positive SPTs had lower ACT scores and reported more frequent use of systemic steroids and admissions to hospital within the past 12 months; however, this effect was not statistically significant (p > 0.05). CONCLUSIONS Sensitization to inhaled allergens is highly prevalent in children with asthma and wheezing episodes in southern Jordan and may be correlated with the severity of the disease. Therefore, appropriate measures to recognize and avoid these allergens are highly recommended. Most children in our study suffered from concomitant allergic rhinitis, indicating that an appropriate diagnosis and treatment of allergic rhinitis could significantly improve asthma control and thus the quality of life of these children. TRIAL REGISTRATION This study is not a clinical trial.
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Affiliation(s)
- Enas M Al-Zayadneh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | | | | | | | - Eman M. Albataineh
- Department of Microbiology and Immunology, University of Mutah, Al-Karak, Jordan
| | - Hani Al-Shagahin
- Department of Special Surgery, University of Mutah, Al-Karak, Jordan
| | | | - Ebaa Alzayadneh
- Department of Physiology and Biochemistry, School of Medicine, The University of Jordan, Amman, Jordan
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Sbihi H, Boutin RCT, Cutler C, Suen M, Finlay BB, Turvey SE. Thinking bigger: How early-life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease. Allergy 2019; 74:2103-2115. [PMID: 30964945 DOI: 10.1111/all.13812] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/27/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023]
Abstract
Imbalance, or dysbiosis, of the gut microbiome of infants has been linked to an increased risk of asthma and allergic diseases. Most studies to date have provided a wealth of data showing correlations between early-life risk factors for disease and changes in the structure of the gut microbiome that disrupt normal immunoregulation. These studies have typically focused on one specific risk factor, such as mode of delivery or early-life antibiotic use. Such "micro-level" exposures have a considerable impact on affected individuals but not necessarily the whole population. In this review, we place these mechanisms under a larger lens that takes into account the influence of upstream "macro-level" environmental factors such as air pollution and the built environment. While these exposures likely have a smaller impact on the microbiome at an individual level, their ubiquitous nature confers them with a large influence at the population level. We focus on features of the indoor and outdoor human-made environment, their microbiomes and the research challenges inherent in integrating the built environment microbiomes with the early-life gut microbiome. We argue that an exposome perspective integrating internal and external microbiomes with macro-level environmental factors can provide a more comprehensive framework to define how environmental exposures can shape the gut microbiome and influence the development of allergic disease.
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Affiliation(s)
- Hind Sbihi
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - Rozlyn CT. Boutin
- Department of Microbiology and Immunology, Michael Smith Laboratories The University of British Columbia Vancouver British Columbia Canada
| | - Chelsea Cutler
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - Mandy Suen
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - B. Brett Finlay
- Department of Microbiology and Immunology, Michael Smith Laboratories The University of British Columbia Vancouver British Columbia Canada
| | - Stuart E. Turvey
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
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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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Ahsen ME, Chun Y, Grishin A, Grishina G, Stolovitzky G, Pandey G, Bunyavanich S. NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers. Sci Rep 2019; 9:12970. [PMID: 31506535 PMCID: PMC6737052 DOI: 10.1038/s41598-019-49498-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 08/27/2019] [Indexed: 12/21/2022] Open
Abstract
Biological and regulatory mechanisms underlying many multi-gene expression-based disease biomarkers are often not readily evident. We describe an innovative framework, NeTFactor, that combines network analyses with gene expression data to identify transcription factors (TFs) that significantly and maximally regulate such a biomarker. NeTFactor uses a computationally-inferred context-specific gene regulatory network and applies topological, statistical, and optimization methods to identify regulator TFs. Application of NeTFactor to a multi-gene expression-based asthma biomarker identified ETS translocation variant 4 (ETV4) and peroxisome proliferator-activated receptor gamma (PPARG) as the biomarker's most significant TF regulators. siRNA-based knock down of these TFs in an airway epithelial cell line model demonstrated significant reduction of cytokine expression relevant to asthma, validating NeTFactor's top-scoring findings. While PPARG has been associated with airway inflammation, ETV4 has not yet been implicated in asthma, thus indicating the possibility of novel, disease-relevant discovery by NeTFactor. We also show that NeTFactor's results are robust when the gene regulatory network and biomarker are derived from independent data. Additionally, our application of NeTFactor to a different disease biomarker identified TF regulators of interest. These results illustrate that the application of NeTFactor to multi-gene expression-based biomarkers could yield valuable insights into regulatory mechanisms and biological processes underlying disease.
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Affiliation(s)
- Mehmet Eren Ahsen
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yoojin Chun
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander Grishin
- Division of Allergy & Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Galina Grishina
- Division of Allergy & Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gustavo Stolovitzky
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- IBM T.J. Watson Research Center, Yorktown Heights, New York, NY, USA
| | - Gaurav Pandey
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Supinda Bunyavanich
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Allergy & Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Dhondalay GK, Rael E, Acharya S, Zhang W, Sampath V, Galli SJ, Tibshirani R, Boyd SD, Maecker H, Nadeau KC, Andorf S. Food allergy and omics. J Allergy Clin Immunol 2019; 141:20-29. [PMID: 29307411 DOI: 10.1016/j.jaci.2017.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 01/06/2023]
Abstract
Food allergy (FA) prevalence has been increasing over the last few decades and is now a global health concern. Current diagnostic methods for FA result in a high number of false-positive results, and the standard of care is either allergen avoidance or use of epinephrine on accidental exposure, although currently with no other approved treatments. The increasing prevalence of FA, lack of robust biomarkers, and inadequate treatments warrants further research into the mechanism underlying food allergies. Recent technological advances have made it possible to move beyond traditional biological techniques to more sophisticated high-throughput approaches. These technologies have created the burgeoning field of omics sciences, which permit a more systematic investigation of biological problems. Omics sciences, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and exposomics, have enabled the construction of regulatory networks and biological pathway models. Parallel advances in bioinformatics and computational techniques have enabled the integration, analysis, and interpretation of these exponentially growing data sets and opens the possibility of personalized or precision medicine for FA.
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Affiliation(s)
- Gopal Krishna Dhondalay
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Efren Rael
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Swati Acharya
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Wenming Zhang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Stephen J Galli
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif
| | - Robert Tibshirani
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, Calif
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Holden Maecker
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Kari Christine Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif.
| | - Sandra Andorf
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
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Wu J, Zhong T, Zhu Y, Ge D, Lin X, Li Q. Effects of particulate matter (PM) on childhood asthma exacerbation and control in Xiamen, China. BMC Pediatr 2019; 19:194. [PMID: 31196028 PMCID: PMC6563520 DOI: 10.1186/s12887-019-1530-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 05/08/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The short-term effects of particulate matter (PM) exposure on childhood asthma exacerbation and disease control rate is not thoroughly assessed in Chinese population yet. The previous toxic effects of PM exposure are either based on long-term survey or experimental data from cell lines or mouse models, which also needs to be validated by real-world evidences. METHODS We evaluated the short-term effects of PM exposure on asthma exacerbation in a Chinese population of 3106 pediatric outpatientsand disease control rate (DCR) in a population of 3344 children using case-crossover design. All the subjects enrolled are non-hospitalized outpatients. All data for this study were collected from the electronic health record (EHR) in the period between January 1, 2016 and June 30, 2018 in Xiamen, China. RESULTS We found that exposure to PM2.5 and PM10 within the past two weeks was significantly associated with elevated risk of exacerbation (OR = 1.049, p < 0.001 for PM2.5and OR = 1.027, p < 0.001 for PM10). In addition, exposure to PM10 was associated with decreased DCR (OR = 0.976 for PM10, p < 0.001). CONCLUSIONS Our results suggest that exposure to both PM10 and PM2.5 has significant short-term effects on childhood asthma exacerbation and DCR, which serves as useful epidemiological parameters for clinical management of asthma risk in the sensitive population.
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Affiliation(s)
- Jinzhun Wu
- Department of Pediatrics, the First Affiliated Hospital of Xiamen University, No.55 Zhenhai Road, Xiamen, 361003 China
| | - Taoling Zhong
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, South Xiang’an Road, Xiamen, 361102 China
| | - Yu Zhu
- Department of Pediatrics, the First Affiliated Hospital of Xiamen University, No.55 Zhenhai Road, Xiamen, 361003 China
| | - Dandan Ge
- Department of Pediatrics, the First Affiliated Hospital of Xiamen University, No.55 Zhenhai Road, Xiamen, 361003 China
| | - Xiaoliang Lin
- Department of Pediatrics, the First Affiliated Hospital of Xiamen University, No.55 Zhenhai Road, Xiamen, 361003 China
| | - Qiyuan Li
- Department of Pediatrics, the First Affiliated Hospital of Xiamen University, No.55 Zhenhai Road, Xiamen, 361003 China
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, South Xiang’an Road, Xiamen, 361102 China
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Oral administration of a mixture of probiotics protects against food allergy via induction of CD103+ dendritic cells and modulates the intestinal microbiota. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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50
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Pecak M, Korošec P, Kunej T. Multiomics Data Triangulation for Asthma Candidate Biomarkers and Precision Medicine. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:392-409. [PMID: 29927718 DOI: 10.1089/omi.2018.0036] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Asthma is a common complex disorder and has been subject to intensive omics research for disease susceptibility and therapeutic innovation. Candidate biomarkers of asthma and its precision treatment demand that they stand the test of multiomics data triangulation before they can be prioritized for clinical applications. We classified the biomarkers of asthma after a search of the literature and based on whether or not a given biomarker candidate is reported in multiple omics platforms and methodologies, using PubMed and Web of Science, we identified omics studies of asthma conducted on diverse platforms using keywords, such as asthma, genomics, metabolomics, and epigenomics. We extracted data about asthma candidate biomarkers from 73 articles and developed a catalog of 190 potential asthma biomarkers (167 human, 23 animal data), comprising DNA loci, transcripts, proteins, metabolites, epimutations, and noncoding RNAs. The data were sorted according to 13 omics types: genomics, epigenomics, transcriptomics, proteomics, interactomics, metabolomics, ncRNAomics, glycomics, lipidomics, environmental omics, pharmacogenomics, phenomics, and integrative omics. Importantly, we found that 10 candidate biomarkers were apparent in at least two or more omics levels, thus promising potential for further biomarker research and development and precision medicine applications. This multiomics catalog reported herein for the first time contributes to future decision-making on prioritization of biomarkers and validation efforts for precision medicine in asthma. The findings may also facilitate meta-analyses and integrative omics studies in the future.
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Affiliation(s)
- Matija Pecak
- 1 Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domzale, Slovenia
| | - Peter Korošec
- 2 Laboratory for Clinical Immunology and Molecular Genetics, University Clinic of Respiratory and Allergic Diseases , Golnik, Slovenia
| | - Tanja Kunej
- 1 Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domzale, Slovenia
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