Retroviral vectors have induced subtle clonal skewing in many gene therapy patients and severe clonal proliferation and leukemia in some of them, emphasizing the need for comprehensive integration site analyses to assess the biosafety and genomic pharmacokinetics of vectors and clonal fate of gene-modified cells in vivo. Integration site analyses such as linear amplification-mediated PCR (LAM-PCR) require a restriction digest generating unevenly small fragments of the genome. Here we show that each restriction motif allows for identification of only a fraction of all genomic integrants, hampering the understanding and prediction of biological consequences after vector insertion. We developed a model to define genomic access to the viral integration site that provides optimal restriction motif combinations and minimizes the percentage of nonaccessible insertion loci. We introduce a new nonrestrictive LAM-PCR approach that has superior capabilities for comprehensive unbiased integration site retrieval in preclinical and clinical samples independent of restriction motifs and amplification inefficiency.

Key Points• CDK6 is a critical effector of MLL fusions in myeloid leukemogenesis.• Genetic and pharmacologic inhibition of CDK6 overcome the differentiation block associated with MLLrearranged AML.Chromosomal rearrangements involving the H3K4 methyltransferase mixed-lineage leukemia (MLL) trigger aberrant gene expression in hematopoietic progenitors and give rise to an aggressive subtype of acute myeloid leukemia (AML). Insights into MLL fusionmediated leukemogenesis have not yet translated into better therapies because MLL is difficult to target directly, and the identity of the genes downstream of MLL whose altered transcription mediates leukemic transformation are poorly annotated. We used a functional genetic approach to uncover that AML cells driven by MLL-AF9 are exceptionally reliant on the cell-cycle regulator CDK6, but not its functional homolog CDK4, and that the preferential growth inhibition induced by CDK6 depletion is mediated through enhanced myeloid differentiation. CDK6 essentiality is also evident in AML cells harboring alternate MLL fusions and a mouse model of MLL-AF9-driven leukemia and can be ascribed to transcriptional activation of CDK6 by mutant MLL. Importantly, the context-dependent effects of lowering CDK6 expression are closely phenocopied by a small-molecule CDK6 inhibitor currently in clinical development. These data identify CDK6 as critical effector of MLL fusions in leukemogenesis that might be targeted to overcome the differentiation block associated with MLL-rearranged AML, and underscore that cell-cycle regulators may have distinct, noncanonical, and nonredundant functions in different contexts. (Blood. 2014;124(1):13-23) Introduction A substantial proportion of acute myeloid leukemia (AML) cases harbor balanced translocations of chromosome 11q23, and AML with t(9;11)(p22;q23) is recognized as a distinct entity by the World Health Organization Classification of Tumors of Hematopoietic and Lymphoid Tissues.1,2 On the molecular level, t(11q23) results in fusion of the MLL gene, which encodes an H3K4 methyltransferase, to a broad spectrum of partner genes, such as MLLT3 (also called AF9), MLLT4 (AF6), MLLT1 (ENL), and MLLT10 (AF10) on chromosomes 9p22, 6q27, 19p13.3, and 10p12, respectively. 3,4 A key functional feature of mixed-lineage leukemia (MLL) rearrangements is their ability to confer leukemia-initiating activity to hematopoietic stem and progenitor cells (HSPC). 5,6 MLL fusions are characterized by loss of the C-terminal H3K4 methyltransferase domain, and their leukemogenic activity is dependent on both features of the remaining N-terminal portion, such as a binding motif for the menin tumor suppressor that mediates the contact between MLL and chromatin as well as aberrant transactivation of target genes through heterologous domains contributed by the various partner proteins.7 For example, MLL fusions involving AF9, ENL, and AF10, which account for the majority of MLLrearranged AML, recruit multiprotein complexes essential for transcriptional activation/elongation...

HSP90 inhibition depletes STK33 in KRAS mutant tumors.

No abstract