EZH2 Is Either Mutated or Downregulated in Patients with Loss of Heterozygosity of Chromosome 7/7q and Leads to Epigenetic Dysregulation Via Histone H3K27.

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 228-228
Author(s):  
Hideki Makishima ◽  
Shahper N Khan ◽  
Anna M Jankowska ◽  
Yuka Sugimoto ◽  
Zhenbo Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Loss Of Heterozygosity ◽  
Cell Lines ◽  
Research Funding ◽  
Negative Impact ◽  
Myeloproliferative Neoplasms ◽  
Chromosome 7 ◽  
Prognostic Impact ◽  
Wild Type ◽  
H3k27 Trimethylation

Abstract Abstract 228 Chromosome 7 abnormalities occur either in isolation or in conjunction with other lesions (del(5q) or del/uniparental disomy (UPD)17p). To date the search for mutations affecting genes located on chromosome 7 has not been successful. By combination of metaphase and single nucleotide polymorphism array based karyotyping, in a cohort of 929 patients with myeloid malignancies (myelodysplastic syndromes (MDS): n=366; myelodysplastic/myeloproliferative neoplasms (MDS/MPN): n=108; MPN: n=206; secondary acute myeloid leukemia (sAML): N=167; primary (p)AML: n=82), loss of heterozygosity (LOH) in chromosome 7q was observed in 11.8% of MDS, 11.3% of MDS/MPN, 8.1% of MPN, 7.6% of sAML and 12.6% of pAML. In addition to somatic interstitial deletions (del7q) and a total loss of chromosome 7 (del7), somatic UPD(7q) was found: UPD(7q) was most frequently observed in MDS/MPN (4.9%). Similar to del(7/7q), UPD(7q) also conveyed a poor prognosis in terms of overall survival (OS). We hypothesized that cases with LOH7q may harbor a mutated gene which would explain clonal malignant evolution. For identification of such a hypothetical gene, we used two strategies: 1) application of a next generation sequencing platform and 2) targeted sequencing of candidate genes in intervals delineated by the presence of somatic microdeletions in specific patients. Both approaches demonstrated that the EZH2 gene can be affected by somatic mutations. Subsequently, screening led to detection of a total of 16 cases with EZH2 mutations, which were present in the majority of UPD(7q) patients, but in only 10% of cases with del(7q). In 4 cases (without LOH7q), we also found heterozygous EZH2 mutations. In addition to mutations, expression of EZH2 was found to be significantly decreased in patients with del(7/7q), likely due to haploinsufficiency, and surprisingly decreased in the entire cohort of patients, including 119/542 cases of AML. EZH2 mutations were observed in MDS/MPN (7.1%) and MPN (6.4%) but less frequently in AML. Further analyses of clinical phenotypes associated with the EZH2 mutation showed a significant negative impact on OS. In particular, the negative impact on OS was evident in the MDS/MPN group (p=0.0005) or in patients older than 60 years (p=0.0086). In the index case (sAML and UPD(7q)), 2 other mutations were detected: ASXL1 and TET2; all mutations were found at initial presentation prior to AML transformation. A concominant ASXL1 mutation was found in 3 other cases, while in 2 other patients, EZH2 mutations were found together with TET2 mutations. We have also investigated the pathogenic mechanisms resulting form EZH2 mutations. Leukemic cells from a patient with a homozygous EZH2 mutation easily initiated xenografts in NSG mice, which within 4 weeks of injection developed massive infiltration of spleen and liver with leukemic blasts. As expected, WB, ELISA and immunohistochemistry performed on these blasts revealed decreased H3K27 trimethylation compared to EZH2 wild type CD34 positive cells. A similar effect was observed in mutant cell line SKM-1 when compared to cell lines with wild type EZH2. When we investigated the effects of EZH2 on the gene expression profile in EZH2 mutant and WT cell lines, we found a significant increase in expression of HOXA9, known to be regulated by EZH2, along with PU.1, CDKN2A, IRF4, RASSF1 and CEBPA. We also investigated the effect of EZH2 mutations on the structural state of chromatin using a PCR-based method using non-denatured chromatin. We set up primers prior to and/or at the beginning of the first exons of MYC, CDKN2A and PU.1 to asses the chromatin plasticity. The EZH2 mutation was associated with more efficient amplification of these genes, suggestive of a relaxed, transcriptionally active state of DNA on the corresponding sites. In sum, mutations of EZH2 are present in patients with MDS/MPN and sAML. The mutations are mostly homozygous and are not commonly associated with del(7/7q). However, decreased expression of wild type EZH2 may be responsible for the pathogenesis associated with del(7/7q). Additionally, they convey a negative prognostic impact on OS. Mechanistically, decreased H3K27 trimethylation mediates downstream effects, such as persistent expression of various genes like HOXA9 and others. Mutations of EZH2 link the genomic instability to epigenetic dysregulation of gene expression. Disclosures: Maciejewski: Celgene: Speakers Bureau; Alexion: Speakers Bureau; Celgene: Research Funding; Eisai: Research Funding; NIH: Research Funding; AA & MDS International Foundation: Research Funding.

scholarly journals HCK Transcription Is Regulated By AP1, NF-Kb and STAT3 Transcription Factors in MYD88 Mutated WM and ABC-DLBCL Cells

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2931-2931
Author(s):  
Xia Liu ◽  
Jiaji G Chen ◽  
Jie Chen ◽  
Lian Xu ◽  
Nicholas Tsakmaklis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cell Lines ◽  
Binding Sites ◽  
Research Funding ◽  
Promoter Activity ◽  
Promoter Sequence ◽  
Wild Type ◽  
Mutation Status ◽  
Bcr Signaling

Abstract Hematopoietic cell kinase (HCK) is a member of the SRC family of tyrosine kinases (SFKs). HCK transcription is aberrantly upregulated in Waldenström's Macroglobulinemia (WM) and Activated B-cell (ABC) subtype Diffuse Large B-cell Lymphoma (DLBCL) in response to activating mutations in MYD88 (Yang et al, Blood 2016). To clarify the mechanism responsible for the aberrant upregulation of HCK transcription inMYD88 mutated cells, we analyzed the promoter sequence of HCK using PROMO and identified consensus binding sites for transcription factors (AP1, NF-kB, STAT3, and IRF1) that are regulated by mutated MYD88 (Ngo et al, Nature 2011; Treon et al, NEJM 2012; Yang et al, Blood 2013; Juilland et al, Blood 2016; Yang et al, Blood 2016). We performed Chromatin Immuno-precipitation (ChIP) assays using ChIP grade antibodies to JunB, c-Jun, NF-kB-p65, STAT3 and IRF1 in MYD88 mutated WM (BCWM.1, MWCL-1) and ABC DLBCL (TMD-8, HBL-1, OCI-Ly3) cells that highly express HCK transcripts, as well as wild type MYD88 expressing GCB DLBCL (OCI-Ly7, OCI-Ly19) cells that show low HCK transcription. Following ChIP, a HCK promoter specific quantitative PCR assay was used to detect HCK promoter sequences. These studies showed that JunB, NF-kB-p65 and STAT3 bound more robustly to the HCK promoter in MYD88 mutated WM and ABC-DLBCL cells versus MYD88 wild type GCB DLBCL cell lines, while c-Jun bound more abundantly to the HCK promoter sequence in all DLBCL cell lines, regardless of MYD88 mutation status. In contrast c-Jun binding was low in MYD88 mutated WM cells. IRF1 binding to the HCK promoter was similar in all cell lines, regardless of the MYD88 mutation status. To further investigate HCK regulation, we developed an HCK promoter driven luciferase reporter vector (WT) with mutated AP-1 binding (AP1-mu-1~6), NF-kB binding (NF-kB-mu-1~5), and STAT3 binding (STAT3-mu) sites and investigated their impact on HCK promoter activity in MYD88 mutated BCWM.1 cells. We observed that mutation of AP1-mu-1,4,5,6; NF-kB-mu-1,4,5, as well as STAT3-mu binding sites greatly reduced HCK promoter activity, thereby supporting a role for AP-1, NF-kB and STAT3 transcription factors in HCK gene expression in MYD88 mutated cells. To further clarify the importance of these transcription factors in aberrant HCK gene expression in MYD88 mutated cells, we treated BCWM.1, MWCL-1, TMD-8 and HBL-1 cells with the AP-1 inhibitor SR 11302; NF-kB inhibitor QNZ; and the STAT3 inhibitor STA-21. Treatment of cells for 2 hours with SR 11302, QNZ, and STA-21 at sub-EC50 concentrations resulted in decreased HCK expression in MYD88 mutated all cell lines. Lastly, we investigated the contribution of BCR signaling to HCK transcription. BCWM.1, MWCL-1, TMD-8, and HBL-1 cells were treated with the Syk kinase inhibitor R406, and HCK transcription levels were then assessed. Differences in HCK expression were observed between MYD88 mutated WM and ABC DLBCL cells following R406, supporting a contributing role for BCR signaling in ABC DLBCL but not WM cells to HCK expression. Our data provide critical new insights into HCK regulation, and a framework for targeting pro-survival HCK signaling in WM and ABC DLBCL cells dependent on activating MYD88 mutations. Disclosures Castillo: Biogen: Consultancy; Otsuka: Consultancy; Millennium: Research Funding; Janssen: Honoraria; Abbvie: Research Funding; Pharmacyclics: Honoraria. Treon:Janssen: Consultancy; Pharmacyclics: Consultancy, Research Funding.

The HDAC INHIBITOR ITF2357 MODULATES KEY HEMATOPOIETIC GENES in JAK2V617F CELLS From MYELOPROLIFERATIVE Neoplasm PATIENTS

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 797-797
Author(s):  
Ariel Amaru ◽  
Katia Todoerti ◽  
Anna Pellicioli ◽  
Luca Donadoni ◽  
Giacomo Tuana ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Molecular Mechanism ◽  
Cell Lines ◽  
Hdac Inhibitor ◽  
Research Funding ◽  
Myeloproliferative Neoplasms ◽  
Differentially Expressed ◽  
Wild Type ◽  
Western Blots ◽  
Erythroid Progenitor

Abstract Abstract 797 We have previously shown that the pan-HDAC inhibitor ITF2357 has strong cytotoxic activity against cells from patients with myeloproliferative neoplasms (MPN) bearing JAK2 mutation at position 617. Indeed ITF2357 inhibited colony growth of JAK2V617F positive cells at doses 5–10 fold lower than those required to block JAK2 wild type cells. We have therefore investigated here the molecular mechanism of this effect. Three cell lines homozygotes (HEL, UKE1) or heterozygotes (SET2) for the JAK2V617F mutation were used along with cell lines bearing JAK2 wild type (K562 and KG1). We confirmed the higher sensitivity of mutated with respect to unmutated cell lines in colony formation assay (mean IC50 42 nM versus 179 nM) and alamar blue assay (mean IC50 84 nM vs 325 nM, respectively). In proliferation assays measuring number of live and dead cells at different time points, we observed that 100 nM ITF2357 blocked the proliferation of both JAK2 mutated and unmutated cell lines to a similar extent, with mean inhibition of 31–69% at 72 hours, but induced apoptosis more efficiently in JAK2 mutated (mean 34%) versus unmutated cells (mean 2%). By cell cycle analysis we could show a block in G1 phase of cell cycle in JAK2V617F cells treated with 100 nM drug. In order to unravel the mechanism of specific inhibition of JAK2 mutated cells by ITF2357, we first investigated expression of HDAC isoforms in the different cell lines. We could detect HDAC1, HDAC2 and HDAC3 proteins in Western blots but these were not differentially expressed in a panel of 3 JAK2 mutated and 3 wild type cell lines. We then set out to analyse the molecular mechanism of action of ITF2357 by global gene expression analysis. Using the Rank Product method with a false positive prediction (pfp) of 0.05 and a 2 fold change cut off parameters, we observed 716 and 863 genes modulated at 6 hours by 250 nM ITF2357 in HEL and UKE-1 cell lines, respectively; 293 of these, (179 up- and 114 down-regulated), were common between both cell lines and 10 were subsequently validated by Q-RT-PCR. Among differentially expressed genes, a number are known to play an important role in the control of proliferation and /or apoptosis, most notably APAF1, BCL2L11, CCNG2, NFKB2, MXD1 and TP53INP1, while additional 6 genes (C-MYB, A-MYB, TAL1, NFE2, MLF1, NOTCH2) are involved in the control of hematopoietic differentiation. Of particular interest is NFE2, which was down modulated 2.7 fold by ITF2357 at 6 hours at the RNA level and by about 2 fold at 24 hours at the protein level. NFE2 has been reported to be hyperexpressed in JAK2V617 MPN patients. We also showed that ITF2357 downmodulated NFE2 expression 2 fold also in CD34+ cells purified from these patients. Given the accepted role of NFE2 in the control of erythroid progenitor cell proliferation and differentiation, and its enhanced expression in MPN patients, our data suggest that NFE2 down-regulation by ITF2357 may at least partially explain the drug effect on growth of MPN progenitor cells. The regulation of NFE2 expression and that of other hematopoietic transcription factors and regulatory proteins in response to ITF2357 is under investigation in our laboratory and data will be presented. Disclosures: Fossati: Italfarmaco SpA: Employment. Rambaldi:Italfarmaco SpA: Research Funding. Golay:Italfarmaco SpA: Research Funding.

Cereblon Binding IMiD Small Molecules Mediate Myeloma Cell Death Via IRF4

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1807-1807
Author(s):  
Yuan Xiao Zhu ◽  
Chang-Xin Shi ◽  
Laura Bruins ◽  
Klaus Martin Kortuem ◽  
Jessica Schmidt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Binding Site ◽  
Cell Lines ◽  
Protein Function ◽  
Research Funding ◽  
Wild Type ◽  
Binding Region ◽  
Down Regulation ◽  
Over Expression

Abstract Abstract 1807 We have recently demonstrated that cereblon (CRBN) mediates the direct anti-myeloma activity of immunomodulatory drugs (IMiDs). However, the genes/pathways downstream of CRBN associated with anti-myeloma activity remain unclear. We, and others, identified interferon regulatory factor 4 (IRF4) as one of the downstream targets of CRBN-associated signaling. Both lenalidomide treatment and CRBN knockdown downregulate IRF4. IRF4 levels return to baseline in IMiD resistant cells surviving CRBN silencing. To determine whether IMiD-induced IRF4 downregulation is critical to anti-MM activity, we overexpressed IRF4 in two IMiD-sensitive human MM cell lines (HMCLs), KMS11 and MM1.S, followed by lenalidomide treatment. Lenalidomide-induced cytotoxicity was greatly impaired in both HMCLs overexpressing IRF4 compared with the control virus infected cells. Further analysis indicated that IRF4 over-expression does not completely prevent lenalidomide-induced growth arrest, but reduces cell death by 70% after lenalidomide treatment. Immunoblotting analysis of KMS11 cells indicated that IRF4 over-expression blocks lenalidomide-induced activation of caspase 8, reduces up-regulation of p21waf and increases CDK6 expression but does not significantly affect lenalidomide-induced MYC down-regulation. Although cereblon and IRF4 are broadly expressed in MM, baseline levels of expression are only weakly correlated (r=0.22) in primary MM patient gene expression analysis. Gene expression studies revealed statistical changes in 1,368 genes when comparing high versus low CRBN expression in primary myeloma samples. Interestingly genes associated with high CRBN expression included cyclin D2, SOCS3 and IL4 while genes associated with low cereblon expression included cyclin D1, FRZB and CD200. In order to understand how CRBN is connected with downstream anti-myeloma signaling, a structure-function study was performed to determine which CRBN domain is required for lenalidomide-induced IRF4 down-regulation and cytotoxicity. Lentiviral constructs expressing wild-type CRBN and a series of mutated CRBN were generated, including mutations at thalidomide binding site (Y384A/W386A), deletion of DDB1 binding region (ΔMid) and truncations at N-terminal and C-terminal. Lentiviruses from these constructs were used to infect IMiDs resistant HMCLs, OCI-MY5 and MM1.S res. Both of these cell lines have very low endogenous CRBN expression and they became sensitive to lenalidomide after introduction of wild-type CRBN. Conversely, introduction of CRBN with mutated thalidomide-binding site or with DDB1 binding region depletion failed to mediate lenalidomide toxicity and down-regulation of IRF4. OCI-MY5 cells expressing either N-terminal or C-terminal truncated CRBN showed substantial reduced responses (more than 50%) to lenalidomide compared with wild-type CRBN expressing cells. Deletion of only 20–30 amino acids at either ends of CRBN greatly impaired the protein function, suggesting that protein folding might be important for CRBN-mediated IMiD response. Our data indicate that IMiD induced myeloma cytotoxicity is largely mediated by modifying CRBN associated E3 ubiqutin ligase and subsequent IRF4 downregulation, suggesting the CRBN-IRF4 axis is a potential target for development of new anti-myeloma drugs. Disclosures: Schmidt: Karyopharm: Research Funding. Stewart:Millenium: Consultancy, Honoraria, Research Funding; Onyx: Consultancy; Celgene: Consultancy.

scholarly journals Gene expression profiling in wild-type and metallothionein mutant fibroblast cell lines

2006 ◽  
Vol 39 (1) ◽  
Author(s):  
ÁNGELA D ARMENDÁRIZ ◽  
FELIPE OLIVARES ◽  
RODRIGO PULGAR ◽  
ALEX LOGUINOV ◽  
VERÓNICA CAMBIAZO ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Cell Lines ◽  
Expression Profiling ◽  
Fibroblast Cell ◽  
Wild Type ◽  
Fibroblast Cell Lines

P4-124: Comparison of gene expression profiles of prion protein-deficient and wild type neuronal cell lines of mice

2006 ◽  
Vol 2 ◽  
pp. S552-S552
Author(s):  
Boe-Hyun Kim ◽  
Jae-Il Kim ◽  
Eun-Kyoung Choi ◽  
Richard I. Carp ◽  
Yong-Sun Kim
Keyword(s):  
Gene Expression ◽  
Prion Protein ◽  
Cell Lines ◽  
Expression Profiles ◽  
Neuronal Cell ◽  
Gene Expression Profiles ◽  
Wild Type ◽  
Neuronal Cell Lines

Activation of the Wnt/β-Catenin Pathway Mediates Lenalidomide Resistance in Multiple Myeloma.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 113-113 ◽  
Author(s):  
Chad C. Bjorklund ◽  
Deborah J. Kuhn ◽  
Jairo A. Matthews ◽  
Michael Wang ◽  
Veerabhadran Baladandayuthapani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Cell Lines ◽  
Expression Profiling ◽  
Fold Increase ◽  
Resistant Cell ◽  
Refractory Disease ◽  
Wild Type ◽  
Myeloma Cells ◽  
Resistant Cells

Abstract Abstract 113 Background: Novel drugs such as the immunomodulatory agent lenalidomide have revolutionized the treatment of multiple myeloma, as evidenced by an increasing overall survival for patients with both newly-diagnosed, and relapsed and/or refractory disease. Despite these improvements, myeloma remains incurable, and is still characterized by a trend for increasing chemoresistance at relapse, with a decreasing duration of benefit from each successive line of therapy. By understanding the mechanisms responsible for the emergence of drug resistance, which have so far not been well characterized in the case of lenalidomide, it may be possible to rationally design novel regimens that could either overcome this resistance, or possibly prevent its emergence altogether. Methods: To improve our understanding of the mechanisms responsible for lenalidomide resistance, we developed cell line models of interleukin (IL)-6-dependent (ANBL-6 and KAS-6/1) and –independent (U266 and MM1.S) lenalidomide-resistant multiple myeloma cells. Starting at a concentration that was 1/10 of the IC50 for lenalidomide's anti-proliferative effects in drug-naïve cells, increasing drug concentrations were used until all the cell lines could proliferate and maintain cell membrane integrity in the presence of 10 μM lenalidomide. These cell lines were then used as an in vitro model of lenalidomide-specific drug resistance, and subjected to further characterization, including with gene expression profiling. Results: Resistance to lenalidomide was evidenced by a dramatic, 100-1000-fold increase in the IC50 values of these myeloma cells. In the case of ANBL-6 cells, for example, drug-naïve cells showed an IC50 of 0.14 μM using tetrazolium dye-based viability assays, but this increased to >100 μM in the drug-resistant cells, as was the case in U266 and MM1.S cells. This resistance was a stable phenotype, since removal of lenalidomide for seven to ninety days from cell culture conditions did not re-sensitize them when 10 μM lenalidomide was reintroduced. Gene expression profiling followed by pathway analysis to examine changes at the transcript level between wild-type parental and lenalidomide-resistant cell lines identified the Wnt/β-catenin pathway as the most altered across all cell lines. Increased expression was seen in several members of the low-density-lipoprotein receptor related protein family, including LRP1 and 5; members of the wingless-type MMTV integrations site family, including WNT3 and 4; β-catenin; and downstream Wnt/β-catenin targets such as CD44. Similar changes were detected in primary samples from a patient who developed clinically lenalidomide-refractory disease. Reporter assays revealed an up to 5-fold increase in LEF/TCF-dependent transcription both in drug-naïve cells acutely exposed to lenalidomide, and in their chronically exposed, lenalidomide-resistant clones. Western blotting and flow cytometry confirmed that these lenalidomide-resistant cells had increased expression by 2-20 fold of β-catenin and CD44, as well as other LEF/TCF targets, including Cyclin D1 and c-Myc. Comparable changes occurred after lenalidomide exposure in myeloma cells grown in the context of bone marrow stroma. Notably, lenalidomide-resistant cells showed decreased expression of casein kinase 1 and increased phosphorylation of glycogen synthase kinase 3 at Ser21/9, both of which would reduce the phosphorylation of β-catenin needed for its later proteasome-mediated degradation. Stimulation of the Wnt/β-catenin pathway with recombinant human Wnt3a resulted in resistance to lenalidomide in wild-type, drug-naïve cells, as evidenced by a 10-fold increase in the IC50. Conversely, exposure of lenalidomide-resistant cell lines to quercetin, a known antagonist of the β-catenin/TCF interaction, induced a partial re-sensitization to lenalidomide. Conclusions: These data support the hypothesis that activation of the Wnt/β-catenin pathway represents a mechanism of both acute and chronic resistance to the anti-proliferative effects of lenalidomide in multiple myeloma. Moreover, they support the development of strategies aimed at suppressing Wnt/β-catenin activity to resensitize multiple myeloma to the effects of this immunomodulatory agent in vivo. Disclosures: No relevant conflicts of interest to declare.

Comparison of Clinical and Biologic Significance of WT1 Mutations in Populations of Older (≥60 years[y]) and Younger (<60 y) Adult Patients (Pts) with Cytogenetically Normal (CN) De Novo Acute Myeloid Leukemia (AML): a Cancer and Leukemia Group B (CALGB) Study.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 326-326
Author(s):  
Heiko Becker ◽  
Guido Marcucci ◽  
Kati Maharry ◽  
Michael D. Radmacher ◽  
Krzysztof Mrózek ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Age Groups ◽  
Stem Cell Marker ◽  
Treatment Intensity ◽  
Prognostic Impact ◽  
Wild Type ◽  
Age Related ◽  
Exon 9 ◽  
Wt1 Mutation

Abstract Abstract 326 Mutations of the Wilms tumor (WT1) gene are found in ∼10% of younger (<60 years[y]) adult pts with de novo CN-AML and impact adversely on their outcome. The clinical significance of WT1 mutations has not yet been evaluated in older (≥60 y) CN-AML pts. Therefore, we analyzed frequency and clinical impact of WT1 mutations in the context of other molecular markers in a relatively large cohort of 243 pts ≥60 y (range, 60-83 y) with de novo CN-AML treated intensively on upfront cytarabine/daunorubicin-based CALGB protocols. Included pts were those with material available for analysis of WT1 mutation status and that of a panel of other validated molecular prognosticators including NPM1, FLT3 (ie, FLT3-ITD, FLT3-TKD) and CEBPA mutations, BAALC and ERG expression levels. Mutations in WT1 “hot spots” (exons 7 and 9) were assessed by DHPLC and sequencing. The results were compared with the findings in younger (18-59 y) CALGB pts (n=207) characterized molecularly in a similar fashion. Gene expression profiles in both populations were assessed centrally using Affymetrix U133 plus 2.0 microchip. Among the 243 older pts, 16 (7%) had WT1 mutations. Of those, 14 had single WT1 mutations in exon 7 [frameshift (n=8), nonsense (n=1), and missense (n=1)] or in exon 9 [missense (n=4)]; 1 pt had 2 frameshift mutations in exon 7, and 1 had 1 frameshift mutation in exon 7 and 1 missense mutation in exon 9. Compared with older WT1 wild-type pts, older WT1 mutated pts more often had FLT3-ITD (P<.001) and had lower hemoglobin (P=.01), and higher WBC (P=.03) and % blood blasts (P=.03). WT1 mutated pts had a trend for lower complete remission (CR) rates (50% v 70%, P=.16) and shorter OS (P=.08; Figure 1), but similar disease-free survival (DFS; P=.59; Figure 2) compared with WT1 wild-type pts. The frequency of WT1 mutations tended to be lower in older than younger pts (7% v 12%, P=.07). Mutation types and pretreatment clinical and molecular characteristics associated with WT1 mutations were similar between the two age groups. Despite differences in treatment intensity, there were no significant differences in younger v older WT1 mutated pts with regard to CR rates (P=.18), or OS (P=.68; Figure 1) or DFS (P=.66; Figure 2) durations. In contrast, younger WT1 wild-type pts had significantly higher CR rates (P<.001), and longer OS (P<.001; Figure 1) and DFS (P<.001; Figure 2) than older WT1 wild-type pts. Although associated with WT1 mutations in both the younger (P=.02) and older age groups, FLT3-ITD had no impact on CR rates (P=.28), or OS (P=.15) or DFS (P=.21) durations of all WT1 mutated pts after controlling for age-related treatment intensity. To provide insights into the molecular features associated with WT1 mutations we analyzed the whole cohort (younger and older) for genes differentially expressed (ie, P≤.001) between WT1 mutated and WT1 wild-type pts. A signature comprising 110 named genes was derived. Among the 71 upregulated genes in WT1 mutated pts, were those encoding the leukemia stem cell marker CD96 and the leukemia fusion protein partners PML and MLL. The most upregulated gene (6.2 fold) was GTSF1, which, like WT1, may be involved in germ cell development. Among the 39 genes downregulated in WT1 mutated pts, were those encoding SNRPN and SNURF, involved in pre-mRNA processing, and the insulin receptor and IRS2, upstream effectors of the PI3K/AKT pathway. In conclusion, WT1 mutations in older CN-AML pts are less frequent than in younger pts. While WT1 mutations independently associate with shorter OS and DFS in younger CN-AML pts, in older CN-AML pts they are only associated with trends for a worse CR rate and shorter OS. This difference appears due to the poor outcome of the older compared to younger WT1 wild-type pts, which reduced the prognostic impact of WT1 mutations in the former. Nevertheless, the outcome of pts with WT1 mutations is equally poor in older and younger pts regardless of differences in treatment, thereby suggesting that WT1 mutated CN-AML may constitute a distinct biologic entity across age groups. The unique gene expression signature associated with WT1 mutations could provide useful insights into WT1 mutation-driven leukemogenic mechanisms across age-related groups, and help in devising novel molecular targeted therapeutic approaches for this subtype of CN-AML. Disclosures: No relevant conflicts of interest to declare.

In Silico Prediction of Novel Drug Combinations to Combat Bortezomib-Resistant Multiple Myeloma

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1344-1344
Author(s):  
Holly A. F. Stessman ◽  
Tian Xia ◽  
Aatif Mansoor ◽  
Raamesh Deshpande ◽  
Linda B. Baughn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Cell Lines ◽  
In Silico ◽  
Research Funding ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Mouse Cell ◽  
Resistant Mouse ◽  
Novel Therapeutic

Abstract Abstract 1344 Bortezomib/VELCADE® (Bz) is a proteasome inhibitor that has been used successfully in the treatment of multiple myeloma (MM) patients. However, acquired resistance to Bz is an emerging problem. Thus, there is a need for novel therapeutic combinations that enhance Bz sensitivity or re-sensitize Bz resistant MM cells to Bz. The Connectivity Map (CMAP; Broad Institute) database contains treatment-induced transcriptional signatures from 1,309 bioactive compounds in 4 human cancer cell lines. An input signature can be used to query the database for correlated drug signatures, a technique that has been used previously to identify drugs that combat chemoresistance in cancer (Wei, et al. Cancer Cell (2006) 10:331). In this study we used in silico bioinformatic screening of gene expression profiles from isogenic pairs of Bz sensitive and resistant mouse cell lines derived from the iMycCα/Bcl-xL mouse model of plasma cell malignancy to identify compounds that combat Bz resistance. We established Bz-induced kinetic gene expression profiles (GEPs) in 3 pairs of Bz sensitive and resistant mouse cell lines over the course of 24 hours. GEPs were collected in the absence of large-scale cell death. The 16 and 24 hour time points were averaged and compared between each Bz sensitive and resistant pair. Genes in the sensitive cell line with a fold change greater than 2, relative to the resistant line, were given the binary distinction of “up” or “down” depending on the direction of change. Genes that met these criteria were assembled into signatures, and then used as inputs for CMAP queries to identify compounds that induce similar transcriptional responses. In all pairs, treatment of the Bz sensitive line correlated with GEPs of drugs that target the proteasome, NF-κB, HSP90 and microtubules, as indicated by positive connectivity scores. However eight compounds, all classified as Topoisomerase (Topo) I and/or II inhibitors, were negatively correlated to our input signature. A negative connectivity score could have two interpretations: (1) this could indicate simply that Topos are upregulated by Bz treatment in Bz sensitive lines, which has been previously reported (Congdan, et al. Biochem. Pharmacol. (2008) 74: 883); or (2) this score could be interpreted as Topos are inhibited in Bz resistant cells upon Bz treatment. This led us to ask whether Topo inhibitors could target Bz resistant MM cells and re-sensitize them to Bz. Indeed, we found that multiple Topo inhibitors were significantly more active against Bz resistant cells as single agents and restored sensitivity to Bz when combined with Bz as a cocktail regimen. This work demonstrates the potential of this in silico bioinformatic approach for identifying novel therapeutic combinations that overcome Bz resistance in MM. Furthermore, it identifies Topo inhibitors – drugs that are already approved for clinical use – as agents that may have utility in combating Bz resistance in refractory MM patients. Disclosures: Stessman: Millennium: The Takeda Oncology Company: Research Funding. Van Ness:Millennium: The Takeda Oncology Company: Research Funding.

Loss of the Histone Demethylase UTX Contributes to Multiple Myeloma and Sensitizes Cells to EZH2 Inhibitors

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 611-611 ◽  
Author(s):  
Teresa Ezponda ◽  
Relja Popovic ◽  
Yupeng Zheng ◽  
Behnam Nabet ◽  
Christine Will ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Cell Lines ◽  
Genetic Alterations ◽  
Histone Demethylase ◽  
Mass Spectrometry Analysis ◽  
Rna Seq ◽  
Wild Type ◽  
Altered Expression ◽  
E Cadherin

Abstract Genetic alterations of epigenetic regulators have become a recurrent theme in hematological malignancies. In particular, aberrations that alter the levels or distribution of methylation of lysine 27 on histone H3 (H3K27me) have emerged as a common feature of a wide variety of cancers, including multiple myeloma (MM). The histone demethylase UTX/KDM6A activates gene expression by removing the H3K27me3 repressive histone mark, counteracting the activity of EZH2, the enzyme that places this modification. UTX somatic inactivating mutations and deletions are found in up to 10% of MM cases; nevertheless, the epigenetic impact of UTX loss in MM and the mechanisms by which it contributes to this disease remain to be elucidated. To ascertain the biological impact of UTX loss, we used a recently identified isogenic cell line pair: ARP-1 (UTX wild-type) and ARD (UTX null). UTX-null ARD cells were engineered to express UTX in a doxycycline-inducible manner. UTX add-back slowed the proliferation rate of ARD cells, without affecting their viability. Soft agar assays demonstrated that UTX-null ARD cells have increased clonogenicity compared to UTX-wild-type ARP-1 cells. Re-expression of UTX partially reversed this effect, decreasing the number and size of colonies formed. ARD cells also showed increased adhesion to Hs-5 bone marrow stromal cells and to fibronectin than ARP-1 cells, an ability associated with cell survival and drug resistance. UTX add-back decreased the adhesive properties of ARD cells demonstrating this effect is dependent on UTX loss. Mass spectrometry analysis of the add-back system and a panel of UTX wild-type and mutant MM cell lines showed that global levels of H3K27me are not altered after UTX loss or upon its add-back. Therefore, UTX depletion may alter H3K27me at specific loci, and control the expression of a limited number of genes. To identify the genes and pathways that are altered upon UTX loss, we performed RNA-sequencing (RNA-seq) on the paired MM cell lines and the add-back system. This analysis revealed approximately 5,000 genes differentially expressed between ARP-1 and ARD cells. Re-expression of UTX in the UTX-null ARD cells reversed the expression of approximately 1,400 genes, most of them being upregulated upon reintroduction of UTX. Gene ontology analysis of genes responsive to UTX manipulation identified pathways such as JAK-STAT, cadherin, integrin and Wnt pathways. Many of these pathways are related to cell adhesion properties, correlating with the effects observed in vitro. Some examples of the genes which expression was restored upon UTX add-back are E-cadherin, whose loss has been associated with MM progression; and PTPN6, a negative regulator of the JAK-STAT pathway. Chromatin immunoprecipitation (ChIP) experiments at UTX target genes revealed a decrease in H3K27me3 and a concomitant increase in H3K4me3 upon UTX add-back, correlating with the observed changes in gene expression. As loss of UTX leads to a failure in the removal of H3K27me3, we hypothesized that UTX-null cells may be more dependent on EZH2 to maintain high H3K27me3 levels at specific loci. Treatment of the paired cell lines with the EZH2 inhibitor GSK343 for 7 days significantly decreased the viability of UTX-null ARD cells, but had no effect on the UTX wild-type ARP-1 cells. This effect was not exclusive to these cell lines, as treatment of a panel of UTX wild-type and mutant MM cells corroborated the increased sensitivity in UTX-mutant cells. RNA-seq of ARD cells treated with GSK343 for 7 days identified approximately 2,000 genes with altered expression in response to this drug, most of them being upregulated upon EZH2 inhibition. These genes partially overlapped with the genes that were responsive to UTX add-back, including E-cadherin, suggesting that treatment with EZH2 inhibitors is somewhat similar to UTX add-back. Collectively, this work demonstrates that loss of UTX alters the epigenetic landscape of MM cells, leading to altered expression of a specific set of genes, ultimately benefiting cells through increased proliferation, clonogenicity and adhesion. Moreover, inhibition of EZH2 partially reverses aberrations promoted by UTX loss and may represent a rationale therapy for the treatment of this type of MM. Disclosures No relevant conflicts of interest to declare.

Recurrent Mutations of the Exportin 1 Gene (XPO1) in Primary Mediastinal B-Cell Lymphoma: A Lysa Study

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 129-129 ◽  
Author(s):  
Fabrice Jardin ◽  
Anais Pujals ◽  
Laura Pelletier ◽  
Elodie Bohers ◽  
Vincent Camus ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Cell Lines ◽  
Nuclear Export ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Wild Type ◽  
U2os Cells ◽  
Aggressive B Cell Lymphoma

Abstract Background and aim of the study Primary mediastinal B-cell lymphoma (PMBL) is an entity of aggressive B-cell lymphoma that is clinically and biologically distinct from the other molecular subtypes of diffuse large B-cell lymphoma (DLBCL). We recently detected by Whole exome sequencing a recurrent point mutation in the XPO1 (exportin 1) gene (also referred to as chromosome region maintenance 1; CRM1), which resulted in the Glu571Lys (p.E571K) missense substitution in 2 refractory/relapsed PMBL (Dubois et al., ICML 2015; Mareschal et al. AACR 2015). XPO1 is a member of the Karyopherin-b superfamily of nuclear transport proteins. XPO1 mediates the nuclear export of numerous RNAs and cellular regulatory proteins, including tumor suppressor proteins. This mutation is in the hydrophobic groove of XPO1 that binds to the leucine-rich nuclear export signal (NES) of cargo proteins. In this study, we investigated the prevalence, specificity, and biological / clinical relevance of XPO1 mutations in PMBL. Patients and methods High-throughput targeted or Sanger sequencing of 117 PMBL patients and 3 PMBL cell lines were performed. PMBL cases were defined either molecularly by gene expression profile (mPMBL cohort) or by standard histological method (hPMBL cohort) and enrolled in various LYSA (LYmphoma Study Association) clinical trials. To assess the frequency and specificity of XPO1 mutations, cases of classical Hodgkin lymphoma (cHL) and primary mediastinal grey zone lymphoma (MGZL) were analysed. Cell experiments were performed to assess the impact of the E571 mutation on the activity of selective inhibitor of nuclear export (SINE) molecules. Results XPO1 mutations were present in 28/117 (24%) PMBL cases but were rare in cHL cases (1/19, 5%) and absent from MGZL cases (0/20). A higher prevalence (50%) of the recurrent codon 571 variant (p.E571K) was observed in PMBL cases defined by gene expression profiling (n = 32), as compared to hPMBL cases (n = 85, 13%). No difference in age, International Prognostic Index (IPI) or bulky mass was observed between the PMBL patients harboring mutant and wild-type XPO1 in the overall cohort whereas a female predominance was noticed in the mPMBL cohort. Based on a median follow-up duration of 42 months, XPO1 mutant patients exhibited significantly decreased PFS (3y PFS = 74% [CI95% 55-100]) compared to wild-type patients (3y PFS = 94% [CI95% 83-100], p=0.049) in the mPMBL cohort. In 4/4 tested cases, the E571K variant was also detected in cell-free circulating plasmatic DNA, suggesting that the mutation can be used as a biomarker at the time of diagnosis and during follow-up. Importantly, the E571K variant was detected as a heterozygous mutation in MedB-1, a PMBL-derived cell line, whereas the two other PMBL cell lines tested, Karpas1106 and U-2940, did not display any variants in XPO1 exon 15. KPT-185, the SINE compound that blocks XPO1-dependent nuclear export, induced a dose-dependent decrease in cell proliferation and increased cell death in the PMBL cell lines harbouring wild type or mutated alleles. To test directly if XPO1 mutation from E571 to E571K alters XPO1 inhibition by SINE compounds, the mutated protein was tested in vitro. The E571XPO1 mutated allele was transiently transfected into osteosarcoma U2OS cells which stably express the fluorescently labelled XPO1 cargo REV. Cells were treated with the clinical SINE compound selinexor, which is currently in phase I/II clinical trials and nuclear localization of REV-GFP was analysed in red transfected cells. The results showed that the nuclear export of the mutated XPO1 protein was inhibited by selinexor similarly to the wild-type XPO1 protein (Figure 1). Conclusion Although the oncogenic properties of XPO1 mutations remain to be determined, their recurrent selection in PMBL strongly supports their involvement in the pathogenesis of this curable aggressive B-cell lymphoma. XPO1 mutations were primarily observed in young female patients who displayed a typical PMBL molecular signature. The E571K XPO1 mutation represents a novel hallmark of PMBL but does not seem to interfere with SINE activity. Rev-GFP (green fluorescent) expressing U2OS cells were transfected with wild type XPO1-RFP (red fluorescent protein), XPO1-C528S-RFP, XPO1-E571K-mCherry, and XPO1-E571G-mCherry. The cells were then treated with 1µM KPT-330 for 8 hours. Figure 1. Rev-GFP expressing U2OS cells transfected with XPO1 variants. Figure 1. Rev-GFP expressing U2OS cells transfected with XPO1 variants. Disclosures Landesman: Karyopharm Therapeutics: Employment. Senapedis:Karyopharm Therapeutics, Inc.: Employment, Patents & Royalties. Argueta:Karyopharm Therapeutics: Employment. Milpied:Celgene: Honoraria, Research Funding.

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