Dissecting the Heterogeneity of Skin Gene Expression Patterns in Systemic Sclerosis

Abstract

Objective To examine the heterogeneity of global transcriptome patterns in systemic sclerosis (SSc) skin in a large sample of patients with SSc and control subjects. Methods Skin biopsy specimens obtained from 61 patients enrolled in the Genetics versus Environment in Scleroderma Outcome Study (GENISOS) cohort and 36 unaffected control subjects with a similar demographic background were examined by Illumina HumanHT-12 bead arrays. Followup experiments using quantitative polymerase chain reaction and immunohistochemical analysis were also performed. Results We identified 2,754 differentially expressed transcripts in SSc patients compared with controls. Clustering analysis revealed 2 prominent transcriptomes in SSc patients: the keratin and fibroinflammatory signatures. Higher keratin transcript scores were associated with shorter disease duration and interstitial lung disease, while higher fibroinflammatory scores were associated with diffuse cutaneous involvement, a higher skin score at the biopsy site, and a higher modified Rodnan skin thickness score. A subgroup of patients with significantly longer disease duration had a normal-like transcript pattern. Analysis of cell type–specific signature scores revealed remarkable heterogeneity across patients. Significantly higher scores were calculated for fibroblasts (72% of patients), microvascular cells (61%), macrophages (54%), and dendritic cells (DCs) (49%). The majority of samples with significantly higher fibroblast scores (35 of 44 [80%]) had significantly increased macrophage and/or DC scores. Further analysis and immunohistochemical staining indicated that the keratin signature was not a general marker of keratinocyte activation but was in fact associated with an activation pattern in hair and adnexal structures. Conclusion Prominent fibroinflammatory and keratin signatures are present in SSc skin. Expression profiles of SSc skin show significant heterogeneity, and this finding might be useful for stratifying patients for targeted therapies or predicting the response to immunosuppression.

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.…”

“…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).…”

Fresh Insights into Disease Etiology and the Role of Microbial Pathogens

“…Among these mediators, the interferons (IFNs) have captured the most attention due to their central role in regulating a multitude of biological functions in the innate immune system, facilitating their primarily antiviral activity [4,5]. Microarray and proteome-wide studies largely documented the presence of BIFN signatures^as a common This article is part of the Topical Collection on Scleroderma theme in most of the organs involved in SSc, such as skin, lungs, and peripheral blood mononuclear cells (PBMCs) [2,3,[6][7][8][9][10][11]. In vitro studies showed that activation of the innate immune response in immune and non-immune cells, including fibroblasts and endothelial cells (ECs), by specific TLR ligands, induced high expression of several IFN-and TGFβ-responsive genes also seen upregulated in SSc skin, such as CXCL9, OAS2, PAI-1, and ET-1 [12][13][14][15][16].…”

Review: Hematopoietic Stem Cell Transplantation for Scleroderma: Effective Immunomodulatory Therapy for Patients With Pulmonary Involvement

“…For example, there is an increased relative risk of SSc in first degree relatives of patients with the condition and a number of human leukocyte antigens are associated with SSc, several of which correlate with specific ethnic populations or clinical features (1). Genomic analyses can differentiate normal from scleroderma skin and disclose associated fibroinflammatory and interferon (IFN)-associated gene signatures (2, 3). Among the chemokines, CXCL4 has been shown to predict the risk and progression of SSc (4).…”