Sheetal Singh

Impaired NHEJ function in Multiple Myeloma

Multiple myeloma (MM) is characterized by multiple chromosomal aberrations. To assess the contribution of DNA repair to this phenotype, ionizing radiation was used to induce DNA double strand breaks in three MM cell lines. Clonogenic survival assays showed U266 (SF4=15.3+6.4%) and RPMI 8226 (SF4=12.6.0+1.7%) were radiation sensitive while OPM2 was resistant (SF4=78.9+4.1%). Addition of the DNA-PK inhibitor NU7026 showed the expected suppression in radiation survival in OPM2 but increased survival in both radiation sensitive cell lines. To examine non-homologous end joining (NHEJ) repair in these lines, the ability of protein extracts to support in vitro DNA repair was measured. Among the three MM cell lines analyzed, RPMI 8226 demonstrated impaired blunt ended DNA ligation using a ligation-mediated PCR technique. In a bacterial based functional assay to rejoin a DNA break within the beta-galactosidase gene, RPMI 8226 demonstrated a 4-fold reduction in rejoining fidelity compared to U266, with OPM2 showing an intermediate capacity. Ionizing radiation induced a robust gamma-H2AX response in OPM2 but only a modest increase in each radiation sensitive cell line perhaps related to the high level of gamma-H2AX in freshly plated cells. Examination of gamma-H2AX foci in RPMI 8226 cells confirmed data from Western blots where a significant number of foci were present in freshly plated untreated cells which diminished over 24h of culture. Based on the clonogenic survival and functional repair assays, all three cell lines exhibited corrupt NHEJ repair. We conclude that suppression of aberrant NHEJ function using the DNA-PK inhibitor NU7026 may facilitate access of DNA ends to an intact homologous recombination repair pathway, paradoxically increasing survival after irradiation. These data provide insight into the deregulation of DNA repair at the site of DNA breaks in MM that may underpin the characteristic genomic instability of this disease.

Estrogen treatment induces MLL aberrations in human lymphoblastoid cells

Epidemiological data indicates increased risk of infant acute leukemia involving MLL gene aberrations with use of oral contraceptives. To determine whether estrogens might be implicated, we examined the effect of estradiol (E2) or 4-OH-E2 in an in vitro model of translocation susceptibility. Genomic DNA from the TK6 human lymphoblastoid cell line was screened by ligation mediated PCR and inverse PCR at a rearrangement hot spot within the MLL breakpoint cluster region to detect DNA aberrations. An increase in DNA double strand breaks was observed within this region after exposure to either E2 or 4-OH-E2. An increase in the frequency of MLL translocations was only found after exposure to E2. Induction of cleavage due to increased activation of apoptotic nucleases was excluded by pre-treatment with the pan-caspase inhibitor, zVAD.fmk. We conclude that concentrations of E2 and 4-OH-E2 that may occur during pregnancy, or during use of oral contraceptives, can cause aberrations of the MLL gene and could thus be a factor in the early events of leukemogenesis occurring in utero.

Rearrangements of the MLL gene are influenced by DNA secondary structure, potentially mediated by topoisomerase II binding

The location of MLL translocation breakpoints within therapy‐related acute myeloid leukemia linked to drugs targeting Topoisomerase II and infant acute leukemia (IAL) are biased toward the intron 11–exon 12 region of MLL, although lacking a comprehensive explanation. To address this, blood samples were taken from breast cancer and lymphoma patients receiving Topoisomerase II inhibitor therapy. Inverse PCR analysis was used to interrogate the exon 12 region of MLL for rearrangements. Eleven of 19 observed translocations showed breakpoint junctions restricted to a single 5 bp location within exon 12. A similarly restricted distribution (11/20 breakpoint junctions) was observed in TK6 cells exposed to either estrogen (linked to IAL) or anti‐CD95 antibody. The translocation hotspot was at the 5′ edge of a 10‐bp tract matched with a perfect palindrome, 101 bp distant. A high stringency Topoisomerase II consensus sequence binding site was noted at the geometric midpoint of the palindromes. Ligation‐mediated PCR to screen TK6 cells exposed to anti‐CD95 antibody showed 14/37 (38%) of DNA breaks adjacent to the 5′ palindrome and 10/37 (27%) at the 3′ partner. We propose a model whereby Topoisomerase II facilitates the organization of nuclease‐sensitive secondary structures, stabilized by palindrome association, which are prone to rearrangement.

Enhancing the effectiveness of androgen deprivation in prostate cancer by inducing Filamin A nuclear localization

As prostate cancer (CaP) is regulated by androgen receptor (AR) activity, metastatic CaP is treated with androgen deprivation therapy (ADT). Despite initial response, patients on ADT eventually progress to castration-resistant CaP (CRPC), which is currently incurable. We previously showed that cleavage of the 280 kDa structural protein Filamin A (FlnA) to a 90 kDa fragment, and nuclear localization of the cleaved product, sensitized CRPC cells to ADT. Hence, treatment promoting FlnA nuclear localization would enhance androgen responsiveness. Here, we show that FlnA nuclear localization induced apoptosis in CRPC cells during ADT, identifying it as a treatment tool in advanced CaP. Significantly, the natural product genistein combined polysaccharide (GCP) had a similar effect. Investigation of the mechanism of GCP-induced apoptosis showed that GCP induced FlnA cleavage and nuclear localization and that apoptosis resulting from GCP treatment was mediated by FlnA nuclear localization. Two main components of GCP are genistein and daidzein: the ability of GCP to induce G2 arrest was due to genistein whereas sensitivity to ADT stemmed from daidzein; hence, both were needed to mediate GCPs effects. FlnA cleavage is regulated by its phosphorylation; we show that ADT enhanced FlnA phosphorylation, which prevented its cleavage, whereas GCP inhibited FlnA phosphorylation, thereby sensitizing CaP cells to ADT. In a mouse model of CaP recurrence, GCP, but not vehicle, impeded relapse following castration, indicating that GCP, when administered with ADT, interrupted the development of CRPC. These results demonstrate the efficacy of GCP in promoting FlnA nuclear localization and enhancing androgen responsiveness in CaP.

Suberoylanilide Hydroxyamic Acid Modification of Chromatin Architecture Affects DNA Break Formation and Repair

PURPOSE Chromatin-modifying compounds that inhibit the activity of histone deacetylases have shown potency as radiosensitizers, but the action of these drugs at a molecular level is not clear. Here we investigated the effect of suberoylanilide hydroxyamic acid (SAHA) on DNA breaks and their repair and induction of rearrangements. METHODS AND MATERIALS The effect of SAHA on both clonogenic survival and repair was assessed using cell lines SCC-25, MCF7, and TK6. In order to study unique DNA double-strand breaks, anti-CD95 antibody was employed to introduce a DNA double-strand break at a known location within the 11q23 region. The effects of SAHA on DNA cleavage and rearrangements were analyzed by ligation-mediated PCR and inverse PCR, respectively. RESULTS SAHA acts as radiosensitizer at 1 microM, with dose enhancement factors (DEFs) at 10% survival of: SCC-25 - 1.24 +/- 0.05; MCF7 - 1.16 +/- 0.09 and TK6 - 1.17 +/- 0.05, and it reduced the capacity of SCC-25 cells to repair radiation induced lesions. Additionally, SAHA treatment diffused site-specific fragmentation over at least 1 kbp in TK6 cells. Chromosomal rearrangements produced in TK6 cells exposed to SAHA showed a reduction in microhomology at the breakpoint between 11q23 and partner chromosomes. CONCLUSIONS SAHA shows efficacy as a radiosensitizer at clinically obtainable levels. In its presence, targeted DNA strand breaks occur over an expanded region, indicating increased chromatin access. The rejoining of such breaks is degraded by SAHA when measured as rearrangements at the molecular level and rejoining that contributes to cell survival.

Localized DNA cleavage secondary to genotoxic exposure adjacent to an Alu inverted repeat

Radiation is a potent inducer of DNA damage leading to both random DNA loss and mutation. As part of a study focused on the mechanism whereby cells undergo loss of heterozygosity (LOH), a region of common LOH telomeric termination at 11q24 was observed in clones of H292 mucoepidermoid cells established after irradiation (IR). A 10‐kbp region including the telomeric extent of LOH termination was analyzed after IR using six sets of ligation‐mediated polymerase chain reaction (PCR) primers to detect the presence of DNA breaks. A cluster of DNA breaks was detected that closely mapped to the telomeric extent of LOH and which were observed up to 8 hr after IR. Repeating the experiment in the presence of the inhibitor of apoptosis, zVAD.fmk, did not change the location or amount of cleavage. A similar distribution of breaks was also seen in the MCF‐10A breast cancer cell line after IR. Further inspection of the involved region showed that 22/32 and 7/7 DNA breaks found in H292 and MCF‐10A cells, respectively, were located either in or immediately adjacent to an AluSx1 sequence, itself ∼1 kbp 5′ to an AluSq2 that was in an inverted orientation to the AluSx1. The region between the inverted Alu repeats was notable for both DNAse hypersensitivity and an open chromatin conformation inferred from histone modification data. These factors may contribute to genomic instability at this location.

Multiple clonal MLL fusions in a patient receiving CHOP-based chemotherapy

MLL rearrangements were analysed in the blood of a patient receiving chemotherapy for diffuse large B‐cell lymphoma using inverse polymerase chain reaction targeting exon 12, parallel sequencing and a custom algorithm design. Of thirteen MLL rearrangements detected, five were capable of generating MLL fusion genes, including MLL‐MLLT3, the most common fusion in acute myeloid leukaemia (AML). Other fusions, all previously clinically unobserved, included MLL‐NKD1, a fusion to the negative regulator of Wnt/β‐catenin signaling, a pathway linked to leukaemic cell proliferation. The majority of the fusions exhibited clonal persistence from before treatment until 6 months post‐chemotherapy, suggesting the fusions may confer a survival advantage to the mutant clone. MLL breakpoints were partly clustered at a specific location, indicating commonality in the process of their formation. Further, the same MLL breakpoint location exhibited a 50–100‐fold increase in C to T transitions, consistent with attack by activation‐induced cytidine deaminase (AICDA). As is also observed in AML and acute lymphoblastic leukaemia, in this single patient setting, MLL is capable of interacting with multiple fusion partners. This finding defines a discrete site of MLL susceptibility to fragmentation, linked to possible deregulation of AICDA function.

11q21.1–11q23.3 is a Site of Intrinsic Genomic Instability Triggered by Irradiation

The chromosome location, 11q21‐23, is linked to loss of heterozygosity (LOH) in multiple tumors including those of breast, lung, and head and neck. To examine the process of LOH induction, the H292 cell line (human muco‐epidermoid carcinoma) was irradiated or treated with anti‐CD95 antibody, and individual clones isolated through two rounds of cloning. Regions of LOH were determined by screening a suite of eight polymorphic microsatellite markers covering 11p15‐11q24 using fluorescent primers and genetic analyzer peak discrimination. LOH induction was observed extending through 11q21.1‐11q23.3 in 6/49 of clones surviving 4 Gy and 8/50 after 8 Gy. Analysis of selected clones by Affymetrix 6.0 single nucleotide polymorphism (SNP) arrays confirmed the initial assessment indicating a consistent 27.3–27.7 Mbp deletion in multiple clones. The telomeric border of LOH mapped to a 1 Mbp region of elevated recombination. Whole genome analysis of SNP data indicated that site‐restricted LOH also occurred across multiple additional genomic locations. These data indicate that 11q21.1‐11q23.3, and potentially other regions of this cell line are sites of intrinsic cell‐specific instability leading to LOH after irradiation. Such deletions may subsequently be propagated by genetic selection and clonal expansion.

Abstract B54: Role of inverted Alu repeats in triggering TMPRSS2-ERG fusions in prostate cancer following irradiation

Radical Prostatectomy and radiation therapy are the two most common treatments for primary prostate cancer (PCa). However, patients treated with radiotherapy are at greater risk for metastases compared to those treated with radical prostatectomy. Among other factors regulating biochemical or clinical recurrence is the formation of gene fusions. Ionizing radiation (IR) can trigger formation of TMPRSS2-ERG in PCa which may facilitate the development of more aggressive clones, especially in men with an intact androgen axis. Bioinformatics analysis has indicated that breakpoint regions of TMPRSS2 and ERG are rich in Alu elements, including inverted Alu repeat that are inherently unstable when in close proximity. Previous work in multiple cell lines showed that adjacent inverted Alu repeats, but not tandem or single Alus, are recombinationally unstable subsequent to IR exposure. Based on these results, we hypothesize that regions containing inverted Alu repeats in the prostate genome are vulnerable to DNA strand breaks and rearrangements in hormone naïve PCa patients undergoing IR therapy. As gene fusions require each gene to be broken prior to fusion, the effect of irradiation on ERG fragmentation was studied using ligation mediated-PCR. Data from two androgen-sensitive PCa cell lines, PC-346C and LNCaP, showed that after irradiation DNA breaks were introduced preferentially in proximity to an Alu inverted repeat, Alu-Y pair, in intron 3 of ERG. To determine if the enhanced fragmentation observed in this region is translated into rearrangements, FISH (fluorescence in-situ hybridization) probes were designed to bracket the area of interest in ERG. In addition, the same region has been analyzed by inverse-PCR to detect ERG rearrangements. Application of these techniques will enable a better understanding of those mechanisms driving the formation of fusion genes in the proximity of Alu repeats.

Abstract 3888: Ionizing radiation destabilizes inverted ALU repeats linked to LOH

Ionizing radiation is a potent inducer of Loss of Heterozygosity (LOH), driven primarily by DNA double strand breaks. Such a process impacts both tumorigenesis through deletion of linked tumor suppressor genes and, similarly, the potential development of radiation resistant tumor clones during radiation therapy. The human mucoepidermoid cell line, H292, was exposed to either 4 or 8 Gy and surviving clones developed from two rounds of cloning analyzed for LOH using polymorphic microsatellite markers. A high level of LOH was observed within individual clones extending from 11q21 to 11q24 (6/49 after 4 Gy and 8/50 after 8Gy). More detailed analysis using a SNP screen on selected LOH positive clones indicated a sharp telomeric termination of LOH adjacent to a common SNP location. The telomeric extent of LOH observed co-mapped to a region of elevated recombination instability documented previously using linkage analysis. Further, SNP analysis showed a region of approximately 1 Mbp LOH that included the region of recombination instability identified through linkage analysis, in some clones isolated either with or without irradiation. The consistency of the telomeric boundary of LOH observed in the irradiated clones permitted a targeted analysis of DNA double strand breaks at this location, using LM-PCR, both before and after 4Gy irradiation of the same cell line. Using a six primer set screen covering a 9 kbp region at the telomeric extent of radiation-induced LOH, a single primer set showed an elevation in DNA breaks from 2-8h after irradiation. The timing and discrete distribution of such breaks indicated that these were not directly induced by the radiation itself. Cells that were unirradiated were not affected. Further inspection of the location demonstrating selective radiation-linked fragmentation showed the presence of an ALU inverted repeat, separated by approximately 1kbp, where the DNA breaks determined by LM-PCR were clustered within the 5’ ALU. Others have shown previously that inverted ALU repeats separated by Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3888. doi:10.1158/1538-7445.AM2011-3888