The transcriptomic landscape and directed chemical interrogation of MLL-rearranged acute myeloid leukemias

Abstract

Using next-generation sequencing of primary acute myeloid leukemia (AML) specimens, we identified to our knowledge the first unifying genetic network common to the two subgroups of KMT2A (MLL)-rearranged leukemia, namely having MLL fusions or partial tandem duplications. Within this network, we experimentally confirmed upregulation of the gene with the most subtype-specific increase in expression, LOC100289656, and identified cryptic MLL fusions, including a new MLL-ENAH fusion. We also identified a subset of MLL fusion specimens carrying mutations in SPI1 accompanied by inactivation of its transcriptional network, as well as frequent RAS pathway mutations, which sensitized the leukemias to synthetic lethal interactions between MEK and receptor tyrosine kinase inhibitors. This transcriptomics-based characterization and chemical interrogation of human MLL-rearranged AML was a valuable approach for identifying complementary features that define this disease.

Chemo-genomic interrogation of CEBPA mutated AML reveals recurrent CSF3R mutations and subgroup sensitivity to JAK inhibitors

“…Normal bone marrow (BM) samples were obtained from the BCLQ and from Lonza, and cord blood from Héma-Québec. 23 …”

“…As part of this project, RNA sequencing of 415 primary AML specimens from various cytogenetic groups was performed, including 110 samples that were also characterized by exome sequencing, as previously described. 23 All leukemia samples and paired normal DNA specimens were collected and characterized by the Quebec Leukemia Cell Bank (BCLQ). Normal bone marrow (BM) samples were obtained from the BCLQ and from Lonza, and cord blood from Héma-Québec.…”

“…Preparation of cell culture from frozen AML mono-nucleated cells and chemical screen were performed as previously described 23,27 using serum-free media supplemented with cytokines, 500 nM SR1 (Alichem) and 500 nM UM729 (Institute for Research in Immunology and Cancer [IRIC]). Compounds were added to seeded cells in serial dilutions (8 dilutions, 1:3, 10 mM down to 4.5 nM) in duplicate wells.…”

“…23 Sequence data were mapped to the reference genome hg19 according to RefSeq annotations (University of California Santa Cruz; April 16th, 2014). Variants were all identified using CASAVA 1.8.2 or km (https://bitbucket.org/iric-soft/km) approaches according to the previously reported pipeline.…”

Genomic profiling and directed ex vivo drug analysis of an unclassifiable myelodysplastic/myeloproliferative neoplasm progressing into acute myeloid leukemia

“…Likewise, the MLL positive NRAS-dependent cell line THP-1 (Burgess et al, 2014) proved highly sensitive, whereas KG-1 was non-responsive despite that fact that it harbors mutant NRAS (Long et al, 2014). Trametinib is a potent MEK inhibitor approved for BRAF mutant unresectable or metastatic melanoma, and has been proposed to have an increased efficacy in NRAS mutant AML (Burgess et al, 2014;Lavallée et al, 2015) and is in clinical trial for AML with mutant NRAS (clinicaltrials.gov identifier NCT01907815). Our data further demonstrate that the AML cells, as well as THP-1 and KG-1, were sensitive towards bortezomib (Horton et al, 2006;Oerlemans et al, 2008).…”