LINC00941 promotes oral squamous cell carcinoma progression via activating CAPRIN2 and canonical WNT/ß-catenin signaling pathway.

Dysregulation of long non-coding RNAs (lncRNAs) has been implicated in many cancer developments. Previous studies showed that lncRNA LINC00941 was aberrantly expressed in oral squamous cell carcinoma (OSCC). However, its role in OSCC development remains elusive. In this study, we demonstrated that in OSCC cells, EP300 activates LINC00941 transcription through up-regulating its promoter H3K27ac modification. Up-regulated LINC00941 in turn activates CAPRIN2 expression by looping to CAPRIN2 promoter. Functional assays suggest that both LINC00941 and CAPRIN2 play pivotal roles in promoting OSCC cell proliferation and colony formation. In vivo assay further confirmed the role of LINC00941 in promoting OSCC cell tumour formation. Lastly, we showed that the role of LINC00941 and CAPRIN2 in OSCC progression was mediated through activating the canonical WNT/ß-catenin signaling pathway. Thus, LINC00941/CAPRIN2/ WNT/ß-catenin signaling pathway provides new therapeutic targets for OSCC treatment.

Alternative Lengthening of Telomeres: Building Bridges To Connect Chromosome Ends.

Alternative lengthening of telomeres (ALT) is a mechanism of telomere maintenance that is observed in many of the most recalcitrant cancer subtypes. Telomeres in ALT cancer cells exhibit a distinctive nucleoprotein architecture shaped by the mismanagement of chromatin that fosters cycles of DNA damage and replicative stress that activate homology-directed repair (HDR). Mutations in specific chromatin-remodeling factors appear to be key determinants of the emergence and survival of ALT cancer cells. However, these may represent vulnerabilities for the targeted elimination of ALT cancer cells that infiltrate tissues and organs to become devastating tumors. In this review we examine recent findings that provide new insights into the factors and mechanisms that mediate telomere length maintenance and survival of ALT cancer cells.

Large-scale DNA organization is a prognostic marker of breast cancer survival.

Breast cancer is the leading cause of cancer-related deaths among women worldwide. We investigated whether changes in large-scale DNA organization (LDO) of tumor epithelial nuclei are an indicator of the aggressiveness of the tumor. We tested our algorithm on a set of 172 duplicates TMA cores samples coming from 95 breast cancer patients. Thirty-five patients died of breast cancer, and 60 were still alive 10 years after surgery. Duplicates cores were used to create training and test set. The TMA slides were stained with Feulgen-thionin and imaged using our in-house high-resolution Imaging system. Automated segmentation of cell nuclei followed by manual selection of intact, in-focus nuclei resulted in an average of 50 cell nuclei per sample available for analysis. Using forward stepwise linear discriminant analysis, a combination of six features that combined linearly gave the best discrimination between the two groups of cells: cells collected from 'deceased' patients TMA specimens and cells collected from "survivors" patients TMA specimens. Five of these features measure the spatial organization of DNA chromatin. The resulting canonical score is named cell LDO score. A patient LDO score, percentage of cell nuclei with a cell LDO score higher than a predefined cutoff value, was processed for the specimens in the test set, and a cutoff value was defined to classify patients with a low or a high LDO score. Using this binary test, 82.1% of patients were correctly classified are "deceased" or "survivors," with a specificity of 79% and a sensitivity of 88%. The relative risk of death of an individual with a high LDO score was nine times higher than for a patient with a low LDO score. When testing the combination of LDO score, node status, histological grade, and tumor grade to predict breast cancer survival, LDO was the most significant predictor. LDO classification was also highly associated with survival for only grade 1 and 2 patients as well as for only grade 3 patients. Our result confirms the potential of LDO to measure phenotypic changes associated with more aggressive disease and could be evaluated to identify patients more likely to benefit from adjuvant therapies.

Replication Fork Slowing and Reversal upon DNA Damage Require PCNA Polyubiquitination and ZRANB3 DNA Translocase Activity.

DNA damage tolerance during eukaryotic replication is orchestrated by PCNA ubiquitination. While monoubiquitination activates mutagenic translesion synthesis, polyubiquitination activates an error-free pathway, elusive in mammals, enabling damage bypass by template switching. Fork reversal is driven in vitro by multiple enzymes, including the DNA translocase ZRANB3, shown to bind polyubiquitinated PCNA. However, whether this interaction promotes fork remodeling and template switching in vivo was unknown. Here we show that damage-induced fork reversal in mammalian cells requires PCNA ubiquitination, UBC13, and K63-linked polyubiquitin chains, previously involved in error-free damage tolerance. Fork reversal in vivo also requires ZRANB3 translocase activity and its interaction with polyubiquitinated PCNA, pinpointing ZRANB3 as a key effector of error-free DNA damage tolerance. Mutations affecting fork reversal also induced unrestrained fork progression and chromosomal breakage, suggesting fork remodeling as a global fork slowing and protection mechanism. Targeting these fork protection systems represents a promising strategy to potentiate cancer chemotherapy.

Time-Lapse Monitoring of DNA Damage Colocalized With Particle Tracks in Single Living Cells.

PURPOSE: Understanding the DNA damage and repair induced by hadron therapy (HT) beams is crucial for developing novel strategies to maximize the use of HT beams to treat cancer patients. However, spatiotemporal studies of DNA damage and repair for beam energies relevant to HT have been challenging. We report a technique that enables spatiotemporal measurement of radiation-induced damage in live cells and colocalization of this damage with charged particle tracks over a broad range of clinically relevant beam energies. The technique uses novel fluorescence nuclear track detectors with fluorescence confocal laser scanning microscopy in the beam line to visualize particle track traversals within the subcellular compartments of live cells within seconds after injury. METHODS AND MATERIALS: We designed and built a portable fluorescence confocal laser scanning microscope for use in the beam path, coated fluorescence nuclear track detectors with fluorescent-tagged live cells (HT1080 expressing enhanced green fluorescent protein tagged to XRCC1, a single-strand break repair protein), placed the entire assembly into a proton therapy beam line, and irradiated the cells with a fluence of ∼1 × 10(6) protons/cm(2). RESULTS: We successfully obtained confocal images of proton tracks and foci of DNA single-strand breaks immediately after irradiation. CONCLUSIONS: This technique represents an innovative method for analyzing biological responses in any HT beam line at energies and dose rates relevant to therapy. It allows precise determination of the number of tracks traversing a subcellular compartment and monitoring the cellular damage therein, and has the potential to measure the linear energy transfer of each track from therapeutic beams.

Multi-marker analysis of circulating cell-free DNA toward personalized medicine for colorectal cancer.

Development of a Q-PCR-based assay for the high-performance analysis of circulating cell-free DNA (ccfDNA) requires good knowledge of its structure and size. In this work, we present the first visual determination of ccfDNA by Atomic Force Microscopy (AFM) on plasma samples from colorectal cancer (CRC) patients and healthy donors. In addition to the examination of fragment size distribution profile as performed by Q-PCR, this analysis confirms that ccfDNA is highly fragmented and that more than 80% of ccfDNA fragments in CRC plasma are below 145 bp. We adapted an Allele-Specific Blocker (ASB) Q-PCR to small ccfDNA fragments to determine simultaneously the total ccfDNA concentration, the presence of point mutation, the proportion of mutated allele, and a ccfDNA integrity index. The data validated analytically these four parameters in 124 CRC clinical samples and 71 healthy individuals. The multi-marker method, termed Intplex, enables sensitive and specific non-invasive analysis of tumor ccfDNA, which has great potential in terms of cost, quality control, and easy implementation in every clinical center laboratory.

Multiscale in situ analysis of the role of dyskerin in lung cancer cells.

Dyskerin is one of the three subunits of the telomerase ribonucleoprotein (RNP) complex. Very little is known about the role of dyskerin in the biology of the telomeres in cancer cells. In this study, we use a quantitative, multiscale 3D image-based in situ method and several molecular techniques to show that dyskerin is overexpressed in lung cancer cell lines. Furthermore, we show that dyskerin expression correlates with telomere length both at the cell population level--cells with higher dyskerin expression have short telomeres--and at the single cell level--the shortest telomeres of the cell are spatially associated with areas of concentration of dyskerin proteins. Using this in vitro model, we also show that exogenous increase in dyskerin expression confers resistance to telomere shortening caused by a telomerase inactivating drug. Finally, we show that resistance is achieved by the recovery of telomerase activity associated with dyskerin. In summary, using a novel multiscale image-based in situ method, we show that, in lung cancer cell lines, dyskerin responds to continuous telomere attrition by increasing the telomerase RNP activity, which in turn provides resistance to telomere shortening.

Potential clinical impact of three-dimensional visualization for fluorescent in situ hybridization image analysis.

Chromosomal translocation is strong indication of cancers. Fluorescent in situ hybridization (FISH) can effectively detect this translocation and achieve high accuracy in disease diagnosis and prognosis assessment. For this purpose, whole chromosome paint probes are utilized to image the configuration of DNA fragments. Although two-dimensional (2-D) microscopic images are typically used in FISH signal analysis, we present a case where the translocation occurs in the depth direction where two probed FISH signals are overlapped in the projected image plane. Thus, the translocation cannot be identified. However, when imaging the whole specimen with a confocal microscope at 27 focal planes with 0.5-µm step interval, the translocation can be clearly identified due to the free rotation capability by the three-dimensional (3-D) visualization. Such a translocation detection error of using 2-D images might be critical in detecting and diagnosing early or subtle disease cases where detecting a small number of abnormal cells can make diagnostic difference. Hence, the underlying implication of this report suggests that utilizing 3-D visualization may improve the overall accuracy of FISH analysis for some clinical cases. However, the clinical efficiency and cost of using 3-D versus 2-D imaging methods are also to be assessed carefully.

Differences in DNA condensation and release by lysine and arginine homopeptides govern their DNA delivery efficiencies.

Designing of nanocarriers that can efficiently deliver therapeutic DNA payload and allow its smooth intracellular release for transgene expression is still a major constraint. The optimization of DNA nanocarriers requires thorough understanding of the chemical and structural characteristics of the vector-nucleic acid complexes and its correlation with the cellular entry, intracellular state and transfection efficiency. L-lysine and L-arginine based cationic peptides alone or in conjugation with other vectors are known to be putative DNA delivery agents. Here we have used L-lysine and L-arginine homopeptides of three different lengths and probed their DNA condensation and release properties by using a multitude of biophysical techniques including fluorescence spectroscopy, gel electrophoresis and atomic force microscopy. Our results clearly showed that although both lysine and arginine based homopeptides condense DNA via electrostatic interactions, they follow different pattern of DNA condensation and release in vitro. While lysine homopeptides condense DNA to form both monomolecular and multimolecular complexes and show differential release of DNA in vitro depending on the peptide length, arginine homopeptides predominantly form multimolecular complexes and show complete DNA release for all peptide lengths. The cellular uptake of the complexes and their intracellular state (as observed through flow cytometry and fluorescence microscopy) seem to be controlled by the peptide chemistry. The difference in the transfection efficiency of lysine and arginine homopeptides has been rationalized in light of these observations.

Abnormal DNA content in oral epithelial dysplasia is associated with increased risk of progression to carcinoma.

BACKGROUND: Oral epithelial dysplasia (OED) is a histologically detectable lesion that may progress to carcinoma but there are no accurate markers that predict progression. This study examined the development of carcinoma from oral dysplastic lesions, and the association between abnormal DNA content and progression to carcinoma. METHODS: Epithelial dysplasias from the Oral Pathology Diagnostic Service were matched against the Ontario Cancer Registry database to identify cases that progressed to carcinoma. A case-control study was conducted to compare DNA image cytometry of dysplasias that progressed with those that have not progressed. For a subset of the progressed dysplasias, DNA content of the carcinoma was also analysed. RESULTS: A total of 8% of epithelial dysplasias progressed to carcinoma after 6-131 months. In all, 28 of 99 dysplasias showed abnormal DNA content by image cytometry. In multivariate analysis of time to progression, abnormal DNA content was a significant predictor with hazard ratio of 3.3 (95% confidence interval: 1.5-7.4) corrected for site and grade of dysplasia. Analysis of sequential samples of dysplasia and carcinoma suggested that epithelial cell populations with grossly abnormal DNA content were transient intermediates during oral cancer development. CONCLUSIONS: Abnormal DNA content is a significant biomarker of a subset of OED that progress to carcinoma.

Subtelomeric DNA methylation and telomere length in human cancer cells.

Subtelomeric epigenetic modifications are known to be associated with telomere length. We examined subtelomeric DNA methylation at seven sites for five chromosomes by methylation-specific PCR (MSP) and two sites for two chromosomes by bisulfite genomic sequencing (BGS) in 20 human cancer cell lines and subsequently analyzed their association with telomere length. Full-methylation (55/140) was more frequently found compared to un-methylation (35/140) (p=0.01). Subtelomeric-methylation patterns varied from region to region; full-methylation and un-methylation were dominant at one of 9q sites (20/20) and 9p (18/20), respectively. MSP and BGS data exhibited no apparent correlation between methylation status and telomere length. In addition, Hep3B subclones that possessed different telomere lengths exhibited no changes in methylation status according to telomeres. In summary, subtelomeres might form distinct chromatin structures from region to region and effect of subtelomeric DNA methylation on telomere regulation might be little.

Quantitative analysis of DNA-damage response factors after sequential ion microirradiation.

Several proteins are known to form foci at DNA sites damaged by ionizing radiation. We study DNA damage response by immunofluorescence microscopy after microirradiation of cells with energetic ions. By using microirradiation, it is possible to irradiate different regions on a single dish at different time-points and to differentiate between cells irradiated earlier and later. This allows to directly compare immunofluorescence intensities in both subsets of cells with little systematic error because both subsets are cultivated and stained under identical conditions. In addition, by using irradiation patterns such as crossing lines, it is possible to irradiate individual cells twice and to differentiate between immunofluorescence signals resulting from the cellular response to the earlier and to the later irradiation event. Here, we describe the quantitative evaluation of immunofluorescence intensities after sequential irradiation.

Preliminary studies on induction of apoptosis by genistein on HepG2 cell line.

Consumption of soy products has been linked to lower the incidence of number of cancers. Genistein, one of the principal soy isoflavones, has been shown to inhibit the growth of a number of tumor cell lines in vitro. In this study, we investigate the effects of genistein on cell growth and apoptosis in human hepatocellular carcinoma HepG2 cell by looking for the formation of nuclear apoptotic bodies and DNA ladder formation. Additionally, flow cytometry analysis with propidium iodide staining has been conducted to detect the apoptotic cells. We found inhibition of cell growth and apoptotic nuclei, DNA fragmentation and increased apoptotic cells after treatment with genistein, indicating apoptotic cell deaths. From these results we observed that genistein inhibits the growth of HepG2 cells and induce apoptosis, however, further definitive studies are needed. These results may support the potentially effective chemopreventive and/or chemotherapeutic of genistein against liver cancer.

Application of microscopic Forster resonance energy transfer to cytological diagnosis of the thyroid tumors.

We propose a novel application of microscopic Forster resonance energy transfer (FRET) to clinical cytological diagnosis based on sensitive measurements of distance changes between fluorescently labeled deoxyribose nucleic acid (DNA) molecules. We have employed the microscopic FRET imaging for investigation of six papillary carcinomas and eight benign cases. In each case the FRET images of 20 cells stained by the AT-specific donor Hoechst 33258 and the GC-specific acceptor 7-aminoactinomycin D were acquired and analyzed by texture analysis. We have not found significant difference of the mean FRET efficiency between the benign and malignant groups. On the other hand, the texture analysis revealed a significant difference of the intranuclear spatial distribution of FRET efficiencies between the benign and malignant groups. The results indicate that despite the similar average distance between the AT- and the GC-rich DNA segments in the papillary carcinomas and the benign cases, the former has more heterogeneous distribution of the AT- and the GC-rich DNA segments in nuclei compared to the benign groups. We have demonstrated that the FRET imaging is a helpful tool for the medical cytological diagnosis of human tumors by giving information on the chromatin topology on the scale below the resolution of conventional optical microscopes. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

Autoschizis: a new form of cell death for human ovarian carcinoma cells following ascorbate:menadione treatment. Nuclear and DNA degradation.

Microscopic aspects, densitometric evaluation of Feulgen-stained DNA, and gel electrophoresis of total DNA have been used to elucidate the effects of 1, 2, and 3 h VC (ascorbic acid), VK3 (menadione), and combined VC:VK3 treatments on the cellular and nuclear morphology and DNA content of a human ovarian carcinoma cell line (MDAH 2774). Optical densitometry showed a significant decrease in cancer cell DNA content directly related to VC and VC:VK3 treatments while VK3 and VC:VK3 treated cells exhibited cytoskeletal changes that included self-excision of cytoplasmic pieces with no membranous organelles. Nuclei decreased in size and exhibited poor contrast consistent with progressive decondensation of their chromatin. Degraded chromatin was also detected in cytoplasmic autophagosomes. Nucleoli segregated their components and fragmented into small pieces. Gel electrophoretic analysis of total DNA revealed evidence of generalized DNA degradation specific to treated tumor cells. These results are consistent with previous observations [Scanning 20 (1998a) 564; Ultrastruct. Pathol. 25 (2001b) 183; J. Histochem. Cytochem. 49 (2001) 109] which demonstrated that the VC:VK3 combination induced autoschizic cell death by a series of cytoplasmic excisions without organelles along with specific nuclear ultrastructural damage.

Structural organisation of nucleic acids from tumour cells.

The DNA from Carcinoma Guerina resistant and sensitive cells of Wistar line rats and their interaction with anti-cancer drugs--cis-platin and doxorubicin (DOX)--have been studied in in vivo experiments. Surface enhanced infrared absorption (SEIRA) in reflectance absorption spectroscopy (RAS) mode was applied for registration of conformational change of the DNA induced by cancer process and anti-cancer drugs. We have registered numerous minor changes in infrared spectra of the DNA from sensitive and resistant cells that could reflect essential changes in molecular structure of DNA from cancer cells. The most significant transformation was undergone by the sugar phosphate backbone of the DNA from cancer cells. The DNA from resistant cancer cells could be characterized as rigid structures and look like the canonical helix form of DNA being practically unchangeable after anti-cancer drug application. The structure of DNA from sensitive cancer cells seems to be flexible and after application of anti-cancer drugs drastically changes and approaches to structure of helix form. It has been shown that doxorubicin strongly influences the DNA structure, leading to DNA stabilization and formation of new H-bonds in DNA doxorubicin complex. We have registered slight cis-platin influence on the DNA structure in in vivo experiment. Principal component analysis of SEIRA spectra can select the DNA from cancer cells.

GammaH2AX foci induced by gamma rays and 125idU decay.

PURPOSE: GammaH2AX foci formation was investigated after gamma irradiation and after accumulating 125IdU decays to study the DNA double strand break (dsb) damage repair response in human breast cancer cells, MCF-7. MATERIALS AND METHODS: Confocal laser scanning microscopy (CLSM) was used to detect yH2AX foci formed in response to DNA dsbs induced by 0, 0.5, 1, 2 and 5 Gy gamma irradiation and 125IdU decays accumulated at -90 degrees C in human breast cancer cells, MCF-7. 125IdU treated cells were labeled with 4 different concentrations of 125IdU and then accumulated decays for 6, 19 or 35 days. gammaH2AX foci formation time for all experiments was 1 hour at 37 degrees C. Visual confirmation of gammaH2AX foci was achieved by digital imaging (histogram analysis or profile analysis) and by standardizing the scored number of foci. The average numbers of gammaH2AX foci formed per cell after gamma irradiation or accumulated (125)IdU decays were determined by counting red voxels or counting gammaH2AX foci in propidium iodide (PI) counterstained nuclei by eye in optically sectioned cells. RESULTS: Control, unirradiated MCF-7 cells had an average of 1.7 gammaH2AX foci per cell and an average of 32 yH2AX foci were scored for cells irradiated with 1 Gy gamma rays. The data for doses up to approximately 1 Gy was a good linear fit (r2 =0.97) indicating that the assay is sensitive to low doses of gamma rays. The average number of gammaH2AX foci scored in control cells that were frozen and thawed but not irradiated (=2.3) was not statistically significantly different from controls that were not frozen and thawed. The average number of yH2AX foci was linearly related (r2 = 0.98) to low numbers (< 200 decays/cell) of 125IdU decays indicating that the assay is also sensitive to low numbers of accumulated 125IdU decays. At 125I decays greater than 200 decays/cell, the average number of yH2AX foci plateaued. Regression analysis of the data for 0-140 125IdU decays per cell was used to calculate the rate of yH2AX foci formation (=0.26 foci per 125I decay). CONCLUSIONS: The gammaH2AX foci formation assay is sensitive to low doses of gamma rays and accumulated 125I decays. When 125IdU decays were accumulated at -90 degrees C (to overcome confounding DNA damage repair processes that occur during simultaneous 125IdU incorporation and decay accumulation at 37 degrees C), 0.26 gammaH2AX foci were formed per 125IdU decay. Methods used to incorporate 125I decay may modulate the number of gammaH2AX foci scored in cells.

The omega-hydroxy palmitic acid induced apoptosis in human lung carcinoma cell lines H596 and A549.

We have found that omega-hydroxy palmitic acid (16-hydroxy palmitic acid, omega-HPA) has both cell growth inhibiting and cell death inducing actions on human lung adenosquamous carcinoma cell line H596 and adenocarcinoma cell line A549. Further, these effects were dose- and time-dependent in both cell lines. However, in squamous carcinoma cell line H226, omega-HPA had no cytotoxic effect. On the other hand, in the human small cell lung carcinoma (SCLC) cell line H128, this compound showed weak cytotoxicity. The sensitivity toward omega-HPA was higher in H596 cells than in A549 cells. In both H596 and A549 cells, cell growth was inhibited to 24.4 and 9.4%, respectively, by treatment with 100 microM omega-HPA for 12 h. In the 24 h treatment cells, growth inhibition was increased to 100 and 38.1%, respectively. In cytotoxicity experiments, the number of dead cells increased with incubation times in the presence of omega-HPA: on three days incubation with 100 microM omega-HPA, viability was 0 and 13.5%, respectively, in H596 and A549 cells. Further, the fragmentation of DNA to oligonucleosomal-sized ladder fragments, which is an index of apoptosis, was observed in both cell lines on treatment with omega-HPA. Therefore, it is assumed that these cell deaths induced by omega-HPA, were apoptosis in these cell lines. Since the number of dead cells following treatment with omega-HPA decreased by treatment with omega-HPA in combination with Z-VAD-fmk, a caspase family inhibitor, it is thought that apoptotic cell death was related to caspase activity.

Rapid upregulation of telomerase activity in human leukemia HL-60 cells treated with clinical doses of the DNA-damaging drug etoposide.

The enzyme telomerase is implicated in cellular resistance to apoptosis, but the mechanism for this resistance remains to be elucidated. The ability of telomerase to synthesize new DNA at telomeres suggests that this enzyme might function in the repair of double-stranded DNA breaks. To distinguish the effects of double-stranded DNA break damage and apoptosis on human telomerase activity, we treated the HL-60 human hematopoietic cancer cell line with clinical doses of the chemotherapeutic drug etoposide (0.5 to 5 microM), which allowed us to distinguish between events associated with DNA damage-induced cell cycle arrest, and events associated with apoptosis. Large (three- to seven-fold) upregulation of telomerase activity occurred soon after etoposide treatment (3 h) in S/G2/M-arresting populations; this upregulation was abolished at onset of apoptotic cell death. No upregulation of telomerase activity was observed in cells treated with a larger dose of etoposide (5 microM) that caused cells to undergo rapid apoptosis without intervening cell cycle arrests. These observations are consistent with a possible role for telomerase upregulation during the DNA damage response.