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The Vista of Application of Specific Anaphylaxis Accurate Diagnosis Based on DNA Single-Nucleotide Methylation Sites. CONTRAST MEDIA & MOLECULAR IMAGING 2021; 2021:8202068. [PMID: 34908915 PMCID: PMC8635942 DOI: 10.1155/2021/8202068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
Anaphylaxis has rapidly spread around the world in the last several decades. Environmental factors seem to play a major role, and epigenetic marks, especially DNA methylation, get more attention. We discussed several GEO opening data classifications with TOP 100 specific methylation region values (normalized M-values on line) by machine learning, which are remarkable to classify specific anaphylaxis after monoallergen exposure. Then, we sequenced the whole-genome DNA methylation of six people (3 wormwood monoallergen atopic rhinitis patients and 3 normal-immune people) during the pollen season and analyzed the difference of the single nucleotide and DNA region. The results' divergences were obvious (the differential single nucleotides were mostly distributed in nongene regions but the differential DNA regions of GWAS, on the other hand), which may have caused most single nucleotides to be concealed in the regions' sequences. Therefore, we suggest that we should conduct more “pragmatic” and directly find special single-nucleotide changes after exposure to atopic allergens instead of complex correlativity. It is possible to try to use DNA methylation marks to accurately diagnose anaphylaxis and form a machine learning classification based on the single methylated CpGs.
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Medda E, Vigone MC, Cassio A, Calaciura F, Costa P, Weber G, de Filippis T, Gelmini G, Di Frenna M, Caiulo S, Ortolano R, Rotondi D, Bartolucci M, Gelsomino R, De Angelis S, Gabbianelli M, Persani L, Olivieri A. Neonatal Screening for Congenital Hypothyroidism: What Can We Learn From Discordant Twins? J Clin Endocrinol Metab 2019; 104:5765-5779. [PMID: 31287502 DOI: 10.1210/jc.2019-00900] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022]
Abstract
CONTEXT Newborn screening program for congenital hypothyroidism (CH) adopting rescreening in at-risk neonates. OBJECTIVES To estimate the concordance rate for CH in twin pairs discordant at the first screening; to verify whether long-term follow-up of healthy cotwins belonging to CH discordant pairs may be useful to diagnose thyroid hypofunction during development; to evaluate the importance of genetic and environmental influences on liability to permanent and transient CH. DESIGN AND PATIENTS Forty-seven screening discordant twin pairs were investigated. Proband was defined as the twin in the pair with a positive test at the first screening and a confirmed diagnosis of CH. RESULTS Seven screening discordant twin pairs became concordant for CH within the first month of life (pairwise concordance of 14.9%) because seven screening negative cotwins showed high TSH values when retested. During long-term follow-up (range, 3 to 21 years), hypothyroidism was diagnosed in two monozygotic screening negative cotwins at the age of 9 months and 12 years, respectively. Furthermore, the twin analysis showed that 95% of liability to transient CH was explained by genetic factors and 5% by environmental (unshared) factors, whereas 64% of phenotypic variance of permanent CH was explained by common environmental factors (shared during the fetal life) and 36% by unshared environmental factors. CONCLUSIONS This study showed that the introduction of rescreening permits the diagnosis of CH in a greater number of twins. It also showed the importance of long-term follow-up in both twins in the pair, and the role of nongenetic factors in the etiology of permanent CH.
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Affiliation(s)
- Emanuela Medda
- Reference Center for Behavioral Sciences and Mental Health, National Institutes of Health, Rome, Italy
| | - Maria Cristina Vigone
- Department of Pediatrics, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandra Cassio
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesca Calaciura
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Pietro Costa
- Department of Maternal and Child Sciences and Urology, University "La Sapienza," Rome, Italy
| | - Giovanna Weber
- Department of Pediatrics, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, Milan, Italy
| | - Tiziana de Filippis
- Division of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Milan, Italy
| | - Giulia Gelmini
- Department of Maternal and Child Sciences and Urology, University "La Sapienza," Rome, Italy
| | - Marianna Di Frenna
- Department of Pediatrics, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, Milan, Italy
| | - Silvana Caiulo
- Department of Pediatrics, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, Milan, Italy
| | - Rita Ortolano
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Daniela Rotondi
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, National Institutes of Health, Rome, Italy
| | - Monica Bartolucci
- Department of Maternal and Child Sciences and Urology, University "La Sapienza," Rome, Italy
| | - Rossella Gelsomino
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Simona De Angelis
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, National Institutes of Health, Rome, Italy
| | - Marco Gabbianelli
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, National Institutes of Health, Rome, Italy
| | - Luca Persani
- Division of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Antonella Olivieri
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, National Institutes of Health, Rome, Italy
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Integrated Analysis of Gene Expression Differences in Twins Discordant for Disease and Binary Phenotypes. Sci Rep 2018; 8:17. [PMID: 29311748 PMCID: PMC5758574 DOI: 10.1038/s41598-017-18585-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/14/2017] [Indexed: 11/08/2022] Open
Abstract
While both genes and environment contribute to phenotype, deciphering environmental contributions to phenotype is a challenge. Furthermore, elucidating how different phenotypes may share similar environmental etiologies also is challenging. One way to identify environmental influences is through a discordant monozygotic (MZ) twin study design. Here, we assessed differential gene expression in MZ discordant twin pairs (affected vs. non-affected) for seven phenotypes, including chronic fatigue syndrome, obesity, ulcerative colitis, major depressive disorder, intermittent allergic rhinitis, physical activity, and intelligence quotient, comparing the spectrum of genes differentially expressed across seven phenotypes individually. Second, we performed meta-analysis for each gene to identify commonalities and differences in gene expression signatures between the seven phenotypes. In our integrative analyses, we found that there may be a common gene expression signature (with small effect sizes) across the phenotypes; however, differences between phenotypes with respect to differentially expressed genes were more prominently featured. Therefore, defining common environmentally induced pathways in phenotypes remains elusive. We make our work accessible by providing a new database (DiscTwinExprDB: http://apps.chiragjpgroup.org/disctwinexprdb/ ) for investigators to study non-genotypic influence on gene expression.
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Abstract
This thesis explores the contribution of twin studies, particularly those studies originating from the Danish Twin Registry, to the understanding of the aetiology of asthma. First, it is explored how twin studies have established the contribution of genetic and environmental factors to the variation in the susceptibility to asthma, and to the variation in several aspects of the clinical expression of the disease such as its age at onset, its symptomatology, its intermediate phenotypes, and its relationship with other atopic diseases. Next, it is explored how twin studies have corroborated theories explaining asthma's recent increase in prevalence, and last, how these fit with the explanations of the epidemiological trends in other common chronic diseases of modernity.
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Gawel DR, Rani James A, Benson M, Liljenström R, Muraro A, Nestor CE, Zhang H, Gustafsson M. The Allergic Airway Inflammation Repository--a user-friendly, curated resource of mRNA expression levels in studies of allergic airways. Allergy 2014; 69:1115-7. [PMID: 24888382 DOI: 10.1111/all.12432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2014] [Indexed: 11/28/2022]
Abstract
Public microarray databases allow analysis of expression levels of candidate genes in different contexts. However, finding relevant microarray data is complicated by the large number of available studies. We have compiled a user-friendly, open-access database of mRNA microarray experiments relevant to allergic airway inflammation, the Allergic Airway Inflammation Repository (AAIR, http://aair.cimed.ike.liu.se/). The aim is to allow allergy researchers to determine the expression profile of their genes of interest in multiple clinical data sets and several experimental systems quickly and intuitively. AAIR also provides quick links to other relevant information such as experimental protocols, related literature and raw data files.
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Affiliation(s)
- D. R. Gawel
- Department of Clinical and Experimental Medicine; Centre for Individualised Medicine; Linköping University; Linköping Sweden
| | - A. Rani James
- Department of Clinical and Experimental Medicine; Centre for Individualised Medicine; Linköping University; Linköping Sweden
| | - M. Benson
- Department of Clinical and Experimental Medicine; Centre for Individualised Medicine; Linköping University; Linköping Sweden
| | - R. Liljenström
- Department of Clinical and Experimental Medicine; Centre for Individualised Medicine; Linköping University; Linköping Sweden
| | - A. Muraro
- Department of Women and Child Health; Referral Centre for Food Allergy Diagnosis and Treatment; Veneto Region; Padua University Hospital; Padua Italy
| | - C. E. Nestor
- Department of Clinical and Experimental Medicine; Centre for Individualised Medicine; Linköping University; Linköping Sweden
| | - H. Zhang
- Department of Clinical and Experimental Medicine; Centre for Individualised Medicine; Linköping University; Linköping Sweden
| | - M. Gustafsson
- Department of Clinical and Experimental Medicine; Centre for Individualised Medicine; Linköping University; Linköping Sweden
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Suojalehto H, Lindström I, Majuri ML, Mitts C, Karjalainen J, Wolff H, Alenius H. Altered microRNA expression of nasal mucosa in long-term asthma and allergic rhinitis. Int Arch Allergy Immunol 2014; 163:168-78. [PMID: 24513959 DOI: 10.1159/000358486] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 01/08/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Asthma and allergic rhinitis (AR) commonly coexist and can be taken as manifestations of one syndrome. Evidence exists that microRNAs (miRNAs) are important in controlling inflammatory processes and they are considered promising biomarkers. However, little is known about the differences in miRNA expression in patients with chronic allergic airway disease. This study evaluated the inflammatory and miRNA profiles of the nasal mucosa of patients with long-term asthma with and without AR. METHODS We analyzed inflammatory cells, cytokines, and miRNAs in nasal biopsies and measured exhaled and nasal nitric oxide levels during the nonpollen season in 117 middle-aged men who had suffered mainly from allergic asthma for approximately 20 years and also in 33 healthy controls. RESULTS The differences in the number of nasal eosinophils and cytokine expression levels were modest in nasal biopsies taken from asthmatics. Downregulation of miR-18a, miR-126, let-7e, miR-155, and miR-224 and upregulation of miR-498, miR-187, miR-874, miR-143, and miR-886-3p were observed in asthmatic patients in comparison to controls. The differences in miRNA expression were mainly similar in asthmatics with and without AR. With regard to asthma severity, a trend of increased miRNA expression in persistent asthma was seen, whereas the downregulation of certain miRNAs was most distinct in nonpersistent-asthma patients. CONCLUSIONS Differences in miRNA expression in the nasal mucosa of subjects with long-term asthma and AR can be seen also when no markers of Th2-type inflammation are detected. Asthma severity had only a minor impact on miRNA expression.
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Affiliation(s)
- Hille Suojalehto
- Control of Hypersensitivity Diseases Team, Finnish Institute of Occupational Health, Helsinki, Finland
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Nestor CE, Barrenäs F, Wang H, Lentini A, Zhang H, Bruhn S, Jörnsten R, Langston MA, Rogers G, Gustafsson M, Benson M. DNA methylation changes separate allergic patients from healthy controls and may reflect altered CD4+ T-cell population structure. PLoS Genet 2014; 10:e1004059. [PMID: 24391521 PMCID: PMC3879208 DOI: 10.1371/journal.pgen.1004059] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 11/11/2013] [Indexed: 12/30/2022] Open
Abstract
Altered DNA methylation patterns in CD4+ T-cells indicate the importance of epigenetic mechanisms in inflammatory diseases. However, the identification of these alterations is complicated by the heterogeneity of most inflammatory diseases. Seasonal allergic rhinitis (SAR) is an optimal disease model for the study of DNA methylation because of its well-defined phenotype and etiology. We generated genome-wide DNA methylation (Npatients = 8, Ncontrols = 8) and gene expression (Npatients = 9, Ncontrols = 10) profiles of CD4+ T-cells from SAR patients and healthy controls using Illumina's HumanMethylation450 and HT-12 microarrays, respectively. DNA methylation profiles clearly and robustly distinguished SAR patients from controls, during and outside the pollen season. In agreement with previously published studies, gene expression profiles of the same samples failed to separate patients and controls. Separation by methylation (Npatients = 12, Ncontrols = 12), but not by gene expression (Npatients = 21, Ncontrols = 21) was also observed in an in vitro model system in which purified PBMCs from patients and healthy controls were challenged with allergen. We observed changes in the proportions of memory T-cell populations between patients (Npatients = 35) and controls (Ncontrols = 12), which could explain the observed difference in DNA methylation. Our data highlight the potential of epigenomics in the stratification of immune disease and represents the first successful molecular classification of SAR using CD4+ T cells. T-cells, a type of white blood cell, are an important part of the immune-system in humans. T-cells allow us to adapt our immune-response to the various infectious agents we encounter during life. However, T-cells can also cause disease when they target the body's own cells, e.g. Psoriasis, or when they react to a harmless particle or ‘antigen’, i.e. allergy. Much evidence supports an environmental, or ‘epigenetic’, component to allergy. Surprisingly, although allergy is viewed as a T-cell disease with an epigenetic component, no studies have identified epigenetic differences between healthy individuals and allergic individuals. Using a state-of-the-art genome-wide approach, we found that we could clearly and robustly separate allergic patients from healthy controls. It is often assumed that these changes reflect changes in DNA methylation in a given type of cell; however such differences can also result from different mixtures of T-cell subtypes in the samples. Indeed, we found that allergic patients had different proportions of T-cell sub-types compared to healthy controls. These changes in T-cell proportions may explain the difference in DNA methylation profile we observed between patients and controls. Our study is the first successful molecular classification of allergy using CD4+ T cells.
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Affiliation(s)
- Colm E. Nestor
- The Centre for Individualized Medicine, Linköping University Hospital, Linköping University, Linköping, Sweden
- * E-mail:
| | - Fredrik Barrenäs
- The Centre for Individualized Medicine, Linköping University Hospital, Linköping University, Linköping, Sweden
| | - Hui Wang
- The Centre for Individualized Medicine, Linköping University Hospital, Linköping University, Linköping, Sweden
- Department of Pediatrics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Antonio Lentini
- The Centre for Individualized Medicine, Linköping University Hospital, Linköping University, Linköping, Sweden
| | - Huan Zhang
- The Centre for Individualized Medicine, Linköping University Hospital, Linköping University, Linköping, Sweden
| | - Sören Bruhn
- The Centre for Individualized Medicine, Linköping University Hospital, Linköping University, Linköping, Sweden
| | - Rebecka Jörnsten
- Mathematical Sciences, Chalmers University of Technology, University of Gothenburg, Gothenburg, Sweden
| | - Michael A. Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Gary Rogers
- National Institute for Computational Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Mika Gustafsson
- The Centre for Individualized Medicine, Linköping University Hospital, Linköping University, Linköping, Sweden
| | - Mikael Benson
- The Centre for Individualized Medicine, Linköping University Hospital, Linköping University, Linköping, Sweden
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