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Kuo TC, Tan CE, Wang SY, Lin OA, Su BH, Hsu MT, Lin J, Cheng YY, Chen CS, Yang YC, Chen KH, Lin SW, Ho CC, Kuo CH, Tseng YJ. Human Breathomics Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5682403. [PMID: 31976536 PMCID: PMC6978997 DOI: 10.1093/database/baz139] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/12/2019] [Accepted: 11/13/2019] [Indexed: 12/11/2022]
Abstract
Breathomics is a special branch of metabolomics that quantifies volatile organic compounds (VOCs) from collected exhaled breath samples. Understanding how breath molecules are related to diseases, mechanisms and pathways identified from experimental analytical measurements is challenging due to the lack of an organized resource describing breath molecules, related references and biomedical information embedded in the literature. To provide breath VOCs, related references and biomedical information, we aim to organize a database composed of manually curated information and automatically extracted biomedical information. First, VOCs-related disease information was manually organized from 207 literature linked to 99 VOCs and known Medical Subject Headings (MeSH) terms. Then an automated text mining algorithm was used to extract biomedical information from this literature. In the end, the manually curated information and auto-extracted biomedical information was combined to form a breath molecule database—the Human Breathomics Database (HBDB). We first manually curated and organized disease information including MeSH term from 207 literatures associated with 99 VOCs. Then, an automatic pipeline of text mining approach was used to collect 2766 literatures and extract biomedical information from breath researches. We combined curated information with automatically extracted biomedical information to assemble a breath molecule database, the HBDB. The HBDB is a database that includes references, VOCs and diseases associated with human breathomics. Most of these VOCs were detected in human breath samples or exhaled breath condensate samples. So far, the database contains a total of 913 VOCs in relation to human exhaled breath researches reported in 2766 publications. The HBDB is the most comprehensive HBDB of VOCs in human exhaled breath to date. It is a useful and organized resource for researchers and clinicians to identify and further investigate potential biomarkers from the breath of patients. Database URL: https://hbdb.cmdm.tw
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Affiliation(s)
- Tien-Chueh Kuo
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.,The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.,Drug Research Center, College of Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan
| | - Cheng-En Tan
- The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.,Drug Research Center, College of Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan.,Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - San-Yuan Wang
- The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.,Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.,Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, No. 250, Wu-Hsing St., Taipei 11031, Taiwan
| | - Olivia A Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Bo-Han Su
- Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Ming-Tsung Hsu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jessica Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Yu-Yen Cheng
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.,The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan
| | - Ciao-Sin Chen
- Department of Pharmacy, School of Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan
| | - Yu-Chieh Yang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital-Yunlin Branch, No. 579, Sec. 2, Yunlin Road, Douliu, Yunlin County 640, Taiwan
| | - Kuo-Hsing Chen
- Department of Oncology, National Taiwan University Hospital, National Taiwan University Cancer Center, No. 1, Sec. 4, Roosevelt Road, Taipei 10048, Taiwan
| | - Shu-Wen Lin
- Graduate Institute of Clinical Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan
| | - Chao-Chi Ho
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei 10002, Taiwan
| | - Ching-Hua Kuo
- The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.,Drug Research Center, College of Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan.,Department of Pharmacy, School of Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan
| | - Yufeng Jane Tseng
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.,The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan.,Drug Research Center, College of Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan.,Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
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Alves AGF, de Azevedo Giacomin MF, Braga ALF, Sallum AME, Pereira LAA, Farhat LC, Strufaldi FL, de Faria Coimbra Lichtenfels AJ, de Santana Carvalho T, Nakagawa NK, Silva CA, Farhat SCL. Influence of air pollution on airway inflammation and disease activity in childhood-systemic lupus erythematosus. Clin Rheumatol 2017; 37:683-690. [PMID: 29098476 DOI: 10.1007/s10067-017-3893-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/14/2017] [Accepted: 10/24/2017] [Indexed: 02/06/2023]
Abstract
Exposure to fine particles may trigger pulmonary inflammation/systemic inflammation. The objective of this study was to investigate the association between daily individual exposure to air pollutants and airway inflammation and disease activity in childhood-onset systemic lupus erythematosus (cSLE) patients. A longitudinal panel study was carried out in 108 consecutive appointments with cSLE patients without respiratory diseases. Over four consecutive weeks, daily individual measures of nitrogen dioxide (NO2), fine particulate matter (PM2.5), ambient temperature, and humidity were obtained. This cycle was repeated every 2.5 months along 1 year, and cytokines of exhaled breath condensate-EBC [interleukins (IL) 6, 8, 17 and tumoral necrose factor-α (TNF-α)], fractional exhaled NO (FeNO), and disease activity parameters were collected weekly. Specific generalized estimation equation models were used to assess the impact of these pollutants on the risk of Systemic Lupus Erythematous Disease Activity Index 2000 (SLEDAI-2K) ≥ 8, EBC cytokines, and FeNO, considering the fixed effects for repetitive measurements. The models were adjusted for inflammatory indicators, body mass index, infections, medication, and weather variables. An IQR increase in PM2.5 4-day moving average (18.12 μg/m3) was associated with an increase of 0.05 pg/ml (95% CI 0.01; 0.09, p = 0.03) and 0.04 pg/ml (95% CI 0.02; 0.06, p = 0.01) in IL-17 and TNF-α EBC levels, respectively. Additionally, a short-term effect on FeNO was observed: the PM2.5 3-day moving average was associated with a 0.75 ppb increase (95% CI 0.38; 1.29, p = 0.03) in FeNO. Also, an increase of 1.47 (95% CI 1.10; 1.84) in the risk of SLEDAI-2K ≥ 8 was associated with PM2.5 7-day moving average. Exposure to inhalable fine particles increases airway inflammation/pulmonary and then systemic inflammation in cSLE patients.
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Affiliation(s)
- Andressa Guariento Ferreira Alves
- Pediatric Rheumatology Unit, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
- Pediatric Department, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo, SP, Brazil
| | - Maria Fernanda de Azevedo Giacomin
- Pediatric Rheumatology Unit, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
- Pediatric Department, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo, SP, Brazil
| | - Alfésio Luis Ferreira Braga
- Environmental Epidemiology Study Group, Laboratory of Experimental Air Pollution, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratory of Experimental Air Pollution, LIM05, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
- Environmental Exposure and Risk Assessment Group, Collective Health Post-graduation Program, Universidade Catolica de Santos, Santos, Brazil
| | - Adriana Maluf Elias Sallum
- Pediatric Rheumatology Unit, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
- Pediatric Department, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo, SP, Brazil
| | - Luiz Alberto Amador Pereira
- Environmental Epidemiology Study Group, Laboratory of Experimental Air Pollution, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratory of Experimental Air Pollution, LIM05, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
- Environmental Exposure and Risk Assessment Group, Collective Health Post-graduation Program, Universidade Catolica de Santos, Santos, Brazil
| | - Luis Carlos Farhat
- Environmental Epidemiology Study Group, Laboratory of Experimental Air Pollution, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Fernando Louzada Strufaldi
- Environmental Epidemiology Study Group, Laboratory of Experimental Air Pollution, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana Julia de Faria Coimbra Lichtenfels
- Laboratory of Experimental Air Pollution, LIM05, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
- Laboratory of Experimental Therapeutics, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Tômas de Santana Carvalho
- Department of Physiotherapy, Communication Science and Disorders, Occupational Therapy, LIM 34, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Naomi Kondo Nakagawa
- Laboratory of Experimental Air Pollution, LIM05, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
- Department of Physiotherapy, Communication Science and Disorders, Occupational Therapy, LIM 34, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Clovis Artur Silva
- Pediatric Rheumatology Unit, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
- Pediatric Department, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo, SP, Brazil
- Division of Rheumatology, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Sylvia Costa Lima Farhat
- Pediatric Department, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo, SP, Brazil.
- Environmental Epidemiology Study Group, Laboratory of Experimental Air Pollution, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
- Laboratory of Experimental Air Pollution, LIM05, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil.
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El Gazzar II, Fathy HM, Gheita TA, Nour El-Din AM, Rasheed EA, Bassyouni RH, Kenawy SA. Tumor necrosis factor-α -308 A/G gene polymorphism in children with juvenile idiopathic arthritis: relation to disease activity, damage, and functional status. Clin Rheumatol 2017; 36:1757-1763. [PMID: 28593608 DOI: 10.1007/s10067-017-3719-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/24/2017] [Accepted: 05/31/2017] [Indexed: 12/12/2022]
Abstract
The study aims to evaluate the clinical significance of serum levels of tumor necrosis factor alpha (TNF-α) and -308 A/G promoter polymorphism in juvenile idiopathic arthritis (JIA) patients and find any association to the subsets, clinical and laboratory features, disease activity, and damage as well as functional disability. Forty-eight JIA children and 30 controls were included in the present study. Juvenile arthritis disease activity score in 27 joints (JADAS-27) was calculated, juvenile arthritis damage index (JADI) was assessed, and Childhood Health Assessment Questionnaire (CHAQ) measured the functional status. Serum TNF-α was assayed by ELISA and gene (-308) promoter polymorphism was determined by polymerase chain reaction. The 48 JIA children (mean age 11.5 ± 2.8 years) were 13 systemic, 17 oligoarticular, and 18 polyarticular onset. The serum TNF-α was significantly higher in patients (90.4 ± 6.3 ng/ml) compared to control (3.5 ± 2.6 ng/ml) (p < 0.0001) with a tendency to be higher in the polyarticular subtype. All controls had TNF-α -308 GG alleles. The frequency of GG genotype tended to be higher in systemic onset compared to oligoarticular and polyarticular subtypes. The serum TNF-α significantly correlated with JADAS-27 (r = 0.32, p = 0.03) and CHAQ (r = 0.37, p = 0.01) and negatively with the presence of GG alleles (r = -0.48, p = 0.001). The GG alleles were significantly negatively associated with C-reactive protein (r = -0.32, p = 0.03) with a tendency to negatively correlate with JADAS-27, CHAQ, and JADI-extrarticular (r = -0.28, p = 0.06; r = -0.25, p = 0.09 and r = -0.25, p = 0.09, respectively). There is evidence of a possible influence of the -308 SNP promoter position on the production of TNF-α, the severity of JIA which may consequently influence the response to anti-TNF-α treatment.
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Affiliation(s)
- Iman I El Gazzar
- Rheumatology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Hanan M Fathy
- Rheumatology Department, Faculty of Medicine, Fayoum University, Faiyum, Egypt
| | - Tamer A Gheita
- Rheumatology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | | | - Enas Abdel Rasheed
- Clinical Pathology Department, National Research Centre (NRC), Giza, Egypt
| | - Rasha H Bassyouni
- Medical Microbiology and Immunology Department, Faculty of Medicine, Fayoum University, Faiyum, Egypt
| | - Sanaa A Kenawy
- Clinical Pharmacology, Faculty of Pharmacy, Cairo University; PhD Royal College of Surgeons, London University, London, UK
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