The implementation of targeted therapies for acute myeloid leukemia has been challenged by complex mutational patterns within and across patients as well as a dearth of pharmacologic agents for most mutational events. Here, we report initial findings from the Beat AML program on a cohort of 672 tumor specimens collected from 562 patients. We assessed these specimens using whole exome sequencing, RNA-sequencing, and ex vivo drug sensitivity analyses. Our data reveal Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

RNA interference pathways may involve amplification of secondary siRNAs by RNA-dependent RNA polymerases. In plants, RDR6-dependent secondary siRNAs arise from transcripts targeted by some microRNA (miRNA). Here, Arabidopsis thaliana secondary siRNA from mRNA, and trans-acting siRNA, are shown to be triggered through initial targeting by 22 nt miRNA that associate with AGO1. In contrast to canonical 21 nt miRNA, 22 nt miRNA primarily arise from foldback precursors containing asymmetric bulges. Using artificial miRNA constructs, conversion of asymmetric foldbacks to symmetric foldbacks resulted in production of 21 nt forms of miR173, miR472 and miR828. Both 21 and 22 nt forms associated with AGO1 and guided accurate slicer activity, but only 22 nt miRNA were competent to trigger RDR6-dependent siRNA from target RNA. These data suggest that AGO1 functions differentially with 21 and 22 nt miRNA to engage the RDR6-associated amplification apparatus.

Transacting siRNA (tasiRNA) biogenesis in Arabidopsis is initiated by microRNA (miRNA) -guided cleavage of primary transcripts. In the case of TAS3 tasiRNA formation, ARGONAUTE7 (AGO7)-miR390 complexes interact with primary transcripts at two sites, resulting in recruitment of RNA-DEPENDENT RNA POLYMERASE6 for dsRNA biosynthesis. An extensive screen for Arabidopsis mutants with specific defects in TAS3 tasiRNA biogenesis or function was done. This yielded numerous ago7 mutants, one dcl4 mutant, and two mutants that accumulated low levels of miR390. A direct genome sequencing-based approach to both map and rapidly identify one of the latter mutant alleles was developed. This revealed a G-to-A point mutation (mir390a-1) that was calculated to stabilize a relatively nonpaired region near the base of the MIR390a foldback, resulting in misprocessing of the miR390/ miR390* duplex and subsequent reduced TAS3 tasiRNA levels. Directed substitutions, as well as analysis of variation at paralogous miR390-generating loci (MIR390a and MIR390b), indicated that base pair properties and nucleotide identity within a region 4-6 bases below the miR390/miR390* duplex region contributed to the efficiency and accuracy of precursor processing.high-throughput sequencing | miRNA | trans-acting siRNA S mall RNAs, including microRNA (miRNA), several classes of endogenous small interfering RNA (siRNA), and Piwiassociated RNA (piRNA), direct silencing activities that shape transcriptomes and proteomes of eukaryotic organisms. miRNAs arise from transcripts containing self-complementary foldback structures that are initially processed to form 21-22nt miRNA/ miRNA* duplexes. In animals, primary transcripts with miRNA foldbacks (pri-miRNA) are processed first by the Microprocessor complex, which contains the RNase III-type protein Drosha and its cofactor Pasha (also known as DGCR8 in humans), then by Dicer, with partners that include the dsRNA-binding domain protein Loquacious (1). Plants orchestrate both pri-miRNA and pre-miRNA processing with the same (or very similar) complex, which includes the RNase-III like enzyme DICER-LIKE1 (DCL1) as the catalytic component (2-5). DCL1 interacts with the dsRNA binding protein HYPONASTIC LEAVES1 (HYL1) and the zinc-finger protein SERRATE (SE), both of which promote efficient and accurate miRNA biogenesis (2, 6-8).The transacting siRNA (tasiRNA) class represents a specialized type of amplification-dependent siRNA (9, 10). Primary tasiRNA-generating transcripts are first processed by miRNAguided cleavage (11,12). Either the 3′ (TAS1, TAS2 and TAS4 families) or 5′ (TAS3 family) cleavage product is stabilized and converted to dsRNA by RNA-DEPENDENT RNA POLY-MERASE6 (RDR6) (9, 10, 12, 13). Phased, 21-nt siRNAs are generated in register with the miRNA-guided cleavage site through sequential processing by DCL4. Routing of TAS3 precursor RNA requires two miRNA-guided events, both of which involve AGO7-miR390 complexes (14, 15). Interaction of AGO7-miR390 at a 3′ proximal target site results in primary transcript...

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Agents that target B-cell receptor (BCR) signaling in lymphoid malignancies including idelalisib (GS-1101) and fostamatinib which inhibit the delta isoform of PI3 kinase (PI3Kd) and spleen tyrosine kinase (Syk) respectively have shown significant clinical activity. By disrupting B-cell signaling pathways, idelalisib treatment has been associated with a dramatic lymph node response, but eradication of disease and relapse in high risk disease remain challenges. Targeting the BCR signaling pathway with simultaneous inhibition of PI3Kd and Syk has not yet been reported. We evaluated the pre-clinical activity of idelalisib combined with the novel and selective Syk inhibitor GS-9973 in primary peripheral blood and bone marrow Chronic Lymphocytic Leukemia (CLL) samples. Both PI3Kd and Syk inhibition reduced CLL survival and in combination induced synergistic growth inhibition and further disrupted chemokine signaling at nanomolar concentrations including in bone marrow derived and poor risk samples. Simultaneous targeting of these kinases may significantly increase clinical activity.