Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and Asthma
BackgroundPreviously, we investigated skin microbiota and blood cell gene expression in Finnish and Russian teenagers with contrasting incidence of allergic conditions. The microbiota and transcriptomic signatures were distinctly different, with high Acinetobacter abundance and suppression of genes...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Allergy |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/falgy.2022.878862/full |
| _version_ | 1818141394015879168 |
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| author | Joseph Ndika Piia Karisola Vilma Lahti Nanna Fyhrquist Tiina Laatikainen Tiina Laatikainen Tari Haahtela Harri Alenius Harri Alenius |
| author_facet | Joseph Ndika Piia Karisola Vilma Lahti Nanna Fyhrquist Tiina Laatikainen Tiina Laatikainen Tari Haahtela Harri Alenius Harri Alenius |
| author_sort | Joseph Ndika |
| collection | DOAJ |
| description | BackgroundPreviously, we investigated skin microbiota and blood cell gene expression in Finnish and Russian teenagers with contrasting incidence of allergic conditions. The microbiota and transcriptomic signatures were distinctly different, with high Acinetobacter abundance and suppression of genes regulating innate immune response in healthy subjects.ObjectiveHere, we investigated long non-coding RNA (lncRNA) expression profiles of blood mononuclear cells (PBMC) from healthy and allergic subjects, to identify lncRNAs that act at the interphase of microbiome-mediated immune homeostasis in allergy/asthma.MethodsGenome-wide co-expression network analyses of blood cell lncRNA/mRNA expression was integrated with skin microbiota profiles of Finnish (69) and Russian (75) subjects. Selected lncRNAs were validated by stimulation of cohort-derived PBMCs and a macrophage cell model with birch pollen allergen (Betv1) or lipopolysaccharide, respectively.ResultsFinnish and Russian PBMCs were differentiated by 3,818 lncRNA transcripts. In the Finnish subjects with high prevalence of allergy and asthma, a subset of 37 downregulated lncRNAs (including, FAM155A-IT1 and LOC400958) were identified. They were part of a co-expression network with 20 genes known to be related to asthma and allergic rhinitis (R > 0.95). Incidentally, all these 20 genes were also components of pathways corresponding to cellular response to bacterium. The Finnish and Russian samples were also differentiated by the abundance of 176 bacterial OTU (operational taxonomic units). The subset of 37 lncRNAs, associated with allergy, was most correlated with the abundance of Acinetobacter (R > +0.5), Jeotgalicoccus (R > +0.5), Corynebacterium (R < −0.5) and Micrococcus (R < −0.5).ConclusionIn Finnish and Russian teenagers with contrasting allergy and asthma prevalence, epigenetic differences in lncRNA expression appear to be important components of the underlying microbiota-immune interactions. Unraveling the functions of the 37 differing lncRNAs may be the key to understanding microbiome-immune crosstalk, and to develop clinically relevant biomarkers. |
| first_indexed | 2024-12-11T10:59:11Z |
| format | Article |
| id | doaj.art-c23ab8caec564a1ba27c2cbb6585cc82 |
| institution | Directory Open Access Journal |
| issn | 2673-6101 |
| language | English |
| last_indexed | 2024-12-11T10:59:11Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Allergy |
| spelling | doaj.art-c23ab8caec564a1ba27c2cbb6585cc822022-12-22T01:09:57ZengFrontiers Media S.A.Frontiers in Allergy2673-61012022-04-01310.3389/falgy.2022.878862878862Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and AsthmaJoseph Ndika0Piia Karisola1Vilma Lahti2Nanna Fyhrquist3Tiina Laatikainen4Tiina Laatikainen5Tari Haahtela6Harri Alenius7Harri Alenius8Human Microbiome Research (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, FinlandHuman Microbiome Research (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, FinlandHuman Microbiome Research (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, FinlandInstitute of Environmental Medicine, Karolinska Institutet, Stockholm, SwedenDepartment of Public Health Solutions, Finnish Institute for Health and Welfare (THL), Helsinki, FinlandInstitute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, FinlandSkin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, FinlandHuman Microbiome Research (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, FinlandInstitute of Environmental Medicine, Karolinska Institutet, Stockholm, SwedenBackgroundPreviously, we investigated skin microbiota and blood cell gene expression in Finnish and Russian teenagers with contrasting incidence of allergic conditions. The microbiota and transcriptomic signatures were distinctly different, with high Acinetobacter abundance and suppression of genes regulating innate immune response in healthy subjects.ObjectiveHere, we investigated long non-coding RNA (lncRNA) expression profiles of blood mononuclear cells (PBMC) from healthy and allergic subjects, to identify lncRNAs that act at the interphase of microbiome-mediated immune homeostasis in allergy/asthma.MethodsGenome-wide co-expression network analyses of blood cell lncRNA/mRNA expression was integrated with skin microbiota profiles of Finnish (69) and Russian (75) subjects. Selected lncRNAs were validated by stimulation of cohort-derived PBMCs and a macrophage cell model with birch pollen allergen (Betv1) or lipopolysaccharide, respectively.ResultsFinnish and Russian PBMCs were differentiated by 3,818 lncRNA transcripts. In the Finnish subjects with high prevalence of allergy and asthma, a subset of 37 downregulated lncRNAs (including, FAM155A-IT1 and LOC400958) were identified. They were part of a co-expression network with 20 genes known to be related to asthma and allergic rhinitis (R > 0.95). Incidentally, all these 20 genes were also components of pathways corresponding to cellular response to bacterium. The Finnish and Russian samples were also differentiated by the abundance of 176 bacterial OTU (operational taxonomic units). The subset of 37 lncRNAs, associated with allergy, was most correlated with the abundance of Acinetobacter (R > +0.5), Jeotgalicoccus (R > +0.5), Corynebacterium (R < −0.5) and Micrococcus (R < −0.5).ConclusionIn Finnish and Russian teenagers with contrasting allergy and asthma prevalence, epigenetic differences in lncRNA expression appear to be important components of the underlying microbiota-immune interactions. Unraveling the functions of the 37 differing lncRNAs may be the key to understanding microbiome-immune crosstalk, and to develop clinically relevant biomarkers.https://www.frontiersin.org/articles/10.3389/falgy.2022.878862/fulllong non-coding RNAimmune homeostasisasthmaallergymicrobiota |
| spellingShingle | Joseph Ndika Piia Karisola Vilma Lahti Nanna Fyhrquist Tiina Laatikainen Tiina Laatikainen Tari Haahtela Harri Alenius Harri Alenius Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and Asthma Frontiers in Allergy long non-coding RNA immune homeostasis asthma allergy microbiota |
| title | Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and Asthma |
| title_full | Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and Asthma |
| title_fullStr | Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and Asthma |
| title_full_unstemmed | Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and Asthma |
| title_short | Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and Asthma |
| title_sort | epigenetic differences in long non coding rna expression in finnish and russian karelia teenagers with contrasting risk of allergy and asthma |
| topic | long non-coding RNA immune homeostasis asthma allergy microbiota |
| url | https://www.frontiersin.org/articles/10.3389/falgy.2022.878862/full |
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