Abstract 4763: Genome-wide CRISPR screening identifies TSC1 as a regulator of sorafenib resistance in acute myeloid leukemia

Drug resistance impedes the long-term effect of targeted therapies in acute myeloid leukemia (AML), necessitating the identification of mechanisms underlying resistance. Approximately 25% of AML patients carry FLT3 mutations and develop post-treatment insensitivity to FLT3 inhibitors, including sorafenib. Using a genome-wide CRISPR screen, we identified LZTR1, NF1, TSC1 or TSC2, negative regulators of the MAPK and MTOR pathways, as mediators of sorafenib resistance. Analyses of ex vivo drug sensitivity assays in FLT3-ITD AML patient samples revealed lower expression of LZTR1, NF1, and TSC2 correlated with sorafenib sensitivity. Importantly, MAPK and/or MTOR complex1 (MTORC1) activity were upregulated in AML cells made resistant to several FLT3 inhibitors, including crenolanib, quizartinib, or sorafenib. These cells were sensitive to MEK inhibitors, and the combination of FLT3 and MEK inhibitors showed enhanced efficacy, suggesting its effectiveness in AML patients with FLT3 mutations and those with resistance to FLT3 inhibitors.

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Genome-wide haplotype association study identify the FGFR2 gene as a risk gene for Acute Myeloid Leukemia

Oncotarget ◽

10.18632/oncotarget.13631 ◽

2016 ◽

Vol 8 (5) ◽

pp. 7891-7899 ◽

Cited By ~ 6

Author(s):

Hongchao Lv ◽

Mingming Zhang ◽

Zhenwei Shang ◽

Jin Li ◽

Shanshan Zhang ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Association Study ◽

Myeloid Leukemia ◽

Haplotype Association ◽

Risk Gene ◽

Genome Wide ◽

Fgfr2 Gene ◽

Acute Myeloid

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Abstract 4763: Genome-wide CRISPR screening identifies TSC1 as a regulator of sorafenib resistance in acute myeloid leukemia

10.1158/1538-7445.sabcs18-4763 ◽

2019 ◽

Author(s):

Alisa Damnernsawad ◽

Tamilla Nechiporuk ◽

Steve E. Kurtz ◽

Wesley R. Horton ◽

Olga Nikolova ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Genome Wide ◽

Acute Myeloid

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Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability

PLoS ONE ◽

10.1371/journal.pone.0173723 ◽

2017 ◽

Vol 12 (3) ◽

pp. e0173723 ◽

Cited By ~ 15

Author(s):

Anna C. Salzberg ◽

Abigail Harris-Becker ◽

Evgenya Y. Popova ◽

Nikki Keasey ◽

Thomas P. Loughran ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Gene Silencing ◽

Myeloid Leukemia ◽

Genome Instability ◽

Genome Wide ◽

Acute Myeloid

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Analysis of genome-wide methylation and gene expression induced by 5-aza-2′-deoxycytidine identifies BCL2L10 as a frequent methylation target in acute myeloid leukemia

Leukemia & Lymphoma ◽

10.3109/10428194.2010.528093 ◽

2010 ◽

Vol 51 (12) ◽

pp. 2275-2284 ◽

Cited By ~ 22

Author(s):

Emiliano Fabiani ◽

Giuseppe Leone ◽

Manuela Giachelia ◽

Francesco D'alo' ◽

Mariangela Greco ◽

...

Keyword(s):

Gene Expression ◽

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Genome Wide ◽

Acute Myeloid

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Parallel Analyses Disclose Novel Genomic Imbalances in Acute Myeloid Leukemia with Complex Karyotypes.

Blood ◽

10.1182/blood.v106.11.2357.2357 ◽

2005 ◽

Vol 106 (11) ◽

pp. 2357-2357

Author(s):

Frank G. Rucker ◽

Lars Bullinger ◽

Hans A. Kestler ◽

Peter Lichter ◽

Konstanze Dohner ◽

...

Keyword(s):

Gene Expression ◽

Acute Myeloid Leukemia ◽

High Resolution ◽

Candidate Genes ◽

Myeloid Leukemia ◽

Parallel Analysis ◽

Genomic Imbalances ◽

Genome Wide ◽

Genomic Regions ◽

Acute Myeloid

Abstract Approximately 10 to 15 % of acute myeloid leukemia (AML) cases exhibit complex karyotypes, i.e., three or more chromosome abnormalities without presence of a specific fusion transcript. To identify novel genomic regions of interest in AML with complex karyotypes we applied comparative genomic hybridization to microarrays (matrix-CGH) allowing high-resolution genome-wide screening of genomic imbalances. We designed a microarray consisting of 2799 different BAC- or PAC-vectors. A set of 1500 of these clones covers the whole human genome with a physical distance of approximately 1.5 Mb. The remaining 1299 clones either contiguously span genomic regions known to be frequently involved in hematologic malignancies (e.g., 1p, 2p, 3q, 7q, 9p, 11q, 12q, 13q, 17p, 18q) (n=600) or contain oncogenes or tumor suppressor genes (n=699). Using this microarray platform, 83 AML cases with complex karyotypes were analyzed. Genomic losses were found more frequently than gains; the most frequent losses were deletions of 5q (71%), 17p (53%), 7q (48%); followed by deletions of 18q (30%), 16q (28%), 3p and 12q (20% each), 12p (18%), 20q (17%), and 11q (12%). The most frequent genomic gains were trisomies of 11q (39%) and 8q (31%); followed by trisomies of 1p (22%), 21q (20%), 9p (14%), 22q (13%), 13q (12%), and 6p (10%). In part, some critical segments were delineated to genomic fragments of 0.8 to a few megabase pairs in size. In lost/gained regions parallel analysis of gene expression using microarray technology detected a gene dosage effect with significant lower/higher average gene expression levels across the genes located in the respective regions. Furthermore, 47 high-level DNA amplifications in 19 different regions were identified; amplifications occurring in at least two cases mapped to (candidate genes in the amplicon) 11q23.3-q24.1 (n=10; ETS, FLI1); 11q23.3 (n=8; MLL, DDX6); 21q22 (n=5; ERG, ETS2); 13q12 (n=3; CDX2, FLT1, FLT3, PAN3); 8q24 (n=3; C8FW, MYC); 9p24 (n=2; JAK2); 12p13 (n=2; FGF6, CCND2); and 20q11 (n=2; ID1, BCL2L1). Parallel analysis displayed overexpressed candidate genes in critical amplified region, e.g., C8FW and MYC in 8q24. In conclusion, using high-resolution genome-wide screening tools such as matrix-CGH allows to unravel the enormous genetic diversity of AML cases with complex karyotypes, and correlation with global gene expression studies facilitates the delineation of disease-related candidate genes located in the critical regions.

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Selective and Titratable Effects On AML Genome Wide Methylation Patterning, Transcription and Clonogenicity Using Very Low Concentrations of 5-Aza-2'deoxycytidine.

Blood ◽

10.1182/blood.v114.22.2385.2385 ◽

2009 ◽

Vol 114 (22) ◽

pp. 2385-2385

Author(s):

Elisabeth Heuston ◽

Jason E. Farrar ◽

Timothy Triche ◽

Jonathan Buckley ◽

Poul Sorensen ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Conflicts Of Interest ◽

Cellular Reprogramming ◽

Transcription Profiles ◽

Genome Wide ◽

Low Concentrations ◽

Xenograft Models ◽

Methylation Patterns ◽

Acute Myeloid

Abstract Abstract 2385 Poster Board II-362 5-Aza-2'deoxycytidine (5AzadC) has significantly contributed to the treatment of myelodysplatic syndromes (MDS) and acute myeloid leukemia (AML). But while the cytotoxic effects of 5AzadC have been well characterized, its influence on methylation-induced cellular reprogramming remains poorly understood. We have treated several AML cell lines at extremely low concentrations of 5AzadC (0 nM to 1.0 nM) over the course of three days, followed by the determination of genome wide methylation changes, alterations in transcription profiles as well as cell viability, proliferation, apoptosis and changes in clonogenicity. The results demonstrate titratable responses on both genomic methylation and transcriptional patterns as well as a selective effect on clonogenicity compared to cytotoxicity. An alternative chemotherapeutic cytosine analog, cytosine arabinofuranoside (AraC), does not show the same selective depletion of clonogenic cells, suggesting that 5AzadC's effects are likely due to altered epigenetic changes associated with cellular reprogramming rather than a direct cytotoxic effect. We are currently evaluating 5AzadC and AraC effects on this population using immunophenotyping methods as well as xenograft models of tumorigenicity. These findings describe a potential role for very low concentrations of 5AzadC in treating acute myeloid leukemia through a selective affect on genome wide methylation patterns leading to altered transcription that differentially effects the clonogenic, leukemic stem cell compartment. Disclosures: No relevant conflicts of interest to declare.

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Genome-Wide Genotyping of Acute Myeloid Leukemia with t(9;11) Reveals New Recurrent Genomic Alterations,

Blood ◽

10.1182/blood.v118.21.3546.3546 ◽

2011 ◽

Vol 118 (21) ◽

pp. 3546-3546

Author(s):

Michael W.M. Kühn ◽

Lars Bullinger ◽

Jennifer Edelmann ◽

Jan Krönke ◽

Gröschel Stefan ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

De Novo ◽

Genetic Alterations ◽

Mixed Lineage Leukemia ◽

Genetic Event ◽

Genome Wide ◽

De Novo Aml ◽

Paired Analysis ◽

Acute Myeloid

Abstract Abstract 3546 Rearrangements of the mixed lineage leukemia (MLL) gene are associated with the development of acute leukemia, and a variety of translocation partners have been described to date. In acute myeloid leukemia (AML), the translocation t(9;11)(p22;q23), resulting in the MLLT3-MLL fusion gene, is the most common genetic event involving MLL. The translocation t(9;11) can occur de novo, or as a consequence of previous chemotherapy (t-AML). Both types exhibit significant biological and clinical heterogeneity, and cooperating genetic events have been implicated underlying these heterogeneous phenotypes. To identify additional genomic abnormalities in AML with t(9;11), we performed high-resolution, genome-wide analysis of DNA copy number alterations (CNA) and copy neutral loss of heterozygosity (CN-LOH) using Affymetrix 6.0 single nucleotide polymorphism (SNP) microarrays in 34 AMLs with t(9;11) [de novo AML, n=22; t-AML, n=12]. Samples were also analyzed for AML-associated mutations: FLT3 [internal tandem duplication (ITD; 2/33); tyrosine kinase domain (TKD; 2/26)], NPM1 (0/28), CEBPA (0/23), IDH1 (0/28), IDH 2 (0/28), DNMT3A (0/19), NRAS (0/6); and deregulated expression of EVI1 (8/16). Control DNA from remission bone marrow or peripheral blood was available for paired analysis in 12 (33%) cases. Data were processed using reference alignment, dChipSNP, and circular binary segmentation. Paired analysis revealed a mean of 1.9 somatic CNAs per case (range: 0–12); 45% of cases lacked any CNAs. Deletions were more common than gains (1.73 losses/case vs. 0.25 gains/case; p =0.04). There were no significant differences in the mean number of CNAs between de novo and therapy-related cases (de novo AML: 1.0, range: 0–2; t-AML: 2.7, range: 0–12; p =0.93). Recurrent deletions were detected at chromosomal bands 7q36.1–36.2 (n=2) and at the chromosomal translocation breakpoint at 11q23 (n=2). The del(7q36.1–36.2) overlapped with a minimally deleted region at 7q36.1 that we previously identified in 8% of core-binding factor AML containing only 4 genes (PRKAG2, GALNT11, GALNTL5 and MLL3). The only gene contained in both regions was MLL3, a member of the mixed-lineage leukemia gene family. The most recurrent CNA was trisomy 8 (n=5), also detected by conventional cytogenetics in all 5 cases. Novel recurrent focal gains were identified at 9p22.1 (n=2; size: 341 Kb) and at 13q21.33-q22.1 (n=2; size: 1021 Kb) with each region containing genes potentially involved in cancer pathogenesis (ACER2 in 9p; KLF5 in 13q). Analysis of CN-LOH revealed no such lesion in any of the cases. In summary, our data provide a comprehensive survey of CNAs in a well characterized cohort of AMLs with t(9;11). These data demonstrate a very low occurrence of CNAs, with no significant differences between de novo and therapy-related cases and complete absence of CN-LOH. Interestingly, a number of novel recurrent secondary genetic alterations were identified. Determining the functional role of these lesions in leukemogenesis and drug resistance should provide new insights into t(9;11)-bearing AMLs. Disclosures: No relevant conflicts of interest to declare.

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