Comparative Gene Profiling of Acute Myeloid Leukemia (AML) and Malignant Melanoma (MEL) Cell Lines Exposed to the MEK Inhibitor PD0325901 Reveals Common Effectors of the MEK/ERK Kinase Module.
Authors: Milella Michele , Chiaretti Sabina , Ricciardi Maria R. , Tavolaro Simona , Ciuffreda Ludovica , Benassi Barbara , Bellacosa Alfonso , Peluso Gianfranco , Bergamo Paola , McCubrey James A. , Cognetti Francesco , Zupi Gabriella , Foà Robert , Tafuri Agostino 
Published: October 2019

Abstract
The MEK/ERK kinase module is frequently deregulated in human malignancies, including AML and MEL, and represents a promising therapeutic target. We have recently demonstrated that PD0325901, a selective MEK inhibitor, potently inhibits the growth of both AML and MEL cell lines (IC50 5–20 nM), through a combination of inhibition of cell cycle progression and induction of apoptosis. In order to identify functionally relevant targets of the activity of the MEK/ERK kinase module, we compared the gene expression profiles of the PD0325901-sensitive cell lines OCI-AML3 (AML, harboring a NPM gene mutation) and M14 (MEL, harboring a BRAF mutation), after exposure to vehicle control or 10 nM PD0325901 for 6 and 24h, using the Affymetrix U133A 2.0 and U133 Plus 2.0 gene chips, respectively. All analyses were conducted using the dChip software. In both models, the unsupervised approach showed a tight clustering that was both treatment- and time-dependent; unsupervised and supervised analyses highlighted that the greatest PD0325901-induced variations in gene expression were observed at 24h and 6h in the OCI-AML3 and M14 models, respectively. Comparison of the results obtained in the OCI-AML3 and M14 cell lines showed that 5 genes were consistently modulated after 6h, including CDC25A, cyclin G2, and DUSP6. Cyclin G2 and DUSP6 were also modulated after 24h, together with cyclin D1, TIMP3, and SEMA6A. On the contrary, MAFB, selected in both models, displayed a discordant behavior, being down-regulated upon treatment in OCI-AML3 and up-regulated in M14: this is consistent with the role of MAFB as an important regulator of hematopoiesis, while it does not appear to play a role in melanogenesis. Given the ability of PD0325901 to cause apoptosis, partly through induction of mitochondrial dysfunction in both AML and MEL models, we next investigated whether MEK inhibition specifically modulated the expression of genes related to mitochondrial homeostasis: also in this specific context, the effects were more rapidly induced in M14 than in OCI-AML3, with the greatest changes observed within 6h in the M14 cell line. Two genes were down-regulated after 24h in both models: PPIF, supposedly involved in apoptosis induction, and GRPEL1, on which little is currently known. In addition to mitochondrion-specific changes in gene expression, expression of the mitochondrial protein CPT1A significantly decreased (2-fold), as assessed by WB, after 6 h of exposure of OCI-AML3 cells to 10 nM PD0325901, under which conditions ß-oxidation was also suppressed by the drug. Overall, these results indicate that MEK inhibition by PD0325901 results in the modulation of the expression of a small number of genes that are common to ontogenetically distant tumor models, thereby representing attractive candidates for a shared, functionally relevant, MAPK activation signature; moreover, MEK inhibition results in profound intracellular metabolic changes that might importantly contribute to the anti-neoplastic effect of PD0325901 in AML and, possibly, in other tumor models. MM and SC equally contributed to the work presented.