Machine Learning Classification of Peripheral Blood Gene Expression Identifies at Baseline Subsets of Patients with Systemic Sclerosis Most Likely to Show Clinical Improvement in Response to Autologous Myeloablative Hematopoietic Stem Cell Transplantation

The SCOT (Scleroderma: Cyclophosphamide or Transplantation) trial demonstrated clinical benefit of autologous hematopoietic stem cell transplant (HSCT) compared to cyclophosphamide (CYC) in scleroderma. We analyzed gene expression from peripheral blood mononuclear cells (PBMCs) of SCOT participants to identify those with differential treatment response. PBMC gene expression data were generated from 63 SCOT participants at baseline and at follow-up timepoints. Participants who completed treatment protocol were stratified by intrinsic gene expression subsets at baseline, evaluated for event-free survival (EFS) and analyzed for differentially expressed genes.