Intrinsic Gene Expression Subsets of Diffuse Cutaneous Systemic Sclerosis Are Stable in Serial Skin Biopsies

Abstract

Skin biopsy gene expression was analyzed by DNA microarray from 13 dSSc patients enrolled in an open label study of rituximab, 9 dSSc patients not treated with rituximab, and 9 healthy controls. These data recapitulate the patient ‘intrinsic’ gene expression subsets described previously including proliferation, inflammatory, and normal-like groups. Serial skin biopsies showed consistent and non-progressing gene expression over time, and importantly, the patients in the inflammatory subset do not move to the fibroproliferative subset, and vice versa. We were unable to detect significant differences in gene expression before and after rituximab treatment, consistent with an apparent lack of clinical response. Serial biopsies from each patient stayed within the same gene expression subset regardless of treatment regimen or the time point at which they were taken. Collectively, these data emphasize the heterogeneous nature of SSc and demonstrate that the intrinsic subsets are an inherent, reproducible and stable feature of the disease that is independent of disease duration. Moreover, these data have fundamental importance for the future development of personalized therapy for SSc; drugs targeting inflammation are likely to benefit those patients with an inflammatory signature, whereas drugs targeting fibrosis are likely to benefit those with a fibroproliferative signature.

Integrated, multicohort analysis of systemic sclerosis identifies robust transcriptional signature of disease severity

“…Given the repeatedly observed clinical and molecular heterogeneity in SSc patients across multiple independent cohorts (8,(10)(11)(12), the robustness of the SSc signatures identified in our analysis is unexpected and significant. Until now, the lack of such a robust signature has hampered development of novel diagnostics and prognostics for monitoring SSc patients in clinics.…”

“…Several studies using whole-genome expression profiles of SSc skin biopsies have demonstrated the molecular heterogeneity between patients with SSc (10-12). Based on this heterogeneity, SSc patients can be classified by their intrinsic subset (10,11). Therefore, we explored whether there is any relationship between 4S and the intrinsic subsets.…”

“…We identified 4 clinical microarray gene expression datasets from the NCBI's Gene Expression Omnibus (GEO) database comprising 282 samples obtained from skin ( Figure 1 and Supplemental Table 1; supplemental material available online with this article; doi:10.1172/jci.insight.89073DS1) (7,(10)(11)(12), which were derived from healthy control subjects, patients with diffuse cutaneous SSc or limited cutaneous SSc, and with various disease duration. Two of these datasets profiled longitudinally collected samples from study participants during treatment with rituximab (10) and nilotinib (7).…”

“…These studies have identified remarkable homogeneity in skin biopsies obtained from the same patient such that transcriptomic profiles of clinically unaffected back and clinically affected forearm biopsies are nearly identical (10)(11)(12). Based on the molecular heterogeneity observed in skin biopsies from SSc patients, 4 SSc subtypes, called intrinsic subsets, have been proposed: (a) normal-like, (b) limited, (c) fibroproliferative, and (d) inflammatory (10,11).…”

“…For instance, strict inclusion and exclusion criteria restrict study participation to reduce the number and effects of confounding factors (8,10). However, this controlled experimental approach typically does not capture the heterogeneity observed in the real-world SSc patient population.…”