Fig. 1: AML primary samples with t(6;9)/DEK::NUP214 display a unique transcriptional signature.
From: DEK::NUP214 acts as an XPO1-dependent transcriptional activator of essential leukemia genes
A RNA-seq unsupervised clustering of 57 cytogenetically poor-risk AML samples [10], including four t(6;9) cases. Different colors represent distinct cytogenetic AML subtypes. B Volcano plot representing differentially expressed genes in t(6;9) primary AML samples vs other cytogenetic AML subtypes (RNA-seq analysis integrating our cohort of 57 poor-risk cases and 691 cases from the Leucegene cohort (Leucegene project, https://leucegene.ca/) (significance determined by Kernel MCC > 0.105 and log2FoldChange (l2fc) > 0.58). Kernel MCC is a shorthand for Matthews Correlation Coefficient of a kernel density estimation (KDE)-based classifier. C mRNA expression levels HOXA and HOXB genes in t(6;9) samples compared to KMT2A-rearranged and other poor-risk AMLs (n = 57). D mRNA expression level of FOXC1 in t(6;9) patients compared to other poor-risk AMLs (n = 57). E FOXC1 protein expression across the AML cell line panel (OCI-AML3, KASUMI-1, THP-1, FKH-1, P31-FUJ, MV4;11 and K562). GAPDH was used as an endogenous control. F Bar chart showing FOXC1 silencing efficiency by RT-qPCR after shRNA/scramble transduction of FKH-1 cells. Relative expression levels were calculated using the ΔCT method, normalized to the average of GAPDH and 18S rRNA. G Representative flow cytometry plot for the apoptosis assay, with FOXC1 knockdown (KD)/scramble (scr) FKH-1 cells stained with Annexin V (X-axis) and DAPI (Y-axis). The bar graph illustrates the percentage of live cells (DAPI– Annexin V–), early apoptosis (DAPI– Annexin V+), late apoptosis (DAPI+ Annexin V+), and dead cells (DAPI+ Annexin V–). H Bar graph representing cell cycle analysis by flow cytometry based on DNA content stained with DAPI of FOXC1 KD/scr FKH-1 cells. Each group of bars indicates the percentage distribution of cells in G0/G1, S, and G2/M phases. I Bar graph showing the number of colonies of FOXC1 KD/scr FKH-1 cells after the colony forming unit (CFU) assay. J Representative images of colonies corresponding to the CFU assay. Asterisks indicate statistical significance (*: p < 0.05, **: p < 0.01, ***: p < 0.001, ****: p < 0.0001 and ‘ns’ denotes non-significant differences).
