Myeloablation Followed by Hematopoietic Stem Cell Transplantation and Long-Term Normalization of Systemic Sclerosis Molecular Signatures

Abstract

Objective: In the randomized Scleroderma: Cyclophosphamide or Transplantation (SCOT) trial, myeloablation, followed by hematopoietic stem cell transplantation (HSCT), led to the normalization of systemic sclerosis (SSc) peripheral blood cell (PBC) gene expression signature at the 26-month visit. Herein, we examined long-term molecular changes ensuing 54 months after randomization for individuals receiving an HSCT or 12 months of intravenous cyclophosphamide (CYC).

Methods: Global PBC transcript studies were performed in study participants at pretreatment baseline and at 38 months and 54 months after randomization, as well as in healthy controls using Illumina HT-12 arrays.

Results: Thirty (HSCT = 19 and CYC = 11) participants had 38-month samples available, and 26 (HSCT = 16 and CYC = 11) had 54-month samples available. In the paired comparison to baseline, a significant down-regulation of interferon modules and an up-regulation of cytotoxic/natural killer module were observed at the 38-month and 54-month visits in the HSCT arm, indicating a long-term normalization of baseline SSc gene expression signature. No differentially expressed modules were detected in the CYC arm. In comparison to samples from healthy controls, 38-month visit samples in the HSCT arm showed an up-regulation of B cell and plasmablast modules and a down-regulation of myeloid and inflammation modules. Importantly, 54-month HSCT samples did not show any differentially expressed modules compared to healthy control samples, suggesting completion of immune reconstitution. Participants in the CYC arm continued to show an SSc transcript signature in comparison to controls at both time points.

Conclusion: Paralleling the observed clinical benefit, HSCT leads to durable long-term normalization of the molecular signature in SSc, with completion of immune resetting to 54 months after HSCT.

Figure 1.

Modular analyses of SCOT participant samples in the HSCT arm at 38 months and 54 months compared to baseline samples or healthy controls A) Pairwise comparisons of HSCT 38-month to baseline samples. B) Comparisons of 38-month HSCT samples to healthy controls. C) Legend of color-coding in panels A, B, D and E demonstrating proportion of module transcripts over/under-expressed. D) Pairwise comparison of 54-month HSCT to baseline samples. E) Comparisons of 54-month HSCT samples to healthy controls. F) Annotation of modules based on known biological function of genes included in a given module. The numbers on Y- and X-axes indicate the main module and sub module designation, respectively. Of note, the module map in this Figure and results in Table 1 are based on two different analytic algorithms (repertoire analysis vs. QuSAGE). HSCT = hematopoietic stem cell transplant; CYC = cyclophosphamide.

Figure 2.

Composite scores of IFN [M1.2, M3.4], neutrophil [M5.15], and cytotoxic/NK cell [M3.6] modules in control and SCOT participants at baseline, 38-, and 54-months post-treatment* Longitudinal measurements of A) M1.2 (IFN module), B) M3.4 (IFN module), C) M5.15 (Neutrophil module), and D) M3.6 (Cytotoxic/NK cell module). *Log2 fold change >0.25 and FDR<0.1 in paired analysis of follow-up to baseline SSc samples in QuSAGE analysis. The displayed data at all time points are restricted to the subgroup of participants who had PBC gene expression data available at the baseline and 38-month-, as well as 54-month visits, in order to compare the gene expression modules from the same individuals at these three-time points (sample size: HSCT arm:14- CYC arm: 8).