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Täubel M, Jalanka J, Kirjavainen PV, Tuoresmäki P, Hyvärinen A, Skevaki C, Piippo-Savolainen E, Pekkanen J, Karvonen AM. Fungi in Early-Life House Dust Samples and the Development of Asthma: A Birth Cohort Study. Ann Am Thorac Soc 2023; 20:1456-1464. [PMID: 37535826 PMCID: PMC10559140 DOI: 10.1513/annalsats.202303-187oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023] Open
Abstract
Rationale: Fungal exposure has been associated with predisposing and protective effects on the development of childhood asthma. Objectives: To study whether early-life house dust mycobiota composition is associated with the development of asthma. Methods: Mycobiota were determined by amplicon sequencing from 382 dust samples collected from living room floors 2 months after birth in homes of the LUKAS cohort. Asthma status by 10.5 years of age was defined from questionnaires and assigned as ever asthma (n = 68) or current asthma (n = 27). Inhalant atopy was clinically determined at the same age. β-composition was analyzed using PERMANOVA-S, and asthma and atopy analyses were performed using discrete time hazard models and logistic regression, respectively. Results: The house dust mycobiota composition based on Bray-Curtis distance was different in the homes of children who later did or did not develop asthma. The first and the fourth axes scores of principal coordinates analysis based on Bray-Curtis were associated with ever asthma. Of the genera with the strongest correlation with these axes, the relative abundance of Boeremia, Cladosporium, Microdochium, Mycosphaerella, and Pyrenochaetopsis showed protective associations with asthma. None of these associations remained significant after mutual adjustment among the five genera or when mutually adjusted for other microbial cell wall markers and previously identified asthma-protective bacterial indices. Neither fungal α-diversity nor load was associated with asthma in the whole population, but higher fungal richness was a risk factor among children on farms. Higher fungal loads (measured via quantitative polymerase chain reaction) in house dust were associated with the risk of inhalant atopy. Conclusions: The results of our analyses from this well-characterized birth cohort suggest that the early-life house dust mycobiota in Finnish homes, characterized via DNA amplicon sequencing, do not have strong predisposing or protective effects on asthma development.
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Affiliation(s)
- Martin Täubel
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Jonna Jalanka
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Pirkka V. Kirjavainen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Pauli Tuoresmäki
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Anne Hyvärinen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
- Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Marburg, Germany
| | | | - Juha Pekkanen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Anne M. Karvonen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
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Lukkarinen M, Kirjavainen PV, Backman K, Gonzales-Inca C, Hickman B, Kallio S, Karlsson H, Karlsson L, Keski-Nisula L, Korhonen LS, Korpela K, Kuitunen M, Kukkonen AK, Käyhkö N, Lagström H, Lukkarinen H, Peltola V, Pentti J, Salonen A, Savilahti E, Tuoresmäki P, Täubel M, Vahtera J, de Vos WM, Pekkanen J, Karvonen AM. Early-life environment and the risk of eczema at 2 years-Meta-analyses of six Finnish birth cohorts. Pediatr Allergy Immunol 2023; 34:e13945. [PMID: 37102387 DOI: 10.1111/pai.13945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/28/2023] [Accepted: 03/07/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Urban-related nature exposures are suggested to contribute to the rising prevalence of allergic diseases despite little supporting evidence. Our aim was to evaluate the impact of 12 land cover classes and two greenness indices around homes at birth on the development of doctor-diagnosed eczema by the age of 2 years, and the influence of birth season. METHODS Data from 5085 children were obtained from six Finnish birth cohorts. Exposures were provided by the Coordination of Information on the Environment in three predefined grid sizes. Adjusted logistic regression was run in each cohort, and pooled effects across cohorts were estimated using fixed or random effect meta-analyses. RESULTS In meta-analyses, neither greenness indices (NDVI or VCDI, 250 m × 250 m grid size) nor residential or industrial/commercial areas were associated with eczema by age of 2 years. Coniferous forest (adjusted odds ratio 1.19; 95% confidence interval 1.01-1.39 for the middle and 1.16; 0.98-1.28 for the highest vs. lowest tertile) and mixed forest (1.21; 1.02-1.42 middle vs. lowest tertile) were associated with elevated eczema risk. Higher coverage with agricultural areas tended to associate with elevated eczema risk (1.20; 0.98-1.48 vs. none). In contrast, transport infrastructure was inversely associated with eczema (0.77; 0.65-0.91 highest vs. lowest tertile). CONCLUSION Greenness around the home during early childhood does not seem to protect from eczema. In contrast, nearby coniferous and mixed forests may increase eczema risk, as well as being born in spring close to forest or high-green areas.
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Affiliation(s)
- Minna Lukkarinen
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Pirkka V Kirjavainen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Katri Backman
- Kuopio Birth Cohort (KuBiCo), University of Eastern Finland, Kuopio, Finland
- Department of Paediatrics, Kuopio University Hospital, Kuopio, Finland
| | | | - Brandon Hickman
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampo Kallio
- FLORA: New Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hasse Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Psychiatry, University of Turku and Turku University Hospital, Turku, Finland
| | - Linnea Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Leea Keski-Nisula
- Kuopio Birth Cohort (KuBiCo), University of Eastern Finland, Kuopio, Finland
- Department of Obstetrics and Gynaecology, Kuopio University Hospital, Kuopio, Finland
| | - Laura S Korhonen
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Kuitunen
- FLORA: New Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anna Kaarina Kukkonen
- FLORA: New Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Niina Käyhkö
- Department of Geography and Geology, University of Turku, Turku, Finland
| | - Hanna Lagström
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Heikki Lukkarinen
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Jaana Pentti
- Department of Public Health, University of Turku, Turku, Finland
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Erkki Savilahti
- FLORA: New Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pauli Tuoresmäki
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Martin Täubel
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Jussi Vahtera
- Department of Public Health, University of Turku, Turku, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juha Pekkanen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anne M Karvonen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
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Hyytiäinen H, Kirjavainen PV, Täubel M, Tuoresmäki P, Casas L, Heinrich J, Herberth G, Standl M, Renz H, Piippo-Savolainen E, Hyvärinen A, Pekkanen J, Karvonen AM. Microbial diversity in homes and the risk of allergic rhinitis and inhalant atopy in two European birth cohorts. Environ Res 2021; 196:110835. [PMID: 33582132 DOI: 10.1016/j.envres.2021.110835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/21/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Microbial exposures in early childhood direct the development of the immune system and their diversity may influence the risk of allergy development. We aimed to determine whether the indoor microbial diversity at early-life is associated with the development of allergic rhinitis and inhalant atopy. METHODS The study population included children within two birth cohorts: Finnish rural-suburban LUKAS (N = 312), and German urban LISA from Munich and Leipzig study centers (N = 248). The indoor microbiota diversity (Chao1 richness and Shannon entropy) was characterized from floor dust samples collected at the child age of 2-3 months by Illumina MiSeq sequencing of bacterial and fungal DNA amplicons. Allergic rhinitis and inhalant atopy were determined at the age of 10 years and analyzed using logistic regression models. RESULTS High bacterial richness (aOR 0.19, 95%CI 0.09-0.42 for middle and aOR 0.12, 95%CI 0.05-0.29 for highest vs. lowest tertile) and Shannon entropy were associated with lower risk of allergic rhinitis in LISA, and similar trend was seen in LUKAS. We observed some significant associations between bacterial and fungal diversity measured and the risk of inhalant atopy, but the associations were inconsistent between the two cohorts. High bacterial diversity tended to be associated with increased risk of inhalant atopy in rural areas, but lower risk in more urban areas. Fungal diversity tended to be associated with increased risk of inhalant atopy only in LISA. CONCLUSIONS Our study suggests that a higher bacterial diversity may reduce the risk of allergic rhinitis later in childhood. The environment-dependent heterogeneity in the associations with inhalant atopy - visible here as inconsistent results between two differing cohorts - suggests that specific constituents of the diversity may be relevant.
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Affiliation(s)
- Heidi Hyytiäinen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Pirkka V Kirjavainen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland; Institute of Public Health and Clinical Nutrition, Department of Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Martin Täubel
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Pauli Tuoresmäki
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Lidia Casas
- Centre for Environment and Health - Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Social Epidemiology and Health Policy, Department of Family Medicine and Population Health, University of Antwerp, Antwerp, Belgium
| | - Joachim Heinrich
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital Munich, Ludwig Maximillians University Munich, Member of German Center for Lung Research (DZL), Munich, Germany
| | - Gunda Herberth
- Department of Environmental Immunology/Core Facility Studies, Helmholtz Centre for Environmental Research- UFZ, Leipzig, Germany
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald Renz
- Department of Clinical Chemistry and Molecular Diagnostics, Philipps University of Marburg, Marburg, Germany; Member of the German Center for Lung Research, Germany
| | - Eija Piippo-Savolainen
- Department of Pediatrics, Kuopio University Hospital, Kuopio, Finland; Department of Pediatrics, University of Eastern Finland, Kuopio; Finland
| | - Anne Hyvärinen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Juha Pekkanen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Anne M Karvonen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland.
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Kuosmanen SM, Kansanen E, Kaikkonen MU, Sihvola V, Pulkkinen K, Jyrkkänen HK, Tuoresmäki P, Hartikainen J, Hippeläinen M, Kokki H, Tavi P, Heikkinen S, Levonen AL. NRF2 regulates endothelial glycolysis and proliferation with miR-93 and mediates the effects of oxidized phospholipids on endothelial activation. Nucleic Acids Res 2018; 46:1124-1138. [PMID: 29161413 PMCID: PMC5815049 DOI: 10.1093/nar/gkx1155] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/12/2017] [Accepted: 11/01/2017] [Indexed: 01/02/2023] Open
Abstract
Phospholipids, such as 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PAPC), are the major components of cell membranes. Their exposure to reactive oxygen species creates oxidized phospholipids, which predispose to the development of chronic inflammatory diseases and metabolic disorders through endothelial activation and dysfunction. Although the effects of oxidized PAPC (oxPAPC) on endothelial cells have been previously studied, the underlying molecular mechanisms evoking biological responses remain largely unknown. Here, we investigated the molecular mechanisms of oxPAPC function with a special emphasis on NRF2-regulated microRNAs (miRNAs) in human umbilical vein endothelial cells (HUVECs) utilizing miRNA profiling, global run-on sequencing (GRO-seq), genome-wide NRF2 binding model, and RNA sequencing (RNA-seq) with miRNA overexpression and silencing. We report that the central regulators of endothelial activity, KLF2 for quiescence, PFKFB3 for glycolysis, and VEGFA, FOXO1 and MYC for growth and proliferation, are regulated by transcription factor NRF2 and the NRF2-regulated miR-106b∼25 cluster member, miR-93, in HUVECs. Mechanistically, oxPAPC was found to induce glycolysis and proliferation NRF2-dependently, and oxPAPC-dependent induction of the miR-106b∼25 cluster was mediated by NRF2. Additionally, several regulatory loops were established between NRF2, miR-93 and the essential regulators of healthy endothelium, collectively implying that NRF2 controls the switch between the quiescent and the proliferative endothelial states together with miR-93.
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Affiliation(s)
- Suvi M Kuosmanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Emilia Kansanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Virve Sihvola
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kati Pulkkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Henna-Kaisa Jyrkkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Pauli Tuoresmäki
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Juha Hartikainen
- School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Heart Centre, Kuopio University Hospital, 70211 Kuopio, Finland
| | | | - Hannu Kokki
- School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Anaesthesia and Operative Services, 70211 Kuopio University Hospital, Kuopio, Finland
| | - Pasi Tavi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Sami Heikkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Anna-Liisa Levonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
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Abstract
The genome-wide analysis of the binding sites of the transcription factor vitamin D receptor (VDR) is essential for a global appreciation the physiological impact of the nuclear hormone 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). Genome-wide analysis of lipopolysaccharide (LPS)-polarized THP-1 human monocytic leukemia cells via chromatin immunoprecipitation sequencing (ChIP-seq) resulted in 1,318 high-confidence VDR binding sites, of which 789 and 364 occurred uniquely with and without 1,25(OH)2D3 stimulation, while only 165 were common. We re-analyzed five public VDR ChIP-seq datasets with identical peak calling settings (MACS, version 2) and found, using a novel consensus summit identification strategy, in total 23,409 non-overlapping VDR binding sites, 75% of which are unique within the six analyzed cellular models. LPS-differentiated THP-1 cells have 22% more genomic VDR locations than undifferentiated cells and both cell types display more overlap in their VDR locations than the other investigated cell types. In general, the intersection of VDR binding profiles of ligand-stimulated cells is higher than those of unstimulated cells. De novo binding site searches and HOMER screening for binding motifs formed by direct repeats spaced by three nucleotides (DR3) suggest for all six VDR ChIP-seq datasets that these sequences are found preferentially at highly ligand responsive VDR loci. Importantly, all VDR ChIP-seq datasets display the same relationship between the VDR occupancy and the percentage of DR3-type sequences below the peak summits. The comparative analysis of six VDR ChIP-seq datasets demonstrated that the mechanistic basis for the action of the VDR is independent of the cell type. Only the minority of genome-wide VDR binding sites contains a DR3-type sequence. Moreover, the total number of identified VDR binding sites in each ligand-stimulated cell line inversely correlates with the percentage of peak summits with DR3 sites.
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Affiliation(s)
- Pauli Tuoresmäki
- Department of Biosciences, University of Eastern Finland, Kuopio, Finland
| | - Sami Väisänen
- Department of Biosciences, University of Eastern Finland, Kuopio, Finland
| | - Antonio Neme
- Department of Biosciences, University of Eastern Finland, Kuopio, Finland
| | - Sami Heikkinen
- Department of Biosciences, University of Eastern Finland, Kuopio, Finland
| | - Carsten Carlberg
- Department of Biosciences, University of Eastern Finland, Kuopio, Finland
- * E-mail:
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