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Introduction SSc is a complex, heterogeneous disease with a high mortality rate. The disease is characterized by vascular dysfunction, tissue fibrosis, and immune dysfunction resulting in autoantibody formation. Cause and effect among these different pathological processes is not known, but they lead to significant skin and internal organ pathology. The purpose of this study was to use the gene expression in skin biopsies to quantify and clarify the heterogeneity in SSc, to identify subgroups within the patient cohort, and to map each subgroup to clinical covariates.
Methods Gene expression was measured with whole-genome DNA microarrays in skin biopsies from 18 patients with diffuse cutaneous SSc (dcSSc), 7 patients with limited cutaneous SSc (lcSSc), 3 patients with morphea and 6 healthy controls. Both lesional forearm and non-lesional back biopsies were analyzed for each patient resulting in 61 skin biopsies; the addition of 14 technical replicates resulted in a total of 75 microarray hybridizations.
Results Skin biopsies from dcSSc, lcSSc, morphea and healthy controls have distinct but overlapping gene expression signatures. 17 out of 22 forearm-back pairs cluster together showing nearly identical patterns of gene expression. Using this property of the gene expression, we selected 995 intrinsic genes and analyzed the data-driven groupings. As previously found, dcSSc skin is easily distinguished from healthy controls. Surprisingly, the skin biopsies of patients with lcSSc demonstrated a unique gene signature and clustered separately from dcSSc and healthy control samples. Most importantly, our data show multiple distinct subgroups among the patients with dcSSc, each with a distinct gene expression signature. Within dcSSc patients, we mapped the gene expression subtypes to clinical covariates and identified specific gene expression signatures correlated with high modified Rodnan skin score (MRSS of 26.34 ± 9.42) and another set with low MRSS (18.11 ± 6.45; p < 0.02). Within dcSSc with high MRSS, we define genes associated with the presence of digital ulcers, interstitial lung disease (ILD) and genes primarily associated with gastrointestinal involvement. Analysis of pathways differentially expressed in each subtype reveals increased expression of a signature for proliferating cells in the subset of the dcSSc patients with high MRSS, a B cell signature and a T cell signature. Combinations of these different signatures define the molecular subtypes of the disease.
Conclusions
Unique and overlapping gene expression signatures are found in the skin of patients with dcSSc, lcSSc and morphea. The samples cluster into distinct subgroups and multiple groups are evident among patients with dcSSc. The genes identified in this study provide gene signatures that could serve as biomarkers of disease activity, and provide insight into the molecular changes occurring in the skin in SSc.
Methods Gene expression was measured with whole-genome DNA microarrays in skin biopsies from 18 patients with diffuse cutaneous SSc (dcSSc), 7 patients with limited cutaneous SSc (lcSSc), 3 patients with morphea and 6 healthy controls. Both lesional forearm and non-lesional back biopsies were analyzed for each patient resulting in 61 skin biopsies; the addition of 14 technical replicates resulted in a total of 75 microarray hybridizations.
Results Skin biopsies from dcSSc, lcSSc, morphea and healthy controls have distinct but overlapping gene expression signatures. 17 out of 22 forearm-back pairs cluster together showing nearly identical patterns of gene expression. Using this property of the gene expression, we selected 995 intrinsic genes and analyzed the data-driven groupings. As previously found, dcSSc skin is easily distinguished from healthy controls. Surprisingly, the skin biopsies of patients with lcSSc demonstrated a unique gene signature and clustered separately from dcSSc and healthy control samples. Most importantly, our data show multiple distinct subgroups among the patients with dcSSc, each with a distinct gene expression signature. Within dcSSc patients, we mapped the gene expression subtypes to clinical covariates and identified specific gene expression signatures correlated with high modified Rodnan skin score (MRSS of 26.34 ± 9.42) and another set with low MRSS (18.11 ± 6.45; p < 0.02). Within dcSSc with high MRSS, we define genes associated with the presence of digital ulcers, interstitial lung disease (ILD) and genes primarily associated with gastrointestinal involvement. Analysis of pathways differentially expressed in each subtype reveals increased expression of a signature for proliferating cells in the subset of the dcSSc patients with high MRSS, a B cell signature and a T cell signature. Combinations of these different signatures define the molecular subtypes of the disease.
Conclusions
Unique and overlapping gene expression signatures are found in the skin of patients with dcSSc, lcSSc and morphea. The samples cluster into distinct subgroups and multiple groups are evident among patients with dcSSc. The genes identified in this study provide gene signatures that could serve as biomarkers of disease activity, and provide insight into the molecular changes occurring in the skin in SSc.
A. Milano, None; S.A. Pendergrass, None; J.L. Sargent, None; X. Dou, None; M.K. Connolly, None; M.L. Whitfield, None.