Early DNA methylation changes in children developing beta cell autoimmunity at a young age

Inna Starskaia; Essi Laajala; Toni Grönroos; Taina Härkönen; Sini Junttila; Roosa Kattelus; Henna Kallionpää; Asta Laiho; Veronika Suni; Vallo Tillmann; Riikka Lund; Laura L. Elo; Harri Lähdesmäki; Mikael Knip; Ubaid Ullah Kalim; Riitta Lahesmaa

doi:10.1007/s00125-022-05657-x

Early DNA methylation changes in children developing beta cell autoimmunity at a young age

Inna Starskaia, Essi Laajala, Toni Grönroos, Taina Härkönen, Sini Junttila, Roosa Kattelus, Henna Kallionpää, Asta Laiho, Veronika Suni, Vallo Tillmann, Riikka Lund, Laura L. Elo, Harri Lähdesmäki, Mikael Knip, Ubaid Ullah Kalim^*, Riitta Lahesmaa^*

^*Corresponding author for this work

Turku Bioscience Centre

Research output: Contribution to journal › Article › Scientific › peer-review

13 Citations (Scopus)

61 Downloads (Pure)

Abstract

Aims/hypothesis: Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. Methods: Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4⁺ T cell, CD8⁺ T cell and CD4⁻CD8⁻ cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. Results: We identified 79, 56 and 45 differentially methylated regions in CD4⁺ T cells, CD8⁺ T cells and CD4⁻CD8⁻ cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4⁺ T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4⁺ T cells. Conclusions/interpretation: These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management. Graphical abstract: [Figure not available: see fulltext.]

Original language	English
Pages (from-to)	844-860
Number of pages	17
Journal	Diabetologia
Volume	65
Issue number	5
DOIs	https://doi.org/10.1007/s00125-022-05657-x
Publication status	Published - May 2022
MoE publication type	A1 Journal article-refereed

Funding

Open Access funding provided by University of Turku (UTU) including Turku University Central Hospital. R Lahesmaa was supported by the Academy of Finland (AoF) (grants 292335, 294337, 319280, 31444, 319280, 329277, 331790) and Business Finland, and grants from JDRF, the Novo Nordisk Foundation (grant NNF19OC0057218), the Sigrid Jusélius Foundation (SJF), the Jane and Aatos Erkko Foundation, the Finnish Diabetes Foundation and the Finnish Cancer Foundation. R Lahesmaa, HL and MK were supported by the AoF Centre of Excellence in Molecular Systems Immunology and Physiology Research (2012–2017), grant 250114 and grant 292482. VT was supported by the Estonian Research Council (grant PRG1428). LLE reports grants from the European Research Council (ERC) (677943), the European Union’s Horizon 2020 research and innovation programme (955321), the AoF (296801, 310561, 314443, 329278, 335434 and 335611) and the SJF. Our research is also supported by the University of Turku Graduate School (UTUGS), Biocenter Finland and the InFLAMES Flagship Programme of the AoF (decision number: 337530). IS was supported by the Turku Doctoral Programme of Molecular Medicine (TuDMM) and the Finnish Diabetes Research Foundation. EL was supported by the TuDMM, the Finnish Cultural Foundation, and the Kyllikki and Uolevi Lehikoinen Foundation. TG was supported by the Academy of Finland (grant 340231). We are grateful to the families for their participation in the DIABIMMUNE study and the clinical personnel for excellent collaboration, work with the families and collection of the samples for the study. We thank M. Hakkarainen and S. Heinonen (Turku Bioscience Centre, University of Turku, Finland) for their excellent technical help. We acknowledge the Turku Bioscience Centre’s core facility, the Finnish Functional Genomics Centre (FFGC), supported by Biocenter Finland, for their assistance. We also acknowledge the Finnish Centre for Scientific Computing (CSC), Elixir Finland and the Aalto Science-IT project for computational resources. The graphical abstract was created with BioRender. We are grateful to the families for their participation in the DIABIMMUNE study and the clinical personnel for excellent collaboration, work with the families and collection of the samples for the study. We thank M. Hakkarainen and S. Heinonen (Turku Bioscience Centre, University of Turku, Finland) for their excellent technical help. We acknowledge the Turku Bioscience Centre’s core facility, the Finnish Functional Genomics Centre (FFGC), supported by Biocenter Finland, for their assistance. We also acknowledge the Finnish Centre for Scientific Computing (CSC), Elixir Finland and the Aalto Science-IT project for computational resources. The graphical abstract was created with BioRender. The authors declare that there are no relationships or activities that might bias, or be perceived to bias, their work.

Keywords

DNA methylation
Epigenetics
T cells
Type 1 diabetes

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10.1007/s00125-022-05657-x

Early DNA methylation changes in children developing beta cell autoimmunity at a young ageFinal published version, 1.68 MBLicence: CC BY

https://urn.fi/URN:NBN:fi-fe2023022228220

Cite this

Starskaia, I., Laajala, E., Grönroos, T., Härkönen, T., Junttila, S., Kattelus, R., Kallionpää, H., Laiho, A., Suni, V., Tillmann, V., Lund, R., Elo, L. L., Lähdesmäki, H., Knip, M., Kalim, U. U., & Lahesmaa, R. (2022). Early DNA methylation changes in children developing beta cell autoimmunity at a young age. Diabetologia, 65(5), 844-860. https://doi.org/10.1007/s00125-022-05657-x

@article{8fe324fe79df4af29d93eaa00e677944,

title = "Early DNA methylation changes in children developing beta cell autoimmunity at a young age",

abstract = "Aims/hypothesis: Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. Methods: Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4+ T cell, CD8+ T cell and CD4−CD8− cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. Results: We identified 79, 56 and 45 differentially methylated regions in CD4+ T cells, CD8+ T cells and CD4−CD8− cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4+ T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4+ T cells. Conclusions/interpretation: These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management. Graphical abstract: [Figure not available: see fulltext.]",

keywords = "DNA methylation, Epigenetics, T cells, Type 1 diabetes",

author = "Inna Starskaia and Essi Laajala and Toni Gr{\"o}nroos and Taina H{\"a}rk{\"o}nen and Sini Junttila and Roosa Kattelus and Henna Kallionp{\"a}{\"a} and Asta Laiho and Veronika Suni and Vallo Tillmann and Riikka Lund and Elo, \{Laura L.\} and Harri L{\"a}hdesm{\"a}ki and Mikael Knip and Kalim, \{Ubaid Ullah\} and Riitta Lahesmaa",

note = "Funding Information: Open Access funding provided by University of Turku (UTU) including Turku University Central Hospital. R Lahesmaa was supported by the Academy of Finland (AoF) (grants 292335, 294337, 319280, 31444, 319280, 329277, 331790) and Business Finland, and grants from JDRF, the Novo Nordisk Foundation (grant NNF19OC0057218), the Sigrid Jus{\'e}lius Foundation (SJF), the Jane and Aatos Erkko Foundation, the Finnish Diabetes Foundation and the Finnish Cancer Foundation. R Lahesmaa, HL and MK were supported by the AoF Centre of Excellence in Molecular Systems Immunology and Physiology Research (2012–2017), grant 250114 and grant 292482. VT was supported by the Estonian Research Council (grant PRG1428). LLE reports grants from the European Research Council (ERC) (677943), the European Union{\textquoteright}s Horizon 2020 research and innovation programme (955321), the AoF (296801, 310561, 314443, 329278, 335434 and 335611) and the SJF. Our research is also supported by the University of Turku Graduate School (UTUGS), Biocenter Finland and the InFLAMES Flagship Programme of the AoF (decision number: 337530). IS was supported by the Turku Doctoral Programme of Molecular Medicine (TuDMM) and the Finnish Diabetes Research Foundation. EL was supported by the TuDMM, the Finnish Cultural Foundation, and the Kyllikki and Uolevi Lehikoinen Foundation. TG was supported by the Academy of Finland (grant 340231). Funding Information: We are grateful to the families for their participation in the DIABIMMUNE study and the clinical personnel for excellent collaboration, work with the families and collection of the samples for the study. We thank M. Hakkarainen and S. Heinonen (Turku Bioscience Centre, University of Turku, Finland) for their excellent technical help. We acknowledge the Turku Bioscience Centre{\textquoteright}s core facility, the Finnish Functional Genomics Centre (FFGC), supported by Biocenter Finland, for their assistance. We also acknowledge the Finnish Centre for Scientific Computing (CSC), Elixir Finland and the Aalto Science-IT project for computational resources. The graphical abstract was created with BioRender. Funding Information: We are grateful to the families for their participation in the DIABIMMUNE study and the clinical personnel for excellent collaboration, work with the families and collection of the samples for the study. We thank M. Hakkarainen and S. Heinonen (Turku Bioscience Centre, University of Turku, Finland) for their excellent technical help. We acknowledge the Turku Bioscience Centre{\textquoteright}s core facility, the Finnish Functional Genomics Centre (FFGC), supported by Biocenter Finland, for their assistance. We also acknowledge the Finnish Centre for Scientific Computing (CSC), Elixir Finland and the Aalto Science-IT project for computational resources. The graphical abstract was created with BioRender. The authors declare that there are no relationships or activities that might bias, or be perceived to bias, their work. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = may,

doi = "10.1007/s00125-022-05657-x",

language = "English",

volume = "65",

pages = "844--860",

journal = "Diabetologia",

issn = "0012-186X",

publisher = "Springer",

number = "5",

}

Starskaia, I, Laajala, E, Grönroos, T, Härkönen, T, Junttila, S, Kattelus, R, Kallionpää, H, Laiho, A, Suni, V, Tillmann, V, Lund, R, Elo, LL, Lähdesmäki, H, Knip, M, Kalim, UU & Lahesmaa, R 2022, 'Early DNA methylation changes in children developing beta cell autoimmunity at a young age', Diabetologia, vol. 65, no. 5, pp. 844-860. https://doi.org/10.1007/s00125-022-05657-x

TY - JOUR

T1 - Early DNA methylation changes in children developing beta cell autoimmunity at a young age

AU - Starskaia, Inna

AU - Laajala, Essi

AU - Grönroos, Toni

AU - Härkönen, Taina

AU - Junttila, Sini

AU - Kattelus, Roosa

AU - Kallionpää, Henna

AU - Laiho, Asta

AU - Suni, Veronika

AU - Tillmann, Vallo

AU - Lund, Riikka

AU - Elo, Laura L.

AU - Lähdesmäki, Harri

AU - Knip, Mikael

AU - Kalim, Ubaid Ullah

AU - Lahesmaa, Riitta

N1 - Funding Information: Open Access funding provided by University of Turku (UTU) including Turku University Central Hospital. R Lahesmaa was supported by the Academy of Finland (AoF) (grants 292335, 294337, 319280, 31444, 319280, 329277, 331790) and Business Finland, and grants from JDRF, the Novo Nordisk Foundation (grant NNF19OC0057218), the Sigrid Jusélius Foundation (SJF), the Jane and Aatos Erkko Foundation, the Finnish Diabetes Foundation and the Finnish Cancer Foundation. R Lahesmaa, HL and MK were supported by the AoF Centre of Excellence in Molecular Systems Immunology and Physiology Research (2012–2017), grant 250114 and grant 292482. VT was supported by the Estonian Research Council (grant PRG1428). LLE reports grants from the European Research Council (ERC) (677943), the European Union’s Horizon 2020 research and innovation programme (955321), the AoF (296801, 310561, 314443, 329278, 335434 and 335611) and the SJF. Our research is also supported by the University of Turku Graduate School (UTUGS), Biocenter Finland and the InFLAMES Flagship Programme of the AoF (decision number: 337530). IS was supported by the Turku Doctoral Programme of Molecular Medicine (TuDMM) and the Finnish Diabetes Research Foundation. EL was supported by the TuDMM, the Finnish Cultural Foundation, and the Kyllikki and Uolevi Lehikoinen Foundation. TG was supported by the Academy of Finland (grant 340231). Funding Information: We are grateful to the families for their participation in the DIABIMMUNE study and the clinical personnel for excellent collaboration, work with the families and collection of the samples for the study. We thank M. Hakkarainen and S. Heinonen (Turku Bioscience Centre, University of Turku, Finland) for their excellent technical help. We acknowledge the Turku Bioscience Centre’s core facility, the Finnish Functional Genomics Centre (FFGC), supported by Biocenter Finland, for their assistance. We also acknowledge the Finnish Centre for Scientific Computing (CSC), Elixir Finland and the Aalto Science-IT project for computational resources. The graphical abstract was created with BioRender. Funding Information: We are grateful to the families for their participation in the DIABIMMUNE study and the clinical personnel for excellent collaboration, work with the families and collection of the samples for the study. We thank M. Hakkarainen and S. Heinonen (Turku Bioscience Centre, University of Turku, Finland) for their excellent technical help. We acknowledge the Turku Bioscience Centre’s core facility, the Finnish Functional Genomics Centre (FFGC), supported by Biocenter Finland, for their assistance. We also acknowledge the Finnish Centre for Scientific Computing (CSC), Elixir Finland and the Aalto Science-IT project for computational resources. The graphical abstract was created with BioRender. The authors declare that there are no relationships or activities that might bias, or be perceived to bias, their work. Publisher Copyright: © 2022, The Author(s).

PY - 2022/5

Y1 - 2022/5

N2 - Aims/hypothesis: Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. Methods: Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4+ T cell, CD8+ T cell and CD4−CD8− cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. Results: We identified 79, 56 and 45 differentially methylated regions in CD4+ T cells, CD8+ T cells and CD4−CD8− cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4+ T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4+ T cells. Conclusions/interpretation: These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management. Graphical abstract: [Figure not available: see fulltext.]

AB - Aims/hypothesis: Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. Methods: Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4+ T cell, CD8+ T cell and CD4−CD8− cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. Results: We identified 79, 56 and 45 differentially methylated regions in CD4+ T cells, CD8+ T cells and CD4−CD8− cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4+ T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4+ T cells. Conclusions/interpretation: These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management. Graphical abstract: [Figure not available: see fulltext.]

KW - DNA methylation

KW - Epigenetics

KW - T cells

KW - Type 1 diabetes

UR - https://www.scopus.com/pages/publications/85124518845

U2 - 10.1007/s00125-022-05657-x

DO - 10.1007/s00125-022-05657-x

M3 - Article

C2 - 35142878

AN - SCOPUS:85124518845

SN - 0012-186X

VL - 65

SP - 844

EP - 860

JO - Diabetologia

JF - Diabetologia

IS - 5

ER -

Early DNA methylation changes in children developing beta cell autoimmunity at a young age

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