title: Differential Gene Expression Profiling of Orbital Adipose Tissue in Thyroid Orbitopathy.
abstract: OBJECTIVE
  We aimed to determine differentially expressed genes relevant to orbital inflammation and orbital fat expansion in thyroid orbitopathy (TO) using microarray gene profiling in a case-control study.
  
  
  METHODS
  Human orbital adipose samples were obtained from individuals with active TO (n = 12), inactive TO (n = 21), and normal controls (n = 21). Gene expression profiles were examined using microarray analysis and were compared between active and inactive TO, and between active TO and normal controls. Top ranked differentially expressed genes were validated by real-time RT-PCR in an additional eight active TO, 13 inactive TO, and 11 normal controls and correlated with gene set enrichment analysis (GSEA) and molecular pathways analysis.
  
  
  RESULTS
  Seven hundred twenty-one probes (683 genes) and 806 probes (735 genes) were significantly differentially expressed in comparing active to inactive TO and in comparing active TO to healthy controls, respectively. All selected genes were confirmed to be differentially expressed by real-time RT-PCR. Multiple top ranked genes in active versus inactive TO comparison are overrepresented by immune and inflammatory response genes. They include defensins (DEFA1, DEFA1B, DEFA3), which were overexpressed by 3.05- to 4.14-fold and TIMD4 by 4.20-fold. Markers for adipogenesis were overexpressed including SCD, FADS1, and SCDP1. Gene set enrichment analysis revealed dysregulation of epigenetic signatures, T-cell activation, Th1 differentiation, defensin pathway, cell adhesion, cytoskeleton organization, apoptosis, cell cycling, and lipid metabolism in active TO.
  
  
  CONCLUSIONS
  Active TO is characterized by upregulation of genes involved in cell-mediated immune, innate immune, and inflammatory response and enhanced orbital adipogenesis. TIMD4, DEFA1, DEFA1B, and DEFA3 genes may be involved in the innate immune-mediated orbital inflammation in TO. Epigenetic mechanisms may play a role in the pathogenesis of TO.
authors.affiliation: Department of Medicine North West Academic Centre, University of Melbourne, St. Albans, Victoria, Australia 2Orbital, Plastics, and Lacrimal Unit, The Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.
authors.forename: Jwu Jin
authors.initials: JJ
authors.lastname: Khong
authors.affiliation: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
authors.forename: Lynn Yuning
authors.initials: LY
authors.lastname: Wang
authors.affiliation: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia 4Department of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Gordon K
authors.initials: GK
authors.lastname: Smyth
authors.affiliation: Orbital, Plastics, and Lacrimal Unit, The Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.
authors.forename: Alan A
authors.initials: AA
authors.lastname: McNab
authors.affiliation: Orbital, Plastics, and Lacrimal Unit, The Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Hardy
authors.affiliation: Department of Ophthalmic and Visual Science, University of Adelaide, South Australia, Australia.
authors.forename: Dinesh
authors.initials: D
authors.lastname: Selva
authors.affiliation: School of Earth and Environmental Sciences, University of Adelaide, South Australia, Australia 7Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia.
authors.forename: Bastien
authors.initials: B
authors.lastname: Llamas
authors.affiliation: VLSCI, Life Sciences Computation Centre, University of Melbourne, Carlton, Victoria, Australia.
authors.forename: Chol-Hee
authors.initials: CH
authors.lastname: Jung
authors.affiliation: Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia.
authors.forename: Shiwani
authors.initials: S
authors.lastname: Sharma
authors.affiliation: Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia 9Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.
authors.forename: Kathryn P
authors.initials: KP
authors.lastname: Burdon
authors.affiliation: Department of Medicine North West Academic Centre, University of Melbourne, St. Albans, Victoria, Australia 10Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia.
authors.forename: Peter R
authors.initials: PR
authors.lastname: Ebeling
authors.affiliation: Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia.
authors.forename: Jamie E
authors.initials: JE
authors.lastname: Craig
mesh_terms: D050156:Adipogenesis / Q000235:genetics*; D000273:Adipose Tissue / Q000378:metabolism* / Q000473:pathology; D023082:Defensins / Q000096:biosynthesis / Q000235:genetics*; D000090943:Delta-5 Fatty Acid Desaturase; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D049970:Graves Ophthalmopathy / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D006801:Humans; D012313:RNA / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D023082:Defensins; D000090943:Delta-5 Fatty Acid Desaturase; D012313:RNA; C000716847:FADS1 protein, human