title: mRNA-Seq reveals novel molecular mechanisms and a robust fingerprint in Graves' disease.
abstract: BACKGROUND
  The immune response in autoimmune thyroid disease has been shown to occur primarily within the thyroid gland in which the most abundant antigens can be found. A variety of capture molecules are known to be expressed by thyroid epithelial cells and serve to attract and help retain an intrathyroidal immune infiltrate.
  
  
  OBJECTIVE
  To explore the entire repertoire of expressed genes in human thyroid tissue, we have deep sequenced the transcriptome (referred to as mRNA-Seq).
  
  
  METHODS
  We applied mRNA-Seq to thyroid tissue from nine patients with Graves' disease subjected to total thyroidectomy and compared the data with 12 samples of normal thyroid tissue obtained from patients having a thyroid nodule removed. The expression for each gene was calculated from the sequencing data by taking the median of the coverage across the length of the gene. The expression levels were quantile normalized and a gene signature was derived from these.
  
  
  RESULTS
  On comparison of expression levels in tissues derived from Graves' patients and controls, there was clear evidence for overexpression of the antigen presentation pathway consisting of HLA and associated genes. We also found a robust disease signature and discovered active innate and adaptive immune signaling networks.
  
  
  CONCLUSIONS
  These data reveal an active immune defense system in Graves' disease, which involves novel molecular mechanisms in its pathogenesis and development.
authors: Thyroid Research Unit (X.Y., S.M., R.L., T.F.D.), Department of Medicine, and Departments of Oncological Science (R.Sa.) and Pathology (R.Sh.), Icahn School of Medicine at Mt Sinai and the James J. Peters Veterans Affairs Medical Center, New York, New York 10468.
authors: Xiaoming
authors: X
authors: Yin
authors: Ravi
authors: R
authors: Sachidanandam
authors: Syed
authors: S
authors: Morshed
authors: Rauf
authors: R
authors: Latif
authors: Ruijin
authors: R
authors: Shi
authors: Terry F
authors: TF
authors: Davies
mesh_terms: D016207:Cytokines / Q000235:genetics / Q000276:immunology; D006111:Graves Disease / Q000235:genetics* / Q000276:immunology* / Q000601:surgery; D006650:Histocompatibility Testing / Q000379:methods; D006801:Humans; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D015398:Signal Transduction / Q000276:immunology; D013961:Thyroid Gland / Q000276:immunology*; D013965:Thyroidectomy; D014015:Tissue Banks; D059467:Transcriptome / Q000235:genetics* / Q000276:immunology
chemical_list: D016207:Cytokines; D012333:RNA, Messenger