Molecular biomarkers of improvement for patients with systemic sclerosis in an open label trial of mycophenolate mofetil

Systemic sclerosis (SSc) is a potentially life-threatening autoimmune disease that presents with a heterogeneous and complex phenotype. Major disease manifestations are skin and internal organ fibrosis, vascular dysfunction, and immune system activation. One in three patients dies within 10 years of diagnosis. There are no validated diagnostic markers, no known curative treatments and disease pathogenesis is poorly understood. The overarching proposal aim is to validate biomarkers in skin and identify circulating factors that will predict and monitor treatment response. The potential for specific gene expression signatures in skin to serve as useful SSc biomarkers has been demonstrated. We previously identified four ‘intrinsic’ gene expression based subsets in SSc skin. These are the inflammatory, fibroproliferative, limited and normal-like subsets. We have established a CLIA-approved laboratory to determine a patients’ intrinsic gene expression subset in skin biopsies. Patients classified in the inflammatory intrinsic subset demonstrate a gene expression signature that is characterized by infiltrating immune cells that include T- and B-lymphocytes and macrophages. We have recently shown that the major pathway driving dermal fibrosis in these patients is the profibrotic IL-13/IL-4 pathway. Translating this discovery to patients with SSc, we demonstrated that SSc patients who map to the inflammatory intrinsic subset show improvement during treatment with mycophenolate mofetil (MMF)/Cellcept, a drug that decreases lymphocyte proliferation. In contrast, patients in the fibroproliferative intrinsic subset did not show clinical improvement during MMF treatment. The finding that gene expression in skin is associated with disparate clinical outcomes is transformative and will usher in a new era of personalized medicine in SSc. Serum proteomics may be able to identify circulating SSc biomarkers that parallel our gene expression findings. In pilot studies, we identified 50+ serum proteins whose levels were significantly different between SSc patients and healthy controls (p<0.05). Patients with progressive skin disease at six months demonstrated significantly different levels in seven analytes in baseline serum samples compared to patients with stable or regressive skin disease. Together these data suggest that circulating factors may be complementary to the gene expression in skin. To validate our finding that the gene expression signatures in skin are associated with clinical improvement during MMF treatment, and to better understand the role of circulating proteins as SSc biomarkers for SSc skin disease, we propose the following two specific aims: Aim 1: Build a multicenter validation cohort in order to test the sensitivity and specificity of gene expression signatures in skin that were associated with clinical improvement during MMF therapy in pilot studies. Aim 2: To identify and validate a core set of serum proteins that are associated with SSc skin fibrosis. Aim 3: Develop a mathematical model that integrates circulating factor measurements and gene expression in a multivariate test to predict clinical endpoints. These experiments are significant because there are no SSc biomarkers to predict treatment response. The experiments are innovative because we will apply a NANostring approach to SSc skin biopsies to identify patients that will benefit from this therapy.