Figure 1

SHH pathway deregulation in chronic myeloid leukemia progression. a. Principal components plots derived from RNA-Seq data for 41 genes in the SHH pathway, from 7 chronic phase (CP; blue triangles) and 6 blast crisis (BC; red circles) untreated subjects, as well as 3 cord blood normal samples (CB; black diamonds) and 3 normal peripheral blood (NPB; black circles). b. Heatmap from unsupervised agglomerative hierarchical clustering of sonic hedgehog (SHH) pathway genes using RNA-Seq data from FACS-purified progenitors (CD34⁺CD38⁺lin⁻PI⁻) from 8 chronic phase (CP) and 9 blast crisis (BC) patients, 3 normal cord blood (CB) and 3 normal peripheral blood (NPB) sample. Samples labeled in bold correspond to patients that received clinical BCR-ABL inhibitor therapy. Red indicates over- and green, under-expression relative to the median RPKM (Log2 scale). Grey represent not expressed (RPKM = 0). c. Network analysis performed on differentially expressed genes between BC and CP revealed GLI2 as a key hub in the SHH pathway. d. Differentially expressed (DE) SHH genes at FDR 5% when comparing Blast crisis (BC) versus chronic phase (CP) or normal (CB and NPB). e. Box plots for GLI2 expression of 7 chronic phase (CP) and 6 blast crisis (BC) non-treated subjects, as well as 3 cord blood normal samples (CB) and 3 normal peripheral blood (NPB). Two-sided Jonckheere-Terpstra trend test: p = 0.014. f. GLI1 and GLI2 transcripts were compared using quantitative RT-PCR in FACS-purified human cord blood and normal peripheral blood CD34⁺CD38⁺Lin⁻PI⁻ progenitor cells (n = 9, black), chronic phase CML (n = 7, blue) and in blast crisis CML (n = 10, red) patient derived samples. Values were normalized to RPL27 or HPRT housekeeping genes, and set to 1 for the normal progenitors. (Student’s t-test *p < 0.05).