Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9

Antoine Weihs; Layal Chaker; Tiphaine c. Martin; Kim v.e. Braun; Purdey j. Campbell; Simon r. Cox; Myriam Fornage; Christian Gieger; Hans j. Grabe; Harald Grallert; Sarah e. Harris; Brigitte Kühnel; Riccardo e. Marioni; Nicholas g. Martin; Daniel l. Mccartney; Allan f. Mcrae; Christa Meisinger; Joyce b.j. Van meurs; Jana Nano; Matthias Nauck; Annette Peters; Holger Prokisch; Michael Roden; Elizabeth Selvin; Marian Beekman; Diana Van heemst; Eline p. Slagboom; Brenton r. Swenson; Adrienne Tin; Pei-Chien Tsai; Andre Uitterlinden; W. edward Visser; Henry Völzke; Melanie Waldenberger; John p. Walsh; Anna Köttgen; Scott g. Wilson; Robin p. Peeters; Jordana t. Bell; Marco Medici; Alexander Teumer

doi:10.1089/thy.2022.0373

Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9

Antoine Weihs, Layal Chaker, Tiphaine c. Martin, Kim v.e. Braun, Purdey j. Campbell, Simon r. Cox, Myriam Fornage, Christian Gieger, Hans j. Grabe, Harald Grallert, Sarah e. Harris, Brigitte Kühnel, Riccardo e. Marioni, Nicholas g. Martin, Daniel l. Mccartney, Allan f. Mcrae, Christa Meisinger, Joyce b.j. Van meurs, Jana Nano, Matthias NauckAnnette Peters, Holger Prokisch, Michael Roden, Elizabeth Selvin, Marian Beekman, Diana Van heemst, Eline p. Slagboom, Brenton r. Swenson, Adrienne Tin, Pei-Chien Tsai, Andre Uitterlinden, W. edward Visser, Henry Völzke, Melanie Waldenberger, John p. Walsh, Anna Köttgen, Scott g. Wilson, Robin p. Peeters, Jordana t. Bell, Marco Medici, Alexander Teumer

Twin Research & Genetic Epidemiology

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4 Citations (Scopus)

Abstract

Background: Thyroid hormones play a key role in differentiation and metabolism and are known regulators of gene expression through both genomic and epigenetic processes including DNA methylation. The aim of this study was to examine associations between thyroid hormones and DNA methylation. Methods: We carried out a fixed-effect meta-analysis of epigenome-wide association study (EWAS) of blood DNA methylation sites from 8 cohorts from the ThyroidOmics Consortium, incorporating up to 7073 participants of both European and African ancestry, implementing a discovery and replication stage. Statistical analyses were conducted using normalized beta CpG values as dependent and log-transformed thyrotropin (TSH), free thyroxine, and free triiodothyronine levels, respectively, as independent variable in a linear model. The replicated findings were correlated with gene expression levels in whole blood and tested for causal influence of TSH and free thyroxine by two-sample Mendelian randomization (MR). Results: Epigenome-wide significant associations (p-value <1.1E-7) of three CpGs for free thyroxine, five for free triiodothyronine, and two for TSH concentrations were discovered and replicated (combined p-values = 1.5E-9 to 4.3E-28). The associations included CpG sites annotated to KLF9 (cg00049440) and DOT1L (cg04173586) that overlap with all three traits, consistent with hypothalamic-pituitary-thyroid axis physiology. Significant associations were also found for CpGs in FKBP5 for free thyroxine, and at CSNK1D/LINCO1970 and LRRC8D for free triiodothyronine. MR analyses supported a causal effect of thyroid status on DNA methylation of KLF9. DNA methylation of cg00049440 in KLF9 was inversely correlated with KLF9 gene expression in blood. The CpG at CSNK1D/LINC01970 overlapped with thyroid hormone receptor alpha binding peaks in liver cells. The total additive heritability of the methylation levels of the six significant CpG sites was between 25% and 57%. Significant methylation QTLs were identified for CpGs at KLF9, FKBP5, LRRC8D, and CSNK1D/LINC01970. Conclusions: We report novel associations between TSH, thyroid hormones, and blood-based DNA methylation. This study advances our understanding of thyroid hormone action particularly related to KLF9 and serves as a proof-of-concept that integrations of EWAS with other -omics data can provide a valuable tool for unraveling thyroid hormone signaling in humans by complementing and feeding classical in vitro and animal studies.

Original language	English
Pages (from-to)	301-311
Number of pages	11
Journal	Thyroid
Volume	33
Issue number	3
Early online date	1 Mar 2023
DOIs	https://doi.org/10.1089/thy.2022.0373
Publication status	Published - 16 Mar 2023

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10.1089/thy.2022.0373

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Weihs, A., Chaker, L., Martin, T. C., Braun, K. V. E., Campbell, P. J., Cox, S. R., Fornage, M., Gieger, C., Grabe, H. J., Grallert, H., Harris, S. E., Kühnel, B., Marioni, R. E., Martin, N. G., Mccartney, D. L., Mcrae, A. F., Meisinger, C., Van meurs, J. B. J., Nano, J., ... Teumer, A. (2023). Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9. Thyroid, 33(3), 301-311. https://doi.org/10.1089/thy.2022.0373

@article{0773b6a7a5eb4d0698b372d897c916a0,

title = "Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9",

abstract = "Background: Thyroid hormones play a key role in differentiation and metabolism and are known regulators of gene expression through both genomic and epigenetic processes including DNA methylation. The aim of this study was to examine associations between thyroid hormones and DNA methylation. Methods: We carried out a fixed-effect meta-analysis of epigenome-wide association study (EWAS) of blood DNA methylation sites from 8 cohorts from the ThyroidOmics Consortium, incorporating up to 7073 participants of both European and African ancestry, implementing a discovery and replication stage. Statistical analyses were conducted using normalized beta CpG values as dependent and log-transformed thyrotropin (TSH), free thyroxine, and free triiodothyronine levels, respectively, as independent variable in a linear model. The replicated findings were correlated with gene expression levels in whole blood and tested for causal influence of TSH and free thyroxine by two-sample Mendelian randomization (MR). Results: Epigenome-wide significant associations (p-value <1.1E-7) of three CpGs for free thyroxine, five for free triiodothyronine, and two for TSH concentrations were discovered and replicated (combined p-values = 1.5E-9 to 4.3E-28). The associations included CpG sites annotated to KLF9 (cg00049440) and DOT1L (cg04173586) that overlap with all three traits, consistent with hypothalamic-pituitary-thyroid axis physiology. Significant associations were also found for CpGs in FKBP5 for free thyroxine, and at CSNK1D/LINCO1970 and LRRC8D for free triiodothyronine. MR analyses supported a causal effect of thyroid status on DNA methylation of KLF9. DNA methylation of cg00049440 in KLF9 was inversely correlated with KLF9 gene expression in blood. The CpG at CSNK1D/LINC01970 overlapped with thyroid hormone receptor alpha binding peaks in liver cells. The total additive heritability of the methylation levels of the six significant CpG sites was between 25% and 57%. Significant methylation QTLs were identified for CpGs at KLF9, FKBP5, LRRC8D, and CSNK1D/LINC01970. Conclusions: We report novel associations between TSH, thyroid hormones, and blood-based DNA methylation. This study advances our understanding of thyroid hormone action particularly related to KLF9 and serves as a proof-of-concept that integrations of EWAS with other -omics data can provide a valuable tool for unraveling thyroid hormone signaling in humans by complementing and feeding classical in vitro and animal studies.",

author = "Antoine Weihs and Layal Chaker and Martin, {Tiphaine c.} and Braun, {Kim v.e.} and Campbell, {Purdey j.} and Cox, {Simon r.} and Myriam Fornage and Christian Gieger and Grabe, {Hans j.} and Harald Grallert and Harris, {Sarah e.} and Brigitte K{\"u}hnel and Marioni, {Riccardo e.} and Martin, {Nicholas g.} and Mccartney, {Daniel l.} and Mcrae, {Allan f.} and Christa Meisinger and {Van meurs}, {Joyce b.j.} and Jana Nano and Matthias Nauck and Annette Peters and Holger Prokisch and Michael Roden and Elizabeth Selvin and Marian Beekman and {Van heemst}, Diana and Slagboom, {Eline p.} and Swenson, {Brenton r.} and Adrienne Tin and Pei-Chien Tsai and Andre Uitterlinden and Visser, {W. edward} and Henry V{\"o}lzke and Melanie Waldenberger and Walsh, {John p.} and Anna K{\"o}ttgen and Wilson, {Scott g.} and Peeters, {Robin p.} and Bell, {Jordana t.} and Marco Medici and Alexander Teumer",

note = "Funding Information: H.J.G. has received travel grants and speakers honoraria from Fresenius Medical Care, Neuraxpharm, Servier, and Janssen Cilag as well as research funding from Fresenius Medical Care not related to this work. R.E.M. has received speaker fees from Illumina and is an advisor to the Epigenetic Clock Development Foundation. All other authors declare no conflicts of interest. Publisher Copyright: {\textcopyright} 2023, Mary Ann Liebert, Inc., publishers.",

year = "2023",

month = mar,

day = "16",

doi = "10.1089/thy.2022.0373",

language = "English",

volume = "33",

pages = "301--311",

journal = "Thyroid",

issn = "1050-7256",

publisher = "Mary Ann Liebert",

number = "3",

}

Weihs, A, Chaker, L, Martin, TC, Braun, KVE, Campbell, PJ, Cox, SR, Fornage, M, Gieger, C, Grabe, HJ, Grallert, H, Harris, SE, Kühnel, B, Marioni, RE, Martin, NG, Mccartney, DL, Mcrae, AF, Meisinger, C, Van meurs, JBJ, Nano, J, Nauck, M, Peters, A, Prokisch, H, Roden, M, Selvin, E, Beekman, M, Van heemst, D, Slagboom, EP, Swenson, BR, Tin, A, Tsai, P-C, Uitterlinden, A, Visser, WE, Völzke, H, Waldenberger, M, Walsh, JP, Köttgen, A, Wilson, SG, Peeters, RP, Bell, JT, Medici, M & Teumer, A 2023, 'Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9', Thyroid, vol. 33, no. 3, pp. 301-311. https://doi.org/10.1089/thy.2022.0373

TY - JOUR

T1 - Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9

AU - Weihs, Antoine

AU - Chaker, Layal

AU - Martin, Tiphaine c.

AU - Braun, Kim v.e.

AU - Campbell, Purdey j.

AU - Cox, Simon r.

AU - Fornage, Myriam

AU - Gieger, Christian

AU - Grabe, Hans j.

AU - Grallert, Harald

AU - Harris, Sarah e.

AU - Kühnel, Brigitte

AU - Marioni, Riccardo e.

AU - Martin, Nicholas g.

AU - Mccartney, Daniel l.

AU - Mcrae, Allan f.

AU - Meisinger, Christa

AU - Van meurs, Joyce b.j.

AU - Nano, Jana

AU - Nauck, Matthias

AU - Peters, Annette

AU - Prokisch, Holger

AU - Roden, Michael

AU - Selvin, Elizabeth

AU - Beekman, Marian

AU - Van heemst, Diana

AU - Slagboom, Eline p.

AU - Swenson, Brenton r.

AU - Tin, Adrienne

AU - Tsai, Pei-Chien

AU - Uitterlinden, Andre

AU - Visser, W. edward

AU - Völzke, Henry

AU - Waldenberger, Melanie

AU - Walsh, John p.

AU - Köttgen, Anna

AU - Wilson, Scott g.

AU - Peeters, Robin p.

AU - Bell, Jordana t.

AU - Medici, Marco

AU - Teumer, Alexander

N1 - Funding Information: H.J.G. has received travel grants and speakers honoraria from Fresenius Medical Care, Neuraxpharm, Servier, and Janssen Cilag as well as research funding from Fresenius Medical Care not related to this work. R.E.M. has received speaker fees from Illumina and is an advisor to the Epigenetic Clock Development Foundation. All other authors declare no conflicts of interest. Publisher Copyright: © 2023, Mary Ann Liebert, Inc., publishers.

PY - 2023/3/16

Y1 - 2023/3/16

N2 - Background: Thyroid hormones play a key role in differentiation and metabolism and are known regulators of gene expression through both genomic and epigenetic processes including DNA methylation. The aim of this study was to examine associations between thyroid hormones and DNA methylation. Methods: We carried out a fixed-effect meta-analysis of epigenome-wide association study (EWAS) of blood DNA methylation sites from 8 cohorts from the ThyroidOmics Consortium, incorporating up to 7073 participants of both European and African ancestry, implementing a discovery and replication stage. Statistical analyses were conducted using normalized beta CpG values as dependent and log-transformed thyrotropin (TSH), free thyroxine, and free triiodothyronine levels, respectively, as independent variable in a linear model. The replicated findings were correlated with gene expression levels in whole blood and tested for causal influence of TSH and free thyroxine by two-sample Mendelian randomization (MR). Results: Epigenome-wide significant associations (p-value <1.1E-7) of three CpGs for free thyroxine, five for free triiodothyronine, and two for TSH concentrations were discovered and replicated (combined p-values = 1.5E-9 to 4.3E-28). The associations included CpG sites annotated to KLF9 (cg00049440) and DOT1L (cg04173586) that overlap with all three traits, consistent with hypothalamic-pituitary-thyroid axis physiology. Significant associations were also found for CpGs in FKBP5 for free thyroxine, and at CSNK1D/LINCO1970 and LRRC8D for free triiodothyronine. MR analyses supported a causal effect of thyroid status on DNA methylation of KLF9. DNA methylation of cg00049440 in KLF9 was inversely correlated with KLF9 gene expression in blood. The CpG at CSNK1D/LINC01970 overlapped with thyroid hormone receptor alpha binding peaks in liver cells. The total additive heritability of the methylation levels of the six significant CpG sites was between 25% and 57%. Significant methylation QTLs were identified for CpGs at KLF9, FKBP5, LRRC8D, and CSNK1D/LINC01970. Conclusions: We report novel associations between TSH, thyroid hormones, and blood-based DNA methylation. This study advances our understanding of thyroid hormone action particularly related to KLF9 and serves as a proof-of-concept that integrations of EWAS with other -omics data can provide a valuable tool for unraveling thyroid hormone signaling in humans by complementing and feeding classical in vitro and animal studies.

AB - Background: Thyroid hormones play a key role in differentiation and metabolism and are known regulators of gene expression through both genomic and epigenetic processes including DNA methylation. The aim of this study was to examine associations between thyroid hormones and DNA methylation. Methods: We carried out a fixed-effect meta-analysis of epigenome-wide association study (EWAS) of blood DNA methylation sites from 8 cohorts from the ThyroidOmics Consortium, incorporating up to 7073 participants of both European and African ancestry, implementing a discovery and replication stage. Statistical analyses were conducted using normalized beta CpG values as dependent and log-transformed thyrotropin (TSH), free thyroxine, and free triiodothyronine levels, respectively, as independent variable in a linear model. The replicated findings were correlated with gene expression levels in whole blood and tested for causal influence of TSH and free thyroxine by two-sample Mendelian randomization (MR). Results: Epigenome-wide significant associations (p-value <1.1E-7) of three CpGs for free thyroxine, five for free triiodothyronine, and two for TSH concentrations were discovered and replicated (combined p-values = 1.5E-9 to 4.3E-28). The associations included CpG sites annotated to KLF9 (cg00049440) and DOT1L (cg04173586) that overlap with all three traits, consistent with hypothalamic-pituitary-thyroid axis physiology. Significant associations were also found for CpGs in FKBP5 for free thyroxine, and at CSNK1D/LINCO1970 and LRRC8D for free triiodothyronine. MR analyses supported a causal effect of thyroid status on DNA methylation of KLF9. DNA methylation of cg00049440 in KLF9 was inversely correlated with KLF9 gene expression in blood. The CpG at CSNK1D/LINC01970 overlapped with thyroid hormone receptor alpha binding peaks in liver cells. The total additive heritability of the methylation levels of the six significant CpG sites was between 25% and 57%. Significant methylation QTLs were identified for CpGs at KLF9, FKBP5, LRRC8D, and CSNK1D/LINC01970. Conclusions: We report novel associations between TSH, thyroid hormones, and blood-based DNA methylation. This study advances our understanding of thyroid hormone action particularly related to KLF9 and serves as a proof-of-concept that integrations of EWAS with other -omics data can provide a valuable tool for unraveling thyroid hormone signaling in humans by complementing and feeding classical in vitro and animal studies.

UR - http://www.scopus.com/inward/record.url?scp=85150751780&partnerID=8YFLogxK

U2 - 10.1089/thy.2022.0373

DO - 10.1089/thy.2022.0373

M3 - Article

SN - 1050-7256

VL - 33

SP - 301

EP - 311

JO - Thyroid

JF - Thyroid

IS - 3

ER -

Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9

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