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  • 1
    Online Resource
    Online Resource
    American Society of Hematology ; 2016
    In:  Blood Vol. 128, No. 22 ( 2016-12-02), p. 2087-2087
    In: Blood, American Society of Hematology, Vol. 128, No. 22 ( 2016-12-02), p. 2087-2087
    Abstract: Homologous recombination (HR) is a DNA repair mechanism that uses extensive sequence homology in the participating DNA molecules for an accurate repair. In a normal cellular environment, HR is the most precise DNA repair mechanism and therefore has a unique role in the maintenance of genomic integrity and stability. Normally HR is tightly regulated, however, as it involves incision and recombination of genomic DNA fragments, if dysregulated or dysfunctional, it can also be deleterious. Consistent with this view, we have shown that elevated HR activity mediates genomic instability and development of drug resistance in MM. Here we have now investigated the mechanism that may contribute to dysregulation of HR and genomic instability in MM, as well as evaluated an agent able to decrease acquisition of new genomic changes. It has been shown that Abl kinase regulates recombinase RAD51 by affecting its expression, stability as well as phosphorylation at Y315. Phosphorylation of RAD51 (at Y315) mediates its dissociation from BCR-ABL1 kinase and migration to the nucleus to form nuclear foci, one of the initial steps in HR. We have evaluated nilotinib, a small molecule inhibitor of Abl kinase and observed that it inhibited HR activity in all MM cell lines tested, in a dose-dependent manner. At 5 µM, nilotinib inhibited HR activity in MM1S, RPMI 8226 and U266 MM cells by 64%, 78% and 80%, respectively. Nilotinib led to reduced phosphorylation of RAD51 at Y315, the phosphorylation which affects RAD51 migration. Nilotinib-mediated inhibition of RAD51 and HR activity was also associated with reduced DNA breaks, as indicated by reduced levels of g-H2AX. To determine the impact of nilotinib on genome stability, MM (RPMI 8226) cells were cultured in the presence of nilotinib for three weeks and the impact of this treatment on appearance of new copy number changes was evaluated using SNP arrays. Using day 0 cells as baseline to identify new copy number events at 3 weeks, the acquisition of new genomic changes was inhibited by 50% in the presence of nilotinib. As we have previously reported that induction of HR helps develop dexamethasone resistance in a short period of time, we investigated whether inhibition of HR by nilotinib may improve efficacy of melphalan and dexamethasone in MM. Nilotinib (at 2.5 µM) significantly increased the efficacy of melphalan (10 µM); and dexamethasone (10 nM) in RPMI 8226 cells. The relation between these observed effects and inhibition of HR is being investigated. In conclusion, we have observed that Abl tyrosine kinase plays an important role in genomic instability in myeloma and its inhibition using nilotinib, suppresses the underlying mechanism of genomic instability and reduces acquisition of new genomic changes with potential for clinical application. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2016
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 2
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 2420-2420
    Abstract: Genomic instability leads to acquisition of mutational changes which underlie development and progression of cancer, including development of drug resistance and poor clinical outcome. Understanding mechanisms of genomic instability is therefore necessary to develop promising strategies for prevention and treatment of disease. Homologous recombination (HR), the most precise DNA repair mechanism, has been previously described to be dysregulated in multiple myeloma (MM) mediating genomic instability. Since nuclease activity, by producing free ends of DNA, can induce DNA recombination leading to genomic rearrangements, we investigated prognostic significance of nuclease activity and nuclease gene expression in MM. We first developed a nuclease gene signature correlating with both the genomic instability and survival in myeloma patients. We used two different myeloma patient datasets (gse26863, n=246 and IFM 170 patient dataset) which had both the gene expression and SNP/CGH array-based copy number information for each patient. Genomic instability in each patient was determined by counting the total number of amplification and/or deletion events; an event was defined as a change in ≥3 and/or 5 consecutive SNPs/probes. We identified 34 nucleases whose elevated expression correlated with increased genomic instability in gse26863 dataset. Of these, the elevated expression of 21 nucleases also correlated with increased genomic instability in 170 dataset. Elevated expression of seven of these genes also correlated with poor overall survival (p=0.00005) as well as event free survival (P=0.0003) in myeloma patients (n=170). We further tested one of these nucleases (APEX2) in both the loss and gain of function studies and found that its suppression significantly reduces DNA breaks and dysregulated HR, an important activity underlying ongoing genomic rearrangements and instability in myeloma. Upregulation of APEX2 was associated with excessive DNA breaks, dysregulation of HR, acquisition of new genomic changes over time in myeloma cells. We also investigated the prognostic significance of nucleolytic activity in cell lines and patient samples using a plasmid degradation assay in which supercoiled DNA is converted to open circular and linear forms by the MM cell lystae prepared from purified CD138+ patient MM cells or MM cell lines. The ratio of supercoiled to total DNA per lane was graphed across successive time points (0, 3, 6, 12, 24 minutes) and analyzed via nonlinear regression using PRISM (statistical software) to calculate a half-life and k-constant. The longer half life suggests lower nuclease activity in MM cells. This assay was able to differentiate MGUS and smoldering myeloma (SMM) patients with long half-life of plasmid (9499 minutes) versus newly diagnosed MM (9 minutes) in which there was variability with some patients with plasmid degradation pattern closer to SMM versus some with significantly higher activity. A large number of (N = 410) clinically annotated sample patients are currently being evaluted for both functional and clinical correlation of nuclease activity. In summary, we show correlation between nucleases activity and genomic instability with impact on survival in MM. The genes in this signature not only provide novel markers to predict clinical outcome but also potential targets for prevention/reduction of genomic evolution. Investigation of the role of each of the seven genes, separately and in combination, in the overall nucleolytic activity, genomic instability, and pathways involved in the regulation of cell cycle, DNA repair/maintenance checkpoints, apoptosis and survival is currently ongoing. Disclosures Avet-Loiseau: jansen: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; celgene: Membership on an entity's Board of Directors or advisory committees; jansen: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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    detail.hit.zdb_id: 80069-7
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  • 3
    In: Journal of Gastroenterology and Hepatology Research, ACT Publishing Group, Vol. 6, No. 1 ( 2017), p. 2286-2295
    Type of Medium: Online Resource
    ISSN: 2224-3992
    Language: English
    Publisher: ACT Publishing Group
    Publication Date: 2017
    detail.hit.zdb_id: 2690046-4
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  • 4
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 3626-3626
    Abstract: Homologous recombination (HR) is a DNA repair mechanism based on extensive sequence homology betyween DNA molecules. In a normal cellular environment, the branch of HR which is utilized to copy missing or altered information from a sister chromatid in the G2 phase of the cell cycle, is one of the most tightly regulated and error-free DNA repair mechanism. Thus HR, especially the one associated with G2 phase of cell cycle, has a unique role in the maintenance of genomic integrity and stability. However, we have previously observed that, in vitro, elevated or dysregulated HR activity mediates genomic instability and development of drug resistance in multiple myeloma (MM). In this study we have now evaluated clinical significance of elevated HR activity in MM. We optimized an in vitro HR assay using cell lysates and demonstrated that evaluation of HR with this assay is consistent with assay conducted with intact cells (R=0.97; P=0.0005). Using this assay, we evaluated HR activity in 100 patient specimens. We found that HR activity was elevated ³2-fold relative to normal PBMC in 69% and ³4-fold in 20% of MM samples. At 47 months 74% of patients with very high HR (³4-fold) had event where as 45% of patients with lower HR had event (P=0.049) To further define genomic signature of elevated HR activity, we performed RNASeq on these patient samples (N=65) and identified 345 genes whose expression correlated with HR activity in MM. Expression of 147 genes correlated positively with HR activity (R, ≥ 0.3; P ≤ 0.01). Higher expression of 65 of these genes significantly associated with poor event free survival (EFS). Expression of 198 genes correlated negatively with HR activity (R, ≥ -0.3; P ≤ 0.01). TP53, a known negative regulator of HR, was among top five in this list. Lower expression of 26 of these potential negative regulators of HR associated with poor EFS. The genes correlating with HR activity in myeloma include novel genes (previously not shown to have association with HR), genes previously known to regulate HR, as well as the genes recently identified as HR regulators in other cancers. Gene network analyses showed that the novel HR genes identified in our signature belonged to a variety of functional groups including those involved in signal transduction by phosphorylation, chromatin organization, chromosome function, cytoskeleton function, cellular response to stimulus, response to stress, DNA/nucleic acid binding, DNA/nucleic acid metabolic process, nuclear metabolic process, nucleolus function, cell cycle, and proliferation. The network analysis is consistent with the view that the novel genes identified in this signature may have roles in DNA repair and genome maintenance. We also tested HR correlating genes for correlation with genomic instability (by investigating copy number changes) in a unique MM dataset (gse26863) and found that 50% of the genes significantly correlated with genomic instability. Elevated expression of MCM5, one of the genes in myeloma HR signature, significantly correlated with hyperdiploidy in MM (P≤0.004). Some of the novel genes, including negative regulators of HR, are currently being confirmed for their impact on HR and genome stability in loss and gain of function studies. In summary, we have developed a novel clinically applicable assay for HR activity and present evidence of prognostic significance of high HR activity in myeloma and have identified novel targets with potential to overcome/reduce dyregulated HR and genomic instability. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 5
    In: Blood, American Society of Hematology, Vol. 128, No. 22 ( 2016-12-02), p. 4440-4440
    Abstract: Multiple myeloma is associated with a marked genomic instability which leads to acquisition of mutational changes, some of which underlie disease progression including development of drug resistance and poor clinical outcome. Understanding mechanisms of genomic instability is, therefore, extremely important to develop novel improved therapeutic strategies. Since dysregulated nuclease activity can induce DNA breaks and genetic recombination eventually disrupting genomic integrity, we have evaluated nuclease activity and specific nucleases for their role in genomic instability in MM. We previously identified a nuclease gene signature correlating with genomic instability in a myeloma patient dataset and tested it for correlation with survival in two other datasets. We showed that expression of these genes associated with poor overall as well as event free survival in both datasets, IFM172 (P 〈 0.00005) and gse24080 (P 〈 0.0008). We have now further refined this signature to a nine gene signature and tested it for correlation with survival in three different MM patient datasets in which gene expression was evaluated either by microarray (GSE39754, n=170; gse24080; n=559) or RNASeq (n=300). Elevated expression of nine gene signature significantly correlated with poor overall survival in all three datasets (P ≤ 1e-06 for IFM70 and gse24080 and P = 0.002 for RNASeq). To biologically and molecularly validate this signature, we conducted an shRNA screen and evaluated impact of all nine genes in signature as well as four additional nucleases on homologous recombination (HR) activity, using a plasmid based assay in which HR produces a functional luciferase gene. Of thirteen nucleases tested, knockdown of seven was associated with ≥50% inhibition of HR activity; the strongest (~80%) inhibition of HR activity was observed by FEN1 knockdown. To further investigate FEN1, we confirmed the role of this nuclease in HR using a different (DRGFP) assay in which homology-based recombination between two mutated genes, generates a functional GFP gene. Using this assay, we showed that FEN1-knockdown in U2OS cells was also associated with a strong (71%) inhibition of HR activity, confirming the role of this nuclease in dysregulation of HR. Evaluation by Western blotting in three different normal PBMC samples and eleven MM cell lines showed that FEN1 was not detected in normal cells, whereas highly expressed in MM cells. Expression profile using microarray also showed that FEN1 is elevated in a subset of MM patient samples. Knockdown of FEN1 in two MM cell lines, RPMI and H929, led to reduction in overall nuclease activity (by ~40%) as assessed by a fluorescence based nuclease activity assay and a similar (~50%) reduction in the levels of gamma-H2AX, a marker of DNA breaks. These data indicate that FEN1 nuclease activity contributes to increased DNA breaks as well as elevated HR activity in MM cells. To further understand the role of FEN1 in dysregulated HR and genome stability in MM, using mass spectrometry, we have identified the interacting proteins. Role of FEN1 in acquisition of new genomic changes over time in MM cells is cuurently being investigated in our laboratory. In summary, we show that FEN1 is an important component of machinery maintaining genomic integrity and plays a significant role in genome dysregulation in myeloma. The FEN1 dysfunction may provide a cellular vulnerability that can be therapeutically exploited. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2016
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 6
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 1218-1218
    Abstract: Understanding mechanisms underlying genomic instability is critical in delineating pathogenesis and development of new treatments for prevention and treatment of cancer. We have previously shown that dysregulated homologous recombination (HR) significantly contributes to genomic instability and progression in multiple myeloma (MM). To identify the regulators of HR and genome stability in MM, we conducted a functional shRNA screen and identified XRCC5 (Ku80) as a novel regulator of HR in MM cells. XRCC5 has been known to work as part of DNA ligase IV-XRCC4 complex in the repair of DNA breaks by non-homologous end joining (NHEJ) and the completion of V(D)J recombination events. Evaluation by Western blotting showed that all myeloma cell lines tested (RPMI, MM1S, OPM2, MM1R, U266, ARP, H929) had elevated expression of XRCC5, ranging from 3- to 10-fold elevation relative to average expression in two normal PBMC samples. Expression profiling showed a wide range of XRCC5 expression in myeloma patients, with a subset of patients with very high expression. To investigate the role of XRCC5 in ongoing acquisition of genomic changes, we investigated the association of XRCC5 with genomic instability using two different patient datasets (gse26863, n=246 and IFM 170 pt dataset) in which both the gene expression and genomic copy number information for each patient was available. Copy events were defined as changes observed in ≥ 3 and/or 5 consecutive SNPs. Higher XRCC5 expression significantly correlated with increase in the number of copy number change events in both the 170 dataset (p ≤ 0.005 for amplifications and p = 0.0001 for deletions) as well as in gse26863 dataset (p ≤ 0.004 for amplifications and p ≤ 0.00003 for deletions). To understand mechanisms by which XRCC5 regulates HR in myeloma cells, we investigatedprotein-protein interactions using a custom protein array coated with antibodies against major DNA repair and cell cycle proteins. Array was sequentially incubated with MM cell lysate and HRP-conjugated anti-XRCC5 antibody, and interacting partners were then identified by their address on the array. Investigation in two different cell lines (RPMI and U266) showed that XRCC5 in myeloma interacts with XRCC4 (an NHEJ protein), a panel of major HR regulators (RAD51, RAD52, BRCA2, BRCA1, BARD1, P73, P53, C-ABL) and with components of cell cycle including CDC42, CDK1 (which controls entry from G2 to mitosis), CDK4, CDK6, CHK, CDC36, CDC34, and cyclins E and H. Consistent with these data, knockdown (KD) of XRCC5 was associated with reduced HR as well as reduced proliferation rate followed by a complete cell death over a period of two to three weeks in different experiments, in all 3 myeloma cell lines tested. Moreover, the investigation in U266 cells showed that XRCC5-KD is associated with 3-fold increase in the fraction of cells in G2 phase of cell cycle. Importantly, the elevated expression of XRCC5 was associated with shorter event free (p 〈 0.013) as well as poor overall survival (p 〈 0.008) in 170 patient dataset. We evaluted the expression and clinical correlation of XRCC5 in RNA-seq data from 311 newly-diagnosed MM patients and observed that the elevated expression of XRCC5 also correlated with event free survival (p = 0.03). In summary, we report that XRCC5, besides its known role in NHEJ, has important roles in HR, cell cycle and may be involved in the crosstalk among these DNA repair pathways. Elevated XRCC5 expression is associated with dysregulation of HR with consequent impact on survival of myeloma patients. Elevated XRCC5 is, therefore, a promising new target to inhibit/reduce genomic evolution as well as MM cell growth. Disclosures Avet-Loiseau: celgene: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; jansen: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; jansen: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 7
    Online Resource
    Online Resource
    Elsevier BV ; 2017
    In:  Clinical Lymphoma Myeloma and Leukemia Vol. 17, No. 1 ( 2017-02), p. e50-e51
    In: Clinical Lymphoma Myeloma and Leukemia, Elsevier BV, Vol. 17, No. 1 ( 2017-02), p. e50-e51
    Type of Medium: Online Resource
    ISSN: 2152-2650
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2017
    detail.hit.zdb_id: 2540998-0
    detail.hit.zdb_id: 2193618-3
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  • 8
    In: Clinical Lymphoma Myeloma and Leukemia, Elsevier BV, Vol. 19, No. 10 ( 2019-10), p. e80-e81
    Type of Medium: Online Resource
    ISSN: 2152-2650
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
    detail.hit.zdb_id: 2540998-0
    detail.hit.zdb_id: 2193618-3
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  • 9
    In: Blood Advances, American Society of Hematology, Vol. 3, No. 23 ( 2019-12-10), p. 3968-3972
    Abstract: UBE2T is frequently amplified and/or overexpressed and is required for homologous recombination activity in multiple myeloma cells. UBE2T is a potential therapeutic target to increase chemosensitivity in multiple myeloma cells.
    Type of Medium: Online Resource
    ISSN: 2473-9529 , 2473-9537
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
    detail.hit.zdb_id: 2876449-3
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  • 10
    In: Developmental Dynamics, Wiley, Vol. 231, No. 3 ( 2004-11), p. 527-541
    Abstract: The zebrafish caudal fin constitutes an important model for studying the molecular basis of tissue regeneration. The cascade of genes induced after amputation or injury, leading to restoration of the lost fin structures, include those responsible for wound healing, blastema formation, tissue outgrowth, and patterning. We carried out a systematic study to identify genes that are up‐regulated during “initiation” (1 day) and “outgrowth and differentiation” (4 days) of fin regeneration by using two complementary methods, suppression subtraction hybridization (SSH) and differential display reverse transcriptase polymerase chain reaction (DDRT‐PCR). We obtained 298 distinct genes/sequences from SSH libraries and 24 distinct genes/sequences by DDRT‐PCR. We determined the expression of 54 of these genes using in situ hybridization. In parallel, gene expression analyses were done in zebrafish embryos and early larvae. The information gathered from the present study provides resources for further investigations into the molecular mechanisms of fin development and regeneration. Developmental Dynamics 231:527–541, 2004. © 2004 Wiley‐Liss, Inc.
    Type of Medium: Online Resource
    ISSN: 1058-8388 , 1097-0177
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2004
    detail.hit.zdb_id: 1473797-8
    SSG: 12
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