Classification analysis of the transcriptosome of nonlesional cultured dermal fibroblasts from systemic sclerosis patients with early disease.
OBJECTIVE
To compare the transcriptosome of early-passage nonlesional dermal fibroblasts from systemic sclerosis (SSc) patients with diffuse disease and matched normal controls in order to gain further understanding of the gene activation patterns that occur in early disease.


METHODS
Total RNA was isolated from early-passage fibroblasts obtained from nonlesional skin biopsy specimens from 21 patients with diffuse SSc (disease duration <5 years in all but 1) and 18 healthy controls who were matched to the cases by age (+/-5 years), sex, and race. Array experiments were performed on a 16,659-oligonucleotide microarray utilizing a reference experimental design. Supervised methods were used to select differentially expressed genes. Quantitative polymerase chain reaction (PCR) was used to independently validate the array results.


RESULTS
Of the 8,324 genes that passed filtering criteria, classification analysis revealed that <5% were differentially expressed between SSc and normal fibroblasts. Individually, differentially expressed genes included COL7A1, COL18A1 (endostatin), DAF, COMP, and VEGFB. Using the panel of genes discovered through classification analysis, a set of model predictors that achieved reasonably high predictive accuracy was developed. Analysis of 1,297 gene ontology (GO) classes revealed 35 classes that were significantly dysregulated in SSc fibroblasts. These GO classes included anchoring collagen (30934), extracellular matrix structural constituent (5201), and complement activation (6958, 6956). Validation by quantitative PCR demonstrated that 7 of 7 genes selected were concordant with the array results.


CONCLUSIONS
Fibroblasts cultured from nonlesional skin of patients with SSc already have detectable abnormalities in a variety of genes and cellular processes, including those involved in extracellular matrix formation, fibrillogenesis, complement activation, and angiogenesis.
Tan
Filemon K
FK
Department of Internal Medicine, University of Texas at Houston Medical School, 77030, USA. filemon.k.tan@uth.tmc.edu <filemon.k.tan@uth.tmc.edu>
Hildebrand
Bernard August
BA
Lester
Malisa S
MS
Stivers
David N
DN
Pounds
Stanley
S
Zhou
Xiaodong
X
Wallis
Debra D
DD
Milewicz
Dianna M
DM
Reveille
John D
JD
Mayes
Maureen D
MD
Jin
Li
L
Arnett
Frank C
FC
D020405:Dermis; D005347:Fibroblasts / Q000502:physiology; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012595:Scleroderma, Systemic / Q000235:genetics*; D015533:Transcriptional Activation / Q000235:genetics