title: Gene profiling of scleroderma skin reveals robust signatures of disease that are imperfectly reflected in the transcript profiles of explanted fibroblasts.
abstract: OBJECTIVE
  To determine whether biopsy specimens obtained from systemic sclerosis (SSc) lesions show a distinctive gene profile, whether that gene profile is maintained in fibroblasts cultured from SSc skin biopsy specimens, and whether results from tissue obtained from multiple clinical centers can be combined to yield useful observations in this rare disease.
  
  
  METHODS
  Biopsy samples and passaged fibroblasts were stored in RNAlater solution prior to processing for RNA. RNA from SSc and control skin biopsy specimens, as well as SSc and control explanted passage 4 fibroblasts, from 9 patients and 9 controls was hybridized to Affymetrix HG-U133A arrays. Data were analyzed using the BRB ArrayTools system. When appropriate, findings were followed up with immunohistochemical analysis or TaqMan studies.
  
  
  RESULTS
  Biopsy samples obtained from patients with SSc had a robust and distinctive gene profile, with approximately 1,800 qualifiers distinguishing normal skin from SSc skin at a significant level. The SSc phenotype was the major driver of sample clusters, independent of origin. Alterations in transforming growth factor beta and Wnt pathways, extracellular matrix proteins, and the CCN family were prominent. Explanted fibroblasts from SSc biopsy samples showed a far smaller subset of changes that were relatively variable between samples, suggesting that either nonfibroblast cell types or other aspects of the dermal milieu are required for full expression of the SSc phenotype.
  
  
  CONCLUSIONS
  SSc has a distinct gene profile that is not confounded by geographic location, indicating that extended multicenter studies may be worthwhile to identify distinct subsets of disease by transcript profiling. Explanted SSc fibroblasts show an incomplete reflection of the SSc phenotype.
authors.affiliation: Biogen Idec, Cambridge, Massachusetts, USA. Humphrey.gardner@novartis.com
authors.forename: Humphrey
authors.initials: H
authors.lastname: Gardner
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Shearstone
authors.forename: Raj
authors.initials: R
authors.lastname: Bandaru
authors.forename: Tom
authors.initials: T
authors.lastname: Crowell
authors.forename: Matthew
authors.initials: M
authors.lastname: Lynes
authors.forename: Maria
authors.initials: M
authors.lastname: Trojanowska
authors.forename: Jaspreet
authors.initials: J
authors.lastname: Pannu
authors.forename: Edwin
authors.initials: E
authors.lastname: Smith
authors.forename: Stefania
authors.initials: S
authors.lastname: Jablonska
authors.forename: Maria
authors.initials: M
authors.lastname: Blaszczyk
authors.forename: Filemon K
authors.initials: FK
authors.lastname: Tan
authors.forename: Maureen D
authors.initials: MD
authors.lastname: Mayes
mesh_terms: D000328:Adult; D001706:Biopsy; D016326:Extracellular Matrix Proteins / Q000378:metabolism; D005260:Female; D005347:Fibroblasts / Q000737:chemistry*; D020869:Gene Expression Profiling; D006801:Humans; D007150:Immunohistochemistry; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D012595:Scleroderma, Systemic / Q000235:genetics*; D012867:Skin / Q000166:cytology*; D016212:Transforming Growth Factor beta / Q000378:metabolism; D051153:Wnt Proteins / Q000378:metabolism
chemical_list: D016326:Extracellular Matrix Proteins; D016212:Transforming Growth Factor beta; D051153:Wnt Proteins