1031P - The EUROSKI biomarker study: Analyzing the mechanisms of treatment-free remission in chronic myeloid leukemia

Abstract

Background: A substantial proportion of chronic myeloid leukemia (CML) patients in deep molecular response (DMR) reach treatment-free remission (TFR) after tyrosine kinase inhibitors (TKI) cessation. The aim of this study is to identify a gene signature predictive for TFR using whole transcriptome expression analyses. Methods: RNA from peripheral blood (PB) leukocytes of 60 CML patients who stopped TKI therapy within the EUROSKI study and 10 healthy controls were isolated. CML patients were divided into two groups of whom n = 30 patients had ongoing TFR, while 30 patients encountered molecular recurrence. RNA was isolated at the last day of TKI intake. In order to investigate differentially expressed genes, whole transcriptome arrays (Clariom D, Affymetrix) were analyzed. Candidate biomarkers were tested in multivariate analyses and gene set enrichment analyses (GSEA). Results: CML patients in DMR compared to healthy controls showed 16000 differentially expressed genes (p < 0.05). The natural killer cell marker CD69 showed overexpression with highest fold change (> 8-fold) for CML patients versus healthy controls. Significant enrichment of NFκB mediated TNFα and TGFβ pathways (FDR<7%, p < 0.03) were found in CML patients. Comparing the CML TFR versus relapse cohort, we found 2600 differentially expressed genes. Most notably the toll-like receptors TLR1, TLR6 and TLR8 were upregulated in the relapse cohort (p < 0.03). Activated downstream signatures of NOD-like, TLR and TNFα pathways, known for their promotion of a protective CML microenvironment, were significantly enriched (p < 0.03, FDR<2%). In contrast, patients in TFR were characterized by an upregulation of T-cell receptor and granzyme gene family members (p < 0.03). Genes of interest showed distinct cut-offs predictive for TFR over a period of 12 months. Conclusions: CML patients in DMR present a considerable inflammatory gene expression pattern in PB leukocytes in contrast to healthy controls. Alike previous studies, genes involved in immune exhaustion and immune surveillance were differentially expressed between patients with TFR and relapse. The specific inflammatory gene signature of the relapse cohort suggests ‘stemness’ as third mechanism and driver for relapse. Legal entity responsible for the study: University Heidelberg Funding: ELN Foundation Disclosure: R. Sébastien: Novartis research fund. S. Saussele: Advisory board: Novartis, Bristol-Myers Squib, Pfizer and ARIAD Fees: Novartis, Bristol-Myers Squib, Pfizer and ARIAD Research grant: Novartis and Bristol-Myers Squib Travel grant: Novartis and Bristol-Myers Squib. All other authors have declared no conflicts of interest.