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CD36 defines CML cells less sensitive to imatinib
teins were also expressed on the CML cell lines KU812 and BV173, whereas fewer displayed expression on K562 and LAMA84 cells. The remaining five candidate markers (IL12RBI, HMMR, ECE1, TNFRSF18, and TYRO3) could not be detected on primary CML cells, possibly due to sub- optimal antibodies or absent or very low cell surface protein expression (Table 1). Finally, CD93, known to be expressed on acute myeloid leukemia (AML) cells and recently report- ed to be upregulated in CML,20,21 was also expressed on primitive CML cells, but did not show a significant upregu-
lation in our gene expression data relative to corresponding NBM cells (Table 1).
CD36 and LEPR are selectively expressed on CD34+CD38low CML cells compared to corresponding NBM cells
Of the newly identified cell surface proteins, CD36, LEPR, ITGB3 and TFRC showed the highest expression on CD34+CD38low CML cells, and were therefore evaluated for expression in NBM. Whereas CD36 and LEPR could not be
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Figure 1. RNA sequencing of sorted primary CML cells from bone marrow of ten newly diagnosed chronic phase patients. (A) Schematic illustration of cell popula- tions analyzed by RNA sequencing. BM aspirates were used to isolate mononuclear cells and then enrich for CD34 expressing cells with subsequent FACS sorting. The cells displaying the lowest 5% according to CD38 expression were defined as the primitive population and the highest 80% as the more mature progenitor pop- ulation. (B) Unsupervised principal component analysis of BM from CML patients (n=10) and healthy donors (n=4) sorted into hematopoietic and leukemic progenitor and primitive cell populations. (C) Heat map showing overexpression of cell surface genes in the primitive CML population (CD34+CD38low) as compared to healthy HSCs as determined by RNA sequencing. (D) Schematic figure of total number of transcribed genes detected, number of cell surface associated genes used to filter the results, number of upregulated genes in the primitive CML cell population, and genes available for validation on protein level. HPC: hematopoietic progenitor cells; HSC: hematopoietic stem cells; CML: chronic myeloid leukemia; RNA-seq: ribonucleic acid sequencing.
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