Research Article
Classification analysis of the transcriptosome of nonlesional cultured dermal fibroblasts from systemic sclerosis patients with early disease
Filemon K. Tan,
Bernard August Hildebrand,
Malisa S. Lester, David N. Stivers,
Stanley Pounds,
Xiaodong Zhou, Debra D. Wallis, Dianna M. Milewicz,
John D. Reveille, Maureen D. Mayes, Li Jin, Frank C. Arnett Jr.,
Corresponding Author
Filemon K. Tan
University of Texas at Houston Medical School
Division of Rheumatology, Department of Internal Medicine, UT Houston Medical School, 6431 Fannin, MSB 5.270, Houston, TX 77030Search for more papers by this authorBernard August Hildebrand
University of Texas at Houston Medical School
Search for more papers by this authorDavid N. Stivers
University of Texas M. D. Anderson Cancer Center, Houston
Search for more papers by this authorStanley Pounds
St. Jude Children's Research Hospital, Memphis, Tennessee
Search for more papers by this authorDianna M. Milewicz
University of Texas at Houston Medical School
Search for more papers by this authorFrank C. Arnett Jr.
University of Texas at Houston Medical School
Search for more papers by this authorFilemon K. Tan,
Bernard August Hildebrand,
Malisa S. Lester, David N. Stivers,
Stanley Pounds,
Xiaodong Zhou, Debra D. Wallis, Dianna M. Milewicz,
John D. Reveille, Maureen D. Mayes, Li Jin, Frank C. Arnett Jr.,
Corresponding Author
Filemon K. Tan
University of Texas at Houston Medical School
Division of Rheumatology, Department of Internal Medicine, UT Houston Medical School, 6431 Fannin, MSB 5.270, Houston, TX 77030Search for more papers by this authorBernard August Hildebrand
University of Texas at Houston Medical School
Search for more papers by this authorDavid N. Stivers
University of Texas M. D. Anderson Cancer Center, Houston
Search for more papers by this authorStanley Pounds
St. Jude Children's Research Hospital, Memphis, Tennessee
Search for more papers by this authorDianna M. Milewicz
University of Texas at Houston Medical School
Search for more papers by this authorFrank C. Arnett Jr.
University of Texas at Houston Medical School
Search for more papers by this authorAbstract
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.
Conclusion
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.
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