Comparison of chronic myeloid leukemia stem cells and hematopoietic stem cells by global proteomic analysis

Tyrosine kinase inhibitors (TKIs) that target BCR-ABL are the standard first-line therapy for patients with chronic-phase CML. However, TKIs cannot eliminate quiescent leukemia stem cells (LSCs) which persist in all patients on long-term therapy and provides a reservoir for disease progression and recurrence. Many researches have confirmed that TKI-resistant LSCs compartment can be captured within CD26 ⁺ fraction. In order to analyze distinctive biological characteristics of TKI-resistant LSCs, we isolated the CD34 ⁺ CD38^-CD26⁺, CD34 ⁺ CD38^-CD26^-and CD34 ⁺ CD38 ⁺ cells from 8 CML patients utilizing magnetic and flow sorting, and analyzed the global proteomic expression through high-resolution LC-MS/MS analysis. In the work, we discovered that a list of dysregulated proteins involved in energy metabolism and carcinogenesis, including PPARD, IL1-RAP, HNF, S15A2, PCLO, VA0D1, CKLF5, were extremely upregulated in the CD26 ⁺ LSCs while some majoring in DNA mismatch repair or related to cell senescence, such as MLH3, NOLC1, were downregulated. Additionally, we verified the upregulation of PPARD in both CML patients-derived CD26 ⁺ LSCs and donor-derived BCR-ABL1 overexpressed HSCs. These results open in turn new therapeutic avenues for targeting TKI-insensitive LSCs.