Modeling Global Genomic Instability in Chronic Myeloid Leukemia (CML) Using Patient-Derived Induced Pluripotent Stem Cells (iPSCs)

SIMPLE SUMMARY: Cancers progress and become resistant to therapies by acquiring novel, unpredictable genomic events. Chronic myeloid leukemia (CML) is a blood cancer characterized by the progression from a chronic phase towards an aggressive acute leukemia called “blast crisis” due to the accumulation of genomic abnormalities in the genetically unstable leukemic clone. The aim of our work was to reproduce these events using induced pluripotent stem cells (iPSCs) harboring the Philadelphia chromosome. These iPSCs with unlimited proliferation potential can be used to generate large numbers of leukemic cells in vitro. We show here that we can also use them for inducing genomic instability by mutagenesis, giving rise to leukemic cells harboring genomic alterations found in a large cohort of patients in blast crisis. We thus show that this iPSC-based “blast crisis in a dish” technology could be used for gene discovery and drug targeting strategies in CML and other hematological malignancies. ABSTRACT: Methods: We used a patient-specific induced pluripotent stem cell (iPSC) line treated with the mutagenic agent N-ethyl-N-nitrosourea (ENU). Genomic instability was validated using γ-H2AX and micronuclei assays and CGH array for genomic events. Results: An increased number of progenitors (x5-Fold), which proliferated in liquid cultures with a blast cell morphology, was observed in the mutagenized condition as compared to the unmutagenized one. CGH array performed for both conditions in two different time points reveals several cancer genes in the ENU-treated condition, some known to be altered in leukemia (BLM, IKZF1, NCOA2, ALK, EP300, ERG, MKL1, PHF6 and TET1). Transcriptome GEO-dataset GSE4170 allowed us to associate 125 of 249 of the aberrations that we detected in CML-iPSC with the CML progression genes already described during progression from chronic and AP to BC. Among these candidates, eleven of them have been described in CML and related to tyrosine kinase inhibitor resistance and genomic instability. Conclusions: These results demonstrated that we have generated, for the first time to our knowledge, an in vitro genetic instability model, reproducing genomic events described in patients with BC.