Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy
BackgroundGraves’ ophthalmopathy (GO) is a frequent extrathyroidal complication of Graves’ hyperthyroidism. Orbital fibroblasts contribute to both orbital tissue inflammation and remodeling in GO, and as such are crucial cellular elements in active GO and inactive GO. However, so far it is largely u...
Main Authors: | , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2021-02-01
|
Series: | Frontiers in Endocrinology |
Subjects: | |
Online Access: | https://www.frontiersin.org/articles/10.3389/fendo.2020.619989/full |
id |
doaj-59861f5dc9a04b719fa6d6c52440a04c |
---|---|
record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Sita Virakul Poorichaya Somparn Poorichaya Somparn Trairak Pisitkun Peter J. van der Spek Virgil A. S. H. Dalm Virgil A. S. H. Dalm Dion Paridaens Dion Paridaens P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen Nattiya Hirankarn Tanapat Palaga Willem A. Dik |
spellingShingle |
Sita Virakul Poorichaya Somparn Poorichaya Somparn Trairak Pisitkun Peter J. van der Spek Virgil A. S. H. Dalm Virgil A. S. H. Dalm Dion Paridaens Dion Paridaens P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen Nattiya Hirankarn Tanapat Palaga Willem A. Dik Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy Frontiers in Endocrinology graves’ ophthalmopathy orbital fibroblast proteomics DNA methylation epigenetics |
author_facet |
Sita Virakul Poorichaya Somparn Poorichaya Somparn Trairak Pisitkun Peter J. van der Spek Virgil A. S. H. Dalm Virgil A. S. H. Dalm Dion Paridaens Dion Paridaens P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen Nattiya Hirankarn Tanapat Palaga Willem A. Dik |
author_sort |
Sita Virakul |
title |
Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy |
title_short |
Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy |
title_full |
Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy |
title_fullStr |
Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy |
title_full_unstemmed |
Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy |
title_sort |
integrative analysis of proteomics and dna methylation in orbital fibroblasts from graves’ ophthalmopathy |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Endocrinology |
issn |
1664-2392 |
publishDate |
2021-02-01 |
description |
BackgroundGraves’ ophthalmopathy (GO) is a frequent extrathyroidal complication of Graves’ hyperthyroidism. Orbital fibroblasts contribute to both orbital tissue inflammation and remodeling in GO, and as such are crucial cellular elements in active GO and inactive GO. However, so far it is largely unknown whether GO disease progression is associated with functional reprogramming of the orbital fibroblast effector function. Therefore, the aim of this study was to compare both the proteome and global DNA methylation patterns between orbital fibroblasts isolated from active GO, inactive GO and healthy controls.MethodsOrbital fibroblasts from inactive GO (n=5), active GO (n=4) and controls (n=5) were cultured and total protein and DNA was isolated. Labelled and fractionated proteins were analyzed with a liquid chromatography tandem-mass spectrometer (LC-MS/MS). Data are available via ProteomeXchange with identifier PXD022257. Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip. In addition, RNA was isolated from the orbital fibroblasts for real-time quantitative (RQ)-PCR. Network and pathway analyses were performed.ResultsOrbital fibroblasts from active GO displayed overexpression of proteins that are typically involved in inflammation, cellular proliferation, hyaluronan synthesis and adipogenesis, while various proteins associated with extracellular matrix (ECM) biology and fibrotic disease, were typically overexpressed in orbital fibroblasts from inactive GO. Moreover, orbital fibroblasts from active GO displayed hypermethylation of genes that linked to inflammation and hypomethylated genes that linked to adipogenesis and autoimmunity. Further analysis revealed networks that contained molecules to which both hypermethylated and hypomethylated genes were linked, including NF-κB, ERK1/2, Alp, RNA polymerase II, Akt and IFNα. In addition, NF-κB, Akt and IFNα were also identified in networks that were derived from the differentially expressed proteins. Generally, poor correlation between protein expression, DNA methylation and mRNA expression was observed.ConclusionsBoth the proteomics and DNA methylation data support that orbital fibroblasts from active GO are involved in inflammation, adipogenesis, and glycosaminoglycan production, while orbital fibroblasts from inactive disease are more skewed towards an active role in extracellular matrix remodeling. This switch in orbital fibroblast effector function may have therapeutic implications and further studies into the underlying mechanism are thus warranted. |
topic |
graves’ ophthalmopathy orbital fibroblast proteomics DNA methylation epigenetics |
url |
https://www.frontiersin.org/articles/10.3389/fendo.2020.619989/full |
work_keys_str_mv |
AT sitavirakul integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT poorichayasomparn integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT poorichayasomparn integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT trairakpisitkun integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT peterjvanderspek integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT virgilashdalm integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT virgilashdalm integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT dionparidaens integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT dionparidaens integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT pmartinvanhagen integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT pmartinvanhagen integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT pmartinvanhagen integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT nattiyahirankarn integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT tanapatpalaga integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy AT willemadik integrativeanalysisofproteomicsanddnamethylationinorbitalfibroblastsfromgravesophthalmopathy |
_version_ |
1724268839806435328 |
spelling |
doaj-59861f5dc9a04b719fa6d6c52440a04c2021-02-15T15:56:22ZengFrontiers Media S.A.Frontiers in Endocrinology1664-23922021-02-011110.3389/fendo.2020.619989619989Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ OphthalmopathySita Virakul0Poorichaya Somparn1Poorichaya Somparn2Trairak Pisitkun3Peter J. van der Spek4Virgil A. S. H. Dalm5Virgil A. S. H. Dalm6Dion Paridaens7Dion Paridaens8P. Martin van Hagen9P. Martin van Hagen10P. Martin van Hagen11Nattiya Hirankarn12Tanapat Palaga13Willem A. Dik14Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, ThailandCenter of Excellence in Systems Biology, Research affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, ThailandTranslational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, ThailandCenter of Excellence in Systems Biology, Research affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, ThailandDepartment of Bioinformatics, Erasmus University Medical Center, Rotterdam, NetherlandsDepartment of Immunology, Laboratory Medical Immunology, Erasmus University Medical Center, Rotterdam, NetherlandsDepartment of Internal Medicine, Division of Clinical Immunology, Erasmus University Medical Center, Rotterdam, NetherlandsRotterdam Eye Hospital, Rotterdam, NetherlandsDepartment of Ophthalmology, Erasmus Medical Center, Rotterdam, NetherlandsDepartment of Immunology, Laboratory Medical Immunology, Erasmus University Medical Center, Rotterdam, NetherlandsDepartment of Internal Medicine, Division of Clinical Immunology, Erasmus University Medical Center, Rotterdam, NetherlandsRotterdam Eye Hospital, Rotterdam, NetherlandsCenter of Excellence in Immunology and Immune Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, ThailandDepartment of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, ThailandDepartment of Immunology, Laboratory Medical Immunology, Erasmus University Medical Center, Rotterdam, NetherlandsBackgroundGraves’ ophthalmopathy (GO) is a frequent extrathyroidal complication of Graves’ hyperthyroidism. Orbital fibroblasts contribute to both orbital tissue inflammation and remodeling in GO, and as such are crucial cellular elements in active GO and inactive GO. However, so far it is largely unknown whether GO disease progression is associated with functional reprogramming of the orbital fibroblast effector function. Therefore, the aim of this study was to compare both the proteome and global DNA methylation patterns between orbital fibroblasts isolated from active GO, inactive GO and healthy controls.MethodsOrbital fibroblasts from inactive GO (n=5), active GO (n=4) and controls (n=5) were cultured and total protein and DNA was isolated. Labelled and fractionated proteins were analyzed with a liquid chromatography tandem-mass spectrometer (LC-MS/MS). Data are available via ProteomeXchange with identifier PXD022257. Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip. In addition, RNA was isolated from the orbital fibroblasts for real-time quantitative (RQ)-PCR. Network and pathway analyses were performed.ResultsOrbital fibroblasts from active GO displayed overexpression of proteins that are typically involved in inflammation, cellular proliferation, hyaluronan synthesis and adipogenesis, while various proteins associated with extracellular matrix (ECM) biology and fibrotic disease, were typically overexpressed in orbital fibroblasts from inactive GO. Moreover, orbital fibroblasts from active GO displayed hypermethylation of genes that linked to inflammation and hypomethylated genes that linked to adipogenesis and autoimmunity. Further analysis revealed networks that contained molecules to which both hypermethylated and hypomethylated genes were linked, including NF-κB, ERK1/2, Alp, RNA polymerase II, Akt and IFNα. In addition, NF-κB, Akt and IFNα were also identified in networks that were derived from the differentially expressed proteins. Generally, poor correlation between protein expression, DNA methylation and mRNA expression was observed.ConclusionsBoth the proteomics and DNA methylation data support that orbital fibroblasts from active GO are involved in inflammation, adipogenesis, and glycosaminoglycan production, while orbital fibroblasts from inactive disease are more skewed towards an active role in extracellular matrix remodeling. This switch in orbital fibroblast effector function may have therapeutic implications and further studies into the underlying mechanism are thus warranted.https://www.frontiersin.org/articles/10.3389/fendo.2020.619989/fullgraves’ ophthalmopathyorbital fibroblastproteomicsDNA methylationepigenetics |