Abstract P2-06-06: ALU and LINE-1 hypomethylation is associated with HER2+/ER- subtype of breast cancer

The changes in DNA methylation status in cancer cells are characterized by hypermethylation of promoter CpG islands and diffuse hypomethylation of non-coding genomic regions. ALU and long interspersed nucleotide element-1 (LINE-1) are non-coding genomic repetitive sequences and methylation of these elements can be used as a surrogate marker for genomewide methylation status. This study was designed to evaluate the changes of ALU and LINE-1 hypomethylation during breast cancer progression from normal to pre-invasive lesions and invasive breast cancer (IBC), and their relations with characteristics of IBC. We analyzed the methylation status of ALU and LINE-1 in 145 cases of breast samples including normal breast tissue (n = 30), atypical ductal hyperplasia/ flat epithelial atypia (ADH/FEA, n = 30), ductal carcinoma in situ (DCIS, n = 35) and IBC (n = 50), and another set of 129 cases of IBC by pyrosequencing. LINE-1 methylation was significantly decreased from normal to ADH/FEA, while ADH/FEA, DCIS and IBC were not different each other. There was no difference in ALU methylation levels during progression of breast cancer. In IBC, ALU hypomethylation was correlated with negative estrogen receptor (ER) status (p = 0.007) and LINE-1 hypomethylation was associated with negative ER status (p<0.001), positive HER2 status (p = 0.005) and p53 overexpression (p = 0.024). ALU-1 and LINE-1 methylation status was significantly different between breast cancer subtype and the HER2+/ER- subtype had significantly lower methylation levels and frequencies than the other subtypes. Our findings suggest that LINE-1 hypomethylation is an early event during breast cancer progression and prominent hypomethylation of ALU and LINE-1 in HER2+/ER- subtype may be related to chromosomal instability of this specific subtype.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-06-06.

Prognostic implication of the CpG island methylator phenotype in colorectal cancers depends on tumour location

BACKGROUND

Colorectal cancer (CRC) is usually categorised as proximal or distal CRC. Recently, many researchers have tried to determine the molecular heterogeneity of CRCs along bowel subsites. However, the differential effects of the CpG island methylator phenotype (CIMP) and microsatellite instability (MSI) on the clinical outcome according to tumour location are not well-known.

METHODS

We analysed clinicopathologic and molecular characteristics, including CIMP, MSI, KRAS and BRAF mutations, in 734 CRCs according to bowel subsites. And the prognostic value of CIMP and MSI was analysed according to tumour location.

RESULTS

We found a linear increase of female predominance, T, N category, stage, differentiation, absence of luminal necrosis, tumour -infiltrating lymphocytes, Crohn's-like lymphoid reaction, serration and mucin production from the rectum to caecum. CpG island methylator phenotype -high and MSI-high gradually increased from the rectum to caecum. CpG island methylator phenotype is a poor prognostic factor of overall survival (hazard ratio (HR): 4.13, 95% confidence interval (CI): 1.27-13.46) and disease-free survival (HR: 2.90, 95% CI: 1.04-8.08) in rectal cancers.

CONCLUSION

Clinicopathologic and molecular profiles of CRCs gradually change along bowel subsites, and the prognostic implication of CIMP is different according to tumour location.

Acoustic emission analysis of tooth-composite interfacial debonding

This study detected tooth-composite interfacial debonding during composite restoration by means of acoustic emission (AE) analysis and investigated the effects of composite properties and adhesives on AE characteristics. The polymerization shrinkage, peak shrinkage rate, flexural modulus, and shrinkage stress of a methacrylate-based universal hybrid, a flowable, and a silorane-based composite were measured. Class I cavities on 49 extracted premolars were restored with 1 of the 3 composites and 1 of the following adhesives: 2 etch-and-rinse adhesives, 2 self-etch adhesives, and an adhesive for the silorane-based composite. AE analysis was done for 2,000 sec during light-curing. The silorane-based composite exhibited the lowest shrinkage (rate), the longest time to peak shrinkage rate, the lowest shrinkage stress, and the fewest AE events. AE events were detected immediately after the beginning of light-curing in most composite-adhesive combinations, but not until 40 sec after light-curing began for the silorane-based composite. AE events were concentrated at the initial stage of curing in self-etch adhesives compared with etch-and-rinse adhesives. Reducing the shrinkage (rate) of composites resulted in reduced shrinkage stress and less debonding, as evidenced by fewer AE events. AE is an effective technique for monitoring, in real time, the debonding kinetics at the tooth-composite interface.

P1-05-04: Distinct Patterns of Promoter CpG Island Methylation of Breast Cancer Subtype Are Associated with Different Stem Cell Phenotype

Background: Although DNA methylation profiles in breast cancer have been connected to breast cancer molecular subtype, there have been no studies of the association of DNA methylation with stem cell phenotype. This study was designed to evaluate promoter CpG islands methylation of 15 genes with regard to breast cancer subtype and to investigate whether the patterns of CpG island methylation in each subtype are associated with cancer stem cell phenotype represented by CD44+/CD24- or ALDH1 expression.

Methods: We performed MethyLight analysis for the methylation status of 15 promoter CpG island loci involved in breast cancer progression (APC, DLEC1, GRIN2B, GSTP1, HOXA1, HOXA10, IGF2, MT1G, RARB, RASSF1A, RUNX3, SCGB3A1, SFRP1, SFRP4, and TMEFF2) and determined cancer stem cell phenotype by CD44/CD24 and ALDH1 immunohistochmeistry in 36 luminal A, 33 luminal B, 30 luminal-HER2, 40 HER2 enriched, and 40 basal-like subtypes of breast cancer.

Results: The number of CpG island loci methylated was significantly different among subtypes and it was highest in luminal-HER2 subtype and lowest in basal-like subtype. Methylation frequencies and levels in 12 out of the 15 genes were significantly different among all subtypes and basal-like subtype showed significantly lower methylation frequencies and levels in nine genes, compared to luminal A, luminal B, HER2 enriched, and luminal-HER2 subtypes. CD44+/CD24- or ALDH1+ putative stem cell populations were most enriched in basal-like subtype. The methylation of promoter CpG islands was significantly lower in CD44+/CD24-cell (+) tumors, compared to CD44+/CD24-cell (−) tumors, even within the basal-like subtype. ALDH1 (+) tumors also had significantly lower methylation, compared to ALDH1 (−) tumors.

Conclusions: Our findings showed that promoter CpG island methylation was significantly different according to breast cancer subtype and stem cell phenotype of tumor, suggesting that breast cancers have different methylation patterns according to molecular subtypes and it is associated with stem cell phenotypes of the tumor.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-05-04.

Anomalous J-modulation effects on amino acids in clinical 3T MR spectroscopy

The signal-intensity loss from anomalous J-modulation effects due to chemical-shift displacement was investigated on amino acid groups (alanine, valine, leucine, and isoleucine) at 3T by using point-resolved (1)H spectroscopy in patients with brain abscess and phantom experiments. With a larger chemical shift between methyl and methine resonances, alanine shows a greater effect of signal-intensity cancellation compared with other amino acids around 0.9 ppm, resulting in noninverted doublets at a TE of 144 ms.

Cell cycle arrest and lytic induction of EBV-transformed B lymphoblastoid cells by a histone deacetylase inhibitor, Trichostatin A

Latent infection of the Epstein-Barr virus (EBV) is strongly associated with the pathogenesis of several human tumor types. The restricted expression of the latent EBV antigens is critical for EBV-associated tumors to escape from immune surveillance. EBV lytic replication can be triggered by various treatments and the induced lytic genes cause strong cytotoxic T lymphocyte (CTL) responses. Histone acetylation or deacetylation is associated with chromatin remodeling and regulates gene expression. Histone deacetylase (HDAC) inhibitors affect cell cycle progression as well as gene expression in a wide variety of transformed cells. We examined whether an HDAC inhibitor, TSA, can affect cell cycle progression and induce EBV lytic replication in EBV-transformed lymphoblastoid cell lines (LCLs). TSA caused cell cycle arrest at low concentrations and induced apoptosis at higher (>300 nM) concentrations in the LCLs and EBV negative BJAB cells. To clarify the underlying mechanism of TSA-induced cell cycle arrest, expression of cell cycle regulatory factors was examined by RNase protection assay and Western blot analysis. Following TSA treatment, a reduced expression of cyclin D2 and an induction of p21 may have played an essential role for G1 arrest in LCLs, while p21 induction might have arrested BJAB cells in G1 phase. A Cdk inhibitor, p57, was increased by 300 nM TSA in both LCLs and BJAB cells, indicating its role in apoptosis. Moreover, immunofluorescene assay and Western blotting showed that TSA induced EBV lytic replication in LCL cells. These results suggest that TSA may exert an enhanced anti-tumor effect for EBV-associated tumors not only by inducing a cell cycle arrest and apoptosis, but also by triggering an EBV lytic cycle.

Hypermethylation of CpG island loci and hypomethylation of LINE-1 and Alu repeats in prostate adenocarcinoma and their relationship to clinicopathological features

Promoter CpG island hypermethylation is an important carcinogenic event in prostate adenocarcinoma. Regardless of tissue type, human cancers have in common both focal CpG island hypermethylation and global genomic hypomethylation. The present study evaluated CpG island loci hypermethylation and LINE-1 and Alu repeat hypomethylation in prostate adenocarcinoma, analysed the relationship between them, and correlated these findings with clinicopathological features. We examined 179 cases of prostate adenocarcinoma and 30 cases of benign prostate hypertrophy for the methylation status of 22 CpG island loci and the methylation levels of LINE-1 and Alu repeats using methylation-specific polymerase chain reaction and combined bisulphite restriction analysis, respectively. The following 16 CpG island loci were found to display cancer-related hypermethylation: RASSF1A, GSTP1, RARB, TNFRSF10C, APC, BCL2, MDR1, ASC, TIG1, RBP1, COX2, THBS1, TNFRSF10D, CD44, p16, and RUNX3. Except for the last four CpG island loci, hypermethylation of each of the remaining 12 CpG island loci displayed a close association with one or more of the prognostic parameters (ie preoperative serum prostate specific antigen level, Gleason score sum, and clinical stage). Prostate adenocarcinoma with hypermethylation of each of ASC, COX2, RARB, TNFRSF10C, MDR1, TIG1, RBP1, NEUROG1, RASSF1A, and GSTP1 showed a significantly lower methylation level of Alu or LINE-1 than prostate adenocarcinoma without hypermethylation. In addition, hypomethylation of Alu or LINE-1 was closely associated with one or more of the above prognostic parameters. These data suggest that in tumour progression a close relationship exists between CpG island hypermethylation and the hypomethylation of repetitive elements, and that CpG island hypermethylation and DNA hypomethylation contribute to cancer progression.

Promoter analysis of the Drosophila melanogaster gene encoding the pterin 4alpha-carbinolamine dehydratase

Pterin-4alpha-carbinolamine dehydratase (PCD) is a key enzyme in the regeneration pathway of tetrahydrobiopterin. Previously, we isolated and reported the Drosophila melanogaster gene encoding PCD. In the present study, we isolated and characterized the Drosophila virilis gene encoding PCD. The Drosophila virilis PCD gene has two introns and an open reading frame to encode a protein of 101 amino acids. The amino acid sequence of Drosophila virilis PCD shows a 83% homology to that of the Drosophila melanogaster PCD protein. From the alignment of the nucleotide sequence in the 5'-flanking region of the Drosophila melanogaster and Drosophila virilis PCD genes, we found four conserved sequences. Using a transient transfection assay, we showed that one of the conserved sequences (-127 to approximately -115) is critical for expression, also the minimal promoter region between -127 and +51 is necessary for the efficient expression of Drosophila melanogaster PCD.

Identification, cloning, and characterization of the bacteriophage N4 gene encoding the single-stranded DNA-binding protein. A protein required for phage replication, recombination, and late transcription

The coliphage N4-coded single-stranded DNA-binding protein (N4SSB) is essential for phage replication and for expression of the phage late genes, which are transcribed by the Escherichia coli sigma 70 RNA polymerase. As a first step in investigating the role of N4SSB in replication and transcriptional activation, we have identified and sequenced the N4SSB gene. The gene encodes a 265-amino acid protein with no apparent sequence homology to other single-stranded DNA-binding proteins. We present data indicating that N4SSB is also essential for phage recombination. Mutational analysis of the carboxyl terminus of the protein indicates that this region is required for protein-protein interactions with the N4 replication, N4 recombination, and E. coli transcriptional machineries, while the rest of the protein contains the determinants for single-stranded DNA binding.

The bacteriophage N4-coded single-stranded DNA-binding protein (N4SSB) is the transcriptional activator of Escherichia coli RNA polymerase at N4 late promoters

Transcription of the 72kb linear double-stranded DNA genome of coliphage N4 is carried out by the sequential activity of three different RNA polymerases. Early and middle viral transcripts are synthesized by two phage-coded RNA polymerases while late transcription is carried out by the Escherichia coli sigma 70-RNA polymerase. We have determined the sequences and sites of initiation of several N4 late transcripts; N4 late promoters share weak homology with the E. coli sigma 70 promoter consensus sequence. Indeed, N4 late promoters are weak templates for the host enzyme. We present evidence that the phage-coded, single-stranded DNA-binding protein (N4SSB), a protein that is required for phage DNA replication and recombination and does not bind with sequence specificity to DNA, is the activator of E. coli RNA polymerase at late N4 promoters. Models for the mechanism of action of N4SSB as a transcriptional activator are discussed.

Different effects of base analog substitutions in BamHI restriction site on recognition by BamHI endonuclease and BamHI methylase

BamHI endonuclease and BamHI methylase were used to investigate their specific interaction with the common recognition sequence, GGATCC. Five derivatives of the oligonucleotide, GACGGATCCGTC, containing a variety of single-base analog substitutions within the hexameric recognition core were synthesized. Steady-state kinetics for the reaction of the endonuclease and the methylase showed that both enzymes recognize the sequences by contacting with functional groups exposed in both major and minor grooves of the site but in different ways. Removal or substitution of the 5-methyl group in thymidine blocked the endonuclease reaction completely but still allowed the methylase reaction with less efficiency. The data also showed that the methylase made a critical minor groove contact with the 2-amino group of the first G but the endonuclease did with that of the second G.

Mutagenesis of Micromonospora rosaria by using protoplasts and mycelial fragments

Both mycelial fragments and protoplasts were successfully employed for mutagenesis of Micromonospora rosaria NRRL 3718, and the results were compared. The optimal conditions and effective procedures for mutagenesis of M. rosaria by a chemical mutagen, N-methyl-N'-nitro-N-nitrosoguanidine, have been determined. Mutation was efficiently induced when mycelial fragments were treated with N-methyl-N'-nitro-N-nitrosoguanidine at a concentration of 0.3 to 0.5 mg/ml in the reaction buffer of pH 7.0. Optimal treatment time was 20 to 40 min. Ampicillin treatment was very effective for enrichment of auxotrophs. Protoplasts showed much higher sensitivity to the lethal effect of N-methyl-N'-nitro-N-nitrosoguanidine. Although protoplasts have some advantage of single cell characteristics, the frequency of auxotrophs obtained was somewhat lower. Up to 4% of the colonies were shown to be auxotrophs under the well-defined conditions. This mutagenesis method with protoplasts or fragmented mycelia (or both) should be applicable to other actinomycetes that have limited or no sporulation.

Genetic recombination in Micromonospora rosaria by protoplast fusion

Auxotrophic strains of Micromonospora rosaria were isolated by N-methyl-N'-nitro-N'-nitrosoguanidine mutagenesis and used in intraspecific recombination by protoplast fusion. High-frequency fusion of protoplasts of M. rosaria strains was induced by polyethylene glycol (molecular weight, 1,000) (PEG 1,000). The optimum concentration of PEG 1,000 for fusion of M. rosaria was 50% (wt/vol). PEG 4,000 was slightly better than PEG 1,000 at concentrations lower than 50% (wt/vol). The recombinant frequency did not increase after treatment with PEG 1,000 (50% [wt/vol]) for longer than 20 min. Under these conditions, fusion with many auxotrophic strains of M. rosaria resulted in a high frequency of formation of true recombinants (sometimes more than 10%). Additionally, when ros (rosamicin nonproducing) strains were crossed by protoplast fusion; about 5% of the resultant prototrophic recombinants were shown to have the ros+ (rosamicin producing) characteristic restored. Rosamicin production by M. rosaria colonies was clearly distinguished by the broth overlay method. The results of fusion experiments between ros and ros+ strains indicated that either the chromosomal mutation or pleiotrophic effect of some auxotrophic markers is involved.