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In Silico Evaluation of Nonsynonymous SNPs in Human ADAM33: The Most Common Form of Genetic Association to Asthma Susceptibility. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1089722. [DOI: 10.1155/2022/1089722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/09/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022]
Abstract
ADAM33 is a zinc-dependent metalloprotease of the ADAM family, which plays a vital biological role as an activator of Th2 cytokines and growth factors. Moreover, this protein is crucial for the normal development of the lung in the fetus two months after gestation leading to determining lung functions all over life. In this regard, mutations in ADAM33 have been linked with asthma risk factors. Consequently, identifying ADAM33 pathogenic nonsynonymous single-nucleotide polymorphisms (nsSNPs) can be very important in asthma treatment. In the present study, 1055 nsSNPs of human ADAM33 were analyzed using biocomputational software, 31 of which were found to be detrimental mutations. Precise structural and stability analysis revealed D219V, C669G, and C606S as the most destabilizing SNPs. Furthermore, MD simulations disclosed higher overall fluctuation and alteration in intramolecular interactions compared with the wild-type structure. Overall, the results suggest D219V, C669G, and C606S detrimental mutations as a starting point for further case-control studies on the ADAM33 protein as well as an essential source for future targeted mechanisms.
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Danielewicz H, Gurgul A, Dębińska A, Myszczyszyn G, Szmatoła T, Myszkal A, Jasielczuk I, Drabik-Chamerska A, Hirnle L, Boznański A. Maternal atopy and offspring epigenome-wide methylation signature. Epigenetics 2021; 16:629-641. [PMID: 32902349 PMCID: PMC8143219 DOI: 10.1080/15592294.2020.1814504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/18/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
The increase in the prevalence of allergic diseases is believed to partially depend on environmental changes. DNA methylation is a major epigenetic mechanism, which is known to respond to environmental factors. A number of studies have revealed that patterns of DNA methylation may potentially predict allergic diseases.Here, we examined how maternal atopy is associated with methylation patterns in the cord blood of neonates.We conducted an epigenome-wide association study in a cohort of 96 mother-child pairs. Pregnant women aged not more than 35 years old, not currently smoking or exposed to environmental tobacco smoke, who did not report obesity before conception were considered eligible. They were further tested for atopy. Converted DNA from cord blood was analysed using Infinium MethylationEPIC; for statistical analysis, RnBeads software was applied. Gestational age and sex were included as covariates in the final analysis.83 DM sites were associated with maternal atopy. Within the top DM sites, there were CpG sites which mapped to genes SCD, ITM2C, NT5C3A and NPEPL1. Regional analysis revealed 25 tiling regions, 4 genes, 3 CpG islands and 5 gene promoters, (including PIGCP1, ADAM3A, ZSCAN12P1) associated with maternal atopy. Gene content analysis revealed pointwise enrichments in pathways related to purine-containing compound metabolism, the G1/S transition of the mitotic cell cycle, stem cell division and cellular glucose homoeostasis.These findings suggest that maternal atopy provides a unique intrauterine environment that may constitute the first environment in which exposure is associated with methylation patterns in newborn.
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Affiliation(s)
- Hanna Danielewicz
- 1st Department of Pediatrics, Allergy and Cardiology, Wroclaw Medical University, Wroclaw, Poland
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Kraków, Poland
| | - Anna Dębińska
- 1st Department of Pediatrics, Allergy and Cardiology, Wroclaw Medical University, Wroclaw, Poland
| | - Grzegorz Myszczyszyn
- 1st Department of Gynecology and Obstetrics, Wroclaw Medical University, Wroclaw, Poland
| | - Tomasz Szmatoła
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Kraków, Poland
| | - Anna Myszkal
- 1st Department of Gynecology and Obstetrics, University Hospital of Jan Mikulicz-Radecki in Wroclaw, Wroclaw, Poland
| | - Igor Jasielczuk
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Kraków, Poland
| | - Anna Drabik-Chamerska
- 1st Department of Pediatrics, Allergy and Cardiology, Wroclaw Medical University, Wroclaw, Poland
| | - Lidia Hirnle
- 1st Department of Gynecology and Obstetrics, Wroclaw Medical University, Wroclaw, Poland
| | - Andrzej Boznański
- 1st Department of Pediatrics, Allergy and Cardiology, Wroclaw Medical University, Wroclaw, Poland
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Association of β2-adrenergic receptor gene polymorphisms (rs1042713, rs1042714, rs1042711) with asthma risk: a systematic review and updated meta-analysis. BMC Pulm Med 2019; 19:202. [PMID: 31699066 PMCID: PMC6836544 DOI: 10.1186/s12890-019-0962-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/17/2019] [Indexed: 01/08/2023] Open
Abstract
Background The published data on the association between β2-adrenergic receptor gene polymorphisms and asthma susceptibility are inconclusive. To derive a more precise estimation of this association, a meta-analysis was performed. Methods A literature search was conducted in PubMed, Web of Science, EMBASE, Wanfang, and the China National Knowledge Infrastructure (CNKI) databases to identify eligible studies. The pooled odds ratios (ORs) with corresponding 95% confidence intervals (CIs) were used to calculate the strength of the association. A sensitivity analysis was performed to evaluate the influence of individual studies on the overall effect estimates, and funnel plots and Egger’s tests were used for indications of publication bias. Results Seventy three studies with three single nucleotide polymorphisms (SNP) (rs1042713, c.G46A, p.Gly16Arg; rs1042714, c.G79C, p.Gln27Glu; rs1042711, c.T-47C, p.Cys19Arg) were finally identified. For the rs1042713 polymorphism, no significant association with asthma risk was found in the overall population. However, a significant protective association was found in the Indian population in the dominant model comparison (OR = 0.72, 95% CI = 0.59–0.87, I2 = 25%, studies = 5, cases = 1190, controls = 1241). A significant risk association was found in the Arab population in the dominant model comparison (OR = 1.75, 95% CI = 1.14–2.70, I2 = 0%, studies = 2, cases = 307, controls = 361) and the homozygote model comparison (OR = 1.88, 95% CI = 1.17–3.02, I2 = 0%, studies = 2, cases = 307, controls = 361), and in the Hispanic-Latino population in the dominant model comparison (OR = 1.68, 95% CI = 1.10–2.55, I2 = 77%, studies = 5, cases = 1026, controls = 1412). For the rs1042714 polymorphism, we found a significant association in the recessive model comparison (OR = 0.83, 95% CI = 0.70–0.98, I2 = 44%, studies = 52, cases = 8242, controls = 16,832), the homozygote genotype comparison (OR = 0.84, 95% CI = 0.72–0.98, I2 = 25%, studies = 52, cases = 8242, controls = 16,832) and the allelic genetic model (OR = 0.91, 95% CI = 0.83–0.99, I2 = 59%, studies = 52, cases = 8242, controls = 16,832) in the overall population. When stratified by age, a significant association was also found in children in the recessive model comparison (OR = 0.59, 95% CI = 0.39–0.88, I2 = 58%, studies = 18, cases = 2498, controls = 2510) and the homozygote genotype comparison (OR = 0.63, 95% CI = 0.43–0.92, I2 = 46%, studies = 18, cases = 2498, controls = 2510), but not in adult. For the rs1042711 polymorphism, no significant associations were found in the any genetic model. Conclusion The meta-analysis suggests that the ADRB2 rs1042714 polymorphism has a protective association with asthma in the overall population and the pediatric subgroup.
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GATA2 and PU.1 Collaborate To Activate the Expression of the Mouse Ms4a2 Gene, Encoding FcεRIβ, through Distinct Mechanisms. Mol Cell Biol 2019; 39:MCB.00314-19. [PMID: 31501274 DOI: 10.1128/mcb.00314-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/02/2019] [Indexed: 12/20/2022] Open
Abstract
GATA factors GATA1 and GATA2 and ETS factor PU.1 are known to function antagonistically during hematopoietic development. In mouse mast cells, however, these factors are coexpressed and activate the expression of the Ms4a2 gene encoding the β chain of the high-affinity IgE receptor (FcεRI). The present study showed that these factors cooperatively regulate Ms4a2 gene expression through distinct mechanisms. Although GATA2 and PU.1 contributed almost equally to Ms4a2 gene expression, gene ablation experiments revealed that simultaneous knockdown of both factors showed neither a synergistic nor an additive effect. A chromatin immunoprecipitation analysis showed that they shared DNA binding to the +10.4-kbp region downstream of the Ms4a2 gene with chromatin looping factor LDB1, whereas the proximal -60-bp region was exclusively bound by GATA2 in a mast cell-specific manner. Ablation of PU.1 significantly reduced the level of GATA2 binding to both the +10.4-kbp and -60-bp regions. Surprisingly, the deletion of the +10.4-kbp region by genome editing completely abolished the Ms4a2 gene expression as well as the cell surface expression of FcεRI. These results suggest that PU.1 and LDB1 play central roles in the formation of active chromatin structure whereas GATA2 directly activates the Ms4a2 promoter.
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Kens OV, Gnateyko OZ, Lukyanenko NS, Vishtak NV, Bergtravm VI. Analysis of molecular genetic study on the polymorphic C-159T locus of the CD14 gene in children with increased risk of recurrent episodes of acute obstructive bronchitis. CYTOL GENET+ 2017. [DOI: 10.3103/s0095452717050036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kens OV, Vishtak NV, Acopyan HR, Bergtravm VI. Allelic polymorphism C-590T of the IL4 gene as a probable genetic marker for the increased predisposition to the development of recurrent episodes of acute obstructive bronchitis in children. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716030051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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White MJ, Risse-Adams O, Goddard P, Contreras MG, Adams J, Hu D, Eng C, Oh SS, Davis A, Meade K, Brigino-Buenaventura E, LeNoir MA, Bibbins-Domingo K, Pino-Yanes M, Burchard EG. Novel genetic risk factors for asthma in African American children: Precision Medicine and the SAGE II Study. Immunogenetics 2016; 68:391-400. [PMID: 27142222 DOI: 10.1007/s00251-016-0914-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/25/2016] [Indexed: 01/06/2023]
Abstract
Asthma, an inflammatory disorder of the airways, is the most common chronic disease of children worldwide. There are significant racial/ethnic disparities in asthma prevalence, morbidity, and mortality among US children. This trend is mirrored in obesity, which may share genetic and environmental risk factors with asthma. The majority of asthma biomedical research has been performed in populations of European decent. We sought to identify genetic risk factors for asthma in African American children. We also assessed the generalizability of genetic variants associated with asthma in European and Asian populations to African American children. Our study population consisted of 1227 (812 asthma cases, 415 controls) African American children with genome-wide single nucleotide polymorphism (SNP) data. Logistic regression was used to identify associations between SNP genotype and asthma status. We identified a novel variant in the PTCHD3 gene that is significantly associated with asthma (rs660498, p = 2.2 × 10(-7)) independent of obesity status. Approximately 5 % of previously reported asthma genetic associations identified in European populations replicated in African Americans. Our identification of novel variants associated with asthma in African American children, coupled with our inability to replicate the majority of findings reported in European Americans, underscores the necessity for including diverse populations in biomedical studies of asthma.
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Affiliation(s)
- Marquitta J White
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA.
| | - O Risse-Adams
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
- Lowell Science Research Program, Lowell High School, San Francisco, CA, USA
| | - P Goddard
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
| | - M G Contreras
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
- SF BUILD, San Francisco State University, San Francisco, CA, USA
| | - J Adams
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
| | - D Hu
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
| | - C Eng
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
| | - S S Oh
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
| | - A Davis
- Children's Hospital and Research Center Oakland, Oakland, CA, USA
| | - K Meade
- Children's Hospital and Research Center Oakland, Oakland, CA, USA
| | - E Brigino-Buenaventura
- Department of Allergy and Immunology, Kaiser Permanente Vallejo Medical Center, Vallejo, CA, USA
| | | | - K Bibbins-Domingo
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
| | - M Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - E G Burchard
- Department of Medicine, University of California, San Francisco, UCSF Box 2911, San Francisco, CA, 94143-2911, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
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Cherednichenko AA, Trifonova EA, Vagaitseva KV, Bocharova AV, Varzari AM, Radzhabov MO, Stepanov VA. Prevalence of gene polymorphisms associated with immune disorders in populations of Northern Eurasia. Mol Biol 2015. [DOI: 10.1134/s0026893315060047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Liu Y, Wang ZH, Zhen W, Lu SJ, Liu Z, Zou LY, Xu JJ. Association between genetic polymorphisms in the ADAM33 gene and asthma risk: a meta-analysis. DNA Cell Biol 2014; 33:793-801. [PMID: 25068505 DOI: 10.1089/dna.2013.2284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The aim of this study was to evaluate the associations between the rs3918396 G>A and rs528557 C>G polymorphisms in the disinterring and metalloproteinase domain 33 (ADAM33) gene and asthma risk. We searched CISCOM, CINAHL, Web of Science, PubMed, Google Scholar, EBSCO, Cochrane Library, and CBM databases from inception through August 1st, 2013 without language restrictions. Meta-analysis was performed using the STATA 12.0 software. Crude odds ratios (ORs) with their 95% confidence intervals (95% CI) were calculated. Thirteen case-control studies were included with a total of 7104 asthma patients and 8172 healthy controls. Our meta-analysis results revealed that ADAM33 rs528557 C>G polymorphism was associated with an increased risk of asthma (all p<0.05). However, we found no correlation between the ADAM33 rs3918396 G>A polymorphism and asthma risk (all p>0.05). Subgroup analysis by ethnicity indicated that the ADAM33 rs528557 C>G polymorphism might be strongly associated with an increased risk of asthma among both Caucasian and Asian populations (All p<0.05). No significant association was found between the ADAM33 rs3918396 G>A polymorphism and the risk of asthma among the studied ethnicities (All p>0.05). The present meta-analysis suggests that the ADAM33 rs528557 C>G polymorphism may contribute to susceptibility to asthma. Thus, the ADAM33 rs528557 C>G polymorphism may be utilized as a biomarker for early diagnosis of asthma.
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Affiliation(s)
- Yu Liu
- 1 Department of Respiratory Medicine, The First Affiliated Hospital of Liaoning Medical University , Jinzhou, People's Republic of China
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Xie H, Cheng Y, Huo Y, Huang G, Su J. Association between β2-adrenoceptor gene polymorphisms and asthma risk: an updated meta-analysis. PLoS One 2014; 9:e101861. [PMID: 24992184 PMCID: PMC4081822 DOI: 10.1371/journal.pone.0101861] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/11/2014] [Indexed: 02/08/2023] Open
Abstract
Background Evidence is increasingly accumulated about multiple roles for the β2-adrenoceptor gene in asthma. The results were inconsistent partly due to small sample sizes. To assess the association between β2-adrenoceptor gene polymorphisms and asthma risk, a meta-analysis was performed. Methods We comprehensively searched the PubMed, EMBASE, BIOSIS Previews databases and extracted data from all eligible articles to estimate the association between β2-adrenoceptor gene polymorphisms and asthma risk. The pooled odds ratio (OR) with 95% confidence intervals (CIs) were calculated. Results Thirty-seven studies involving 6648 asthma patients and 15943 controls were included in the meta-analysis. Overall, significant associations were found in allelic genetic model (OR = 1.06, 95% CI = 1.01∼1.12), recessive genetic model (OR = 1.11, 95% CI = 1.02∼1.21) for Arg/Gly16. Stratified by ethnicity and age, significant associations were also found in Asian population in allelic genetic model, recessive genetic model and addictive model. For Gln/Glu27, no significant association was found when we combined all eligible studies. Age stratification showed significant associations in adults in allelic genetic model and recessive genetic model, but no significant association was found among Asians and Caucasians in ethnicity stratification. Conclusions This meta-analysis implied that the β2-adrenoceptor Arg/Gly16 polymorphism was likely to contribute to asthma risk in Asian population. Gln/Glu27 polymorphism might be a contributor to asthma susceptibility for adults.
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Affiliation(s)
- Haojun Xie
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuanxiong Cheng
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- * E-mail:
| | - Yating Huo
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Guohua Huang
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jin Su
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Chen RX, Lu WM, Zhu LP, Lu MP, Wang ML, Wang YL, Chen XY, Zhu XJ, Yin M, Zhang ZD, Cheng L. Association study on ADAM33 polymorphisms in mite-sensitized persistent allergic rhinitis in a Chinese population. PLoS One 2014; 9:e95033. [PMID: 24751681 PMCID: PMC3994017 DOI: 10.1371/journal.pone.0095033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 03/23/2014] [Indexed: 02/04/2023] Open
Abstract
Background The ADAM33 gene has been identified as a potentially important asthma candidate gene and polymorphisms in this gene have been shown to be associated with asthma and seasonal allergic rhinitis. Objective To assess whether the ADAM33 polymorphisms are associated with persistent allergic rhinitis (PER) due to house dust mites in a Chinese population. Methods In a hospital-based case-control study of 515 patients with mite-sensitized PER and 495 healthy controls, we genotyped seven single nucleotide polymorphisms (SNPs) in ADAM33. Serum levels of eosinophil cationic protein, total IgE and allergen-specific IgE against Dermatophagoides pteronyssinus and Dermatophagoides farinae were measured by the ImmunoCAP assays. Results In the single-locus analysis, three polymorphisms, rs3918392 (F1), rs528557 (S2) and rs2787093, were significantly associated with mite-sensitized PER. SNP S2 was associated with significantly increased risk both of asthmatic and nonasthmatic mite-sensitized PER. In the combined genotypes analysis, individuals with 2–4 risk alleles had a significantly higher risk of mite-sensitized PER (adjusted OR = 1.99, 95% CI = 1.50–2.62) than those with 0–1 risk alleles. Haplotype-based association analysis revealed that the ACAGCCT haplotype might have potential to protect against mite-sensitized PER (adjusted OR = 0.67; 95% CI = 0.49–0.90). Conclusions Polymorphisms in the ADAM33 gene may contribute to susceptibility of mite-sensitized PER in this Chinese population.
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Affiliation(s)
- Ruo-Xi Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Wen-Min Lu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Lu-Ping Zhu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Mei-Ping Lu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Mei-Lin Wang
- Department of Molecular and Genetic Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yun-Li Wang
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Xin-Yuan Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Xin-Jie Zhu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Min Yin
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
- International Centre for Allergy Research, Nanjing Medical University, Nanjing, China
| | - Zheng-Dong Zhang
- Department of Molecular and Genetic Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lei Cheng
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
- International Centre for Allergy Research, Nanjing Medical University, Nanjing, China
- * E-mail:
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