bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3585: KIF11 silencing or inhibition induces chromosome instability
Authors: Asbaghi Yasamin , Lichtensztejn Zelda , Thompson Laura , McManus Kirk 
Published: July 2016

Abstract
Chromosome Instability (CIN) is defined as an increase in the rate at which whole chromosomes or large parts are gained or lost. CIN is not only associated with virtually all tumor types, but it is associated with aggressive tumors, the acquisition of multi-drug resistance and consequently poor patient prognosis. Despite these associations, the genes and molecular defects that contribute to CIN are only poorly understood. Recently, we performed a high content screen that identified KIF11, a microtubule associated motor protein, as a candidate CIN gene. Here, we couple RNAi-based gene silencing with biochemistry and cell biology to show that diminished KIF11 expression and/or function induce CIN. HCT116 cells were employed, as they are a karyotypically stable colorectal cancer cell line of epithelial origin that has been used for similar CIN studies. KIF11 was either silenced (both individual and pooled siRNA duplexes) or inhibited (Monostrol) and expression levels were determined by Western blots. To determine whether KIF11 silencing or inhibition affects DNA content, two phenotypes frequently associated with CIN, namely increases in nuclear area and micronucleus formation were evaluated. Fluorescence microscopy was employed on DAPI-counterstained samples and revealed statistically significant increases both nuclear area and micronucleus formation following KIF11 silencing and inhibition relative to controls. Next, flow cytometry was performed on propidium iodide labeled samples to assess whether increases in DNA content were associated with the changes in nuclear area. As predicted, increases in the proportion of cells with &gt;G2/M DNA content occurred within the KIF11 silenced populations. Finally, mitotic chromosome spreads were generated and chromosomes were manually enumerated from 100 spreads per condition/control. Subsequent Kolmogorov-Smirnov tests identified statistically significant increases in the cumulative distribution frequencies of mitotic chromosome numbers within the spreads generated from the KIF11 silenced cells relative to controls. To extend our findings beyond the colorectal cancer cell context employed above, analogous studies were performed in hTERT cells (karyotypically stable fibroblast cell line) with very similar results. Collectively, these data indicate that KIF11 expression and function are normally required to maintain genome integrity. They further suggest that the loss of KIF11 expression and/or function may be a contributing factor in the etiology of tumorigenesis in colorectal cancer and perhaps other tumor types as well.
Citation Format: Yasamin Asbaghi, Zelda Lichtensztejn, Laura Thompson, Kirk McManus. KIF11 silencing or inhibition induces chromosome instability. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3585.
Abstract 3586: Overexpression of Emi1 causes chromosomal instability and cancer
Authors: Vaidyanathan Srividya , Cato Kathleen , Pavey Sandra , Haass Nikolas K. , Gabrielli Brian G. , Duijf. Pascal HG 
Published: July 2016

Abstract
Chromosomal Instability (CIN) is a common occurrence in solid cancer associated with poor survival in patients. A significant percentage of these tumors show abnormal chromosomes with near-triploid or tetraploid numbers exhibiting numerical CIN (nCIN). nCIN is caused mainly due to deregulation of cell cycle proteins. Early Mitotic Inhibitor 1 (Emi1) is a cell cycle protein that regulates the activity of E3 ubiquitin ligase, Anaphase Promoting Complex/Cyclosome (APC/C), which targets many cell cycle proteins for degradation. Emi1 is overexpressed in many solid tumors but not blood cancers.
Unpublished data from our lab has shown that Emi1 overexpression in mouse models causes more penetrant and metastatic tumor than control tumors. Breast cancer tissues show significantly high expression of Emi1 at protein level as compared to control breast tissue samples, in agreement with the microarray data from The Cancer Genome Atlas (TCGA). In addition, Emi1 expression from breast cancer TCGA data strongly correlated with the chromosomal instability signature than many of the well-established genes known to promote CIN phenotype. To understand the mechanisms of CIN due to Emi1 overexpression, we overexpressed Emi1 in HeLa cells expressing GFP-tagged histone protein to monitor the cells during mitosis by live cell imaging.
HeLa cells overexpressing Emi1 show CIN following delays in both chromosome alignment at the metaphase plate and, subsequently, anaphase onset (p = 0.0008 and p = 0.0028). There is a significant increase in CIN phenotypes and abnormal mitoses such as anaphase bridges/lagging chromosomes, mitotic arrest and cell death. These results indicate that Emi1 overexpression actively drives tumorigenesis.
Citation Format: Srividya Vaidyanathan, Kathleen Cato, Sandra Pavey, Nikolas K. Haass, Brian G. Gabrielli, Pascal HG Duijf. Overexpression of Emi1 causes chromosomal instability and cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3586.
Abstract 3589: Nucleotide excision repair is elevated in stage IV commonly used breast cancer cell lines as compared to stage I breast tumor explants
Authors: As Sobeai Homood , Johnson Jennifer M. , Lalanne Nancy , Ibrahim Omar , Grant Stephen G. , Wenger Sharon L. , Latimer Jean J. 
Published: July 2016

Abstract
Genomic instability is a hallmark of human carcinogenesis. We have previously published that sporadic stage I breast tumors exhibit deficient Nucleotide Excision Repair (NER) capacity relative to non-diseased breast reduction primary cultures (Latimer et al., 2010). In the present work, we hypothesized that this feature of early human breast cancer would not be maintained in cell lines established from late stage tumors. Our objective was to determine functional NER capacity and relative NER gene expression in a series of commonly used stage IV breast cancer-derived cell lines relative to stage I breast cancer explants and cell lines. NER capacity was determined using the functional unscheduled DNA synthesis (UDS) assay in six established breast cancer cell lines (MCF-7, MCF-7LY2, MDA-MB-231, SK-BR-3, CAMA-1, BT-20). JL BTL-12 (Jean Latimer Breast Tumor Line-12), derived from a stage III breast tumor, was included to represent an advanced stage tumor cell line established using our culture system. The NER capacity of the cell lines was compared to that of 19 stage I breast tumor primary cultures. NER gene expression was determined by expression microarray using the Affymetrix HG U-133 plus 2.0 chip in five of these established cell lines (MCF-7, MDA-MB-231, SK-BR-3, CAMA-1, BT-20), JL BTL-12 and a representative stage I tumor-derived cell line (JL BTL-8, Breast Tumor Line-8). The stage IV cell lines and JL BTL-12 all manifested significantly higher NER capacity than explants of stage I breast cancer. Unsupervised as well as supervised analyses, based on expression of the canonical 20 NER genes, placed JL BTL-12 and the five stage IV commercial cell lines in one cluster, while JL BTL-8 clustered separately. Four NER genes were significantly upregulated in JL BTL-12 and all commercial cell lines relative to JL BTL-8. In conclusion, based on NER these five cell lines commonly used in breast cancer research are more representative of late stage disease than early stage breast cancer, regardless of the type of breast cancer they represent. The most commonly diagnosed stage of breast cancer in the U.S. is now stage I, and it is now possible to study stage I cell lines or explants.
Citation Format: Homood As Sobeai, Jennifer M. Johnson, Nancy Lalanne, Omar Ibrahim, Stephen G. Grant, Sharon L. Wenger, Jean J. Latimer. Nucleotide excision repair is elevated in stage IV commonly used breast cancer cell lines as compared to stage I breast tumor explants. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3589.
Abstract 3591: Expression of 14-3-3 gamma stabilizes polyploidization in NSCLC cells
Authors: Gomes Cecil J. , Harman Michael , Centuori Sara , Wolgemuth Charles , Martinez Jesse 
Published: July 2016

Abstract
In normal lung tissue the expression levels of 14-3-3 gamma are very low and tightly regulated, however, in cancer it is evident that 14-3-3 gamma's expression patterns become deregulated and significantly elevated. In patients with advanced non-small cell lung cancer (NSCLC), increased expression of this isoform is associated with poorer survival and significantly correlates with lymph node and distant metastasis. These data prompted us to analyze TCGA's NSCLC gene expression dataset, and it is clear that 14-3-3 gamma's expression continues to increase in the progression from early to late stage cancers. Taken together, these data suggest that overexpression of 14-3-3 gamma is correlated with a more aggressive tumor phenotype, an observation also seen with breast and hepatocellular carcinoma. The focus of this study is to elucidate the mechanism(s) causing these more aggressive cancer phenotypes. We have previously shown that overexpressing 14-3-3 gamma in human lung cancer cells harboring very low levels of endogenous 14-3-3 gamma and no wildtype p53 results in a stable subpopulation of cells with polyploid DNA content. Interestingly, approximately 40% of lung adenocarcinomas present with hyper-triploid karyotypes, and even a higher percentage, 40-60%, have inactivation of p53. It is well established that polyploid tumors have the capacity to increase tumorigenicity by allowing resistance to conventional therapies and also permitting elevated tolerance to chromosomal instability (CIN). This leads us to hypothesize that in the absence of p53, NSCLC tumors overexpressing 14-3-3 gamma result in a polyploid population of cells that may be influencing the aggressiveness of the tumor. Further in vitro analysis of these 14-3-3 gamma induced tetraploid cells show that they have a prolonged mitosis with significantly more lagging chromosomes in anaphase than their diploid counterparts, indicating an increase in chromosomal instability (CIN). After isolating isogenic tetraploid clones with or without 14-3-3 gamma expression, the stability of the tetraploid cell state was assessed. Clones not expressing 14-3-3 gamma quickly reverted back to a pseudo-diploid state, whereas overexpression of 14-3-3 gamma significantly prolonged the tolerance of tetraploidy and eventually resulted in an aneuploid cell state. Our data suggests that overexpression of 14-3-3 gamma increases tumorigenicity through the stabilization of a polyploid cell state.
Citation Format: Cecil J. Gomes, Michael Harman, Sara Centuori, Charles Wolgemuth, Jesse Martinez. Expression of 14-3-3 gamma stabilizes polyploidization in NSCLC cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3591.
Abstract 3592: BaP induces chromosome missegregation through mitotic spindle defects in normal lung epithelial cells
Authors: Thaiparambil Jose T. , El-Zein Randa 
Published: July 2016

Abstract
Lung cancer remains the leading cause of cancer related deaths in the United States. Cancer results from an accumulation of multiple genetic events leading to genomic instability that is a crucial early event in carcinogenesis. Aneuploidy is the most frequently identified genomic abnormality in cancer. We have previously reported a significantly higher level of aneuploidy in smokers who developed lung cancer as compared to smoker controls. Benzo(a)pyrene [B(a)P], a polycyclic aromatic hydrocarbon, is a pulmonary carcinogen and one of 60 different carcinogens found in tobacco smoke. In this study, we hypothesize that B(a)P disrupts mitotic spindle assembly that impairs the fidelity of mitosis leading to chromosome missegregation and aneuploidy.
To test our hypothesis, we use confocal imaging in combination with traditional molecular biology techniques to dissect the precise mechanism by which B[a]P induces chromosome missegregation and aneuploidy. Mitotic spindle defects in the form of chromosome lags and bridges, monopolar and multipolar spindles, were assessed in normal lung epithelial cells after treatment with 10μM B[a]P for 6 hrs. Spindle defects were assessed at 24, 48, 72 and 96 hours after treatment. Immunofluorescence revealed abnormal mitosis in the prometaphase through the telophase stage of mitosis. Our result show that B[a]P exposure induced abnormal spindles in the form of monopolar (14%) and multipolar (4%) spindles. High resolution confocal images further revealed that B[a]P exposure led to misoriented mitotic spindles with an abnormal spindle angle [-380] relative to normal plane [180]. Chromosome lagging at both metaphase (17%) and anaphase (9%) has also been recorded in response to B[a]P exposure, observations that result from defects in the mitotic apparatus and kinetochores. Furthermore, we assessed the extent of B[a]P induced genetic instability [in the form of double strand DNA breaks] using gama-H2AX in order to elucidate the underlying mechanism associated with accumulated genetic damage and chromosome missegregation. Our data indicate that B[a]P results in accumulation of mitotic abnormalities and gama-H2AX foci (22%) peaks at 48 hr compared to other time points.
Taken together, our data show that B[a]P potently induces mitotic abnormalities by disrupting kinetochore microtubules. The induction of mitotic abnormalities by B[a]P leading to chromosome missegregation and aneuploidy, would unravel a novel targetable molecular mechanism of cigarette smoke induced lung tumorigenesis.
Citation Format: Jose T. Thaiparambil, Randa El-Zein. BaP induces chromosome missegregation through mitotic spindle defects in normal lung epithelial cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3592.
Abstract 3595: Improved therapeutics for hepatocellular carcinoma
Authors: Zavadil Jessica A. , Walter Christi A. 
Published: July 2016

Abstract
Eighty percent of hepatocellular carcinoma (HCC) within the USA is diagnosed late when chemotherapy provides only 2 months increased survival. We fortuitously found that treatment with an alkylating agent, methylnitrosurea (MNU), prior to tumorigenesis reduced tumor prevalence later in life by ∼50% in C3HeB/FeJ male mice, a model of spontaneous HCC. A similar effect was observed with temozolomide (TMZ), a glioblastoma therapy that induces the same DNA damage at similar proportions to MNU. O6-methylguanine-DNA methyltransferase (MGMT) repairs the highly mutagenic and cytotoxic O6-methylguanine lesions induced by TMZ, and MGMT abundance influences therapy response in glioblastoma. MGMT is reduced in 1/3 of human HCC, leading us to hypothesize that TMZ could be effective in treating HCC. We proposed to combine TMZ with suberoylanilide hydroxamic acid (SAHA), a histone deacetylase inhibitor, to maximize efficacy, reasoning that SAHA would allow TMZ greater access to DNA to induce greater levels of damage. We tested this drug combination in two human HCC cell lines, Huh7, with reduced MGMT expression, and SNU398, with higher expression. TMZ and SAHA synergistically reduced cell viability in both cell lines with multiple dose combinations. Based on this outcome, we tested the drugs in tumor-bearing C3HeB/FeJ mice. Surprisingly, DMSO treated solvent control mice showed reduced tumor burden. The DMSO treatment was repeated adding a sham control group and confirmed that DMSO significantly reduces tumor burden. The TMZ cohort also displayed a significantly lower tumor burden compared to the sham cohort, but no significant difference was found with SAHA alone or SAHA+TMZ. We previously showed that a hMGMT transgene protects from hepatocarcinogenesis in C3HeB/FeJ mice, but surprisingly, there is not additional protection when transgenic mice are treated with MNU. These results suggest that the more prevalent cytotoxic lesions induced by MNU and TMZ, e.g. N7-methylguanine, may be more important in HCC than O6-methylguanine. These lesions are recognized by methylpurine-DNA glycosylase (MPG) and repaired through base excision repair. Therefore, we directly tested the role of MPG in TMZ therapy through altered expression of MPG in Huh7 and SNU398 cell lines and showed that it does affect sensitivity to TMZ.
Citation Format: Jessica A. Zavadil, Christi A. Walter. Improved therapeutics for hepatocellular carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3595.
Abstract 3598: Laser micro-irradiations of large amounts of cells for high content applications
Authors: Mistrik Martin , Vesela Eva , Furst Tomas , Frydrych Ivo , Gursky Jan , Bartek Jiri 
Published: July 2016

Abstract
A new methodical approach for the evaluation of photo-manipulated samples is presented and tested in various biological setups. The method is based on an atypical setting of a standard laser-scanning microscope (LSM) and image-processing software solution. Newly, a whole population of several dozen of cells is simultaneously micro-irradiated by a laser beam in a precisely defined pattern of collinear rays. Such laser induced striation pattern is automatically analyzed by specialized software routine providing quantitative assessment of various photo-manipulations, such as DNA-damage induced protein translocations or modifications, in both live and fixed cells. Automation of the process reduces workload and opens new possibilities for various dynamic studies and/or high content experiments. Results obtained during the testing of the method are presented and offer an insight into several DNA damage recognition and response pathways.
Citation Format: Martin Mistrik, Eva Vesela, Tomas Furst, Ivo Frydrych, Jan Gursky, Jiri Bartek. Laser micro-irradiations of large amounts of cells for high content applications. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3598.
Abstract 3604: Validated structural variant detection with prioritisation of known cancer related changes
Authors: Ahdesmäki Miika , Chapman Brad , Luke Sally , Carr Hedley , Stetson Daniel , Hofmann Oliver , Johnson Justin 
Published: July 2016

Abstract
Reliable detection of structural variation (SV) is playing an increasingly important role in cancer diagnostics and treatments. We introduce a best practice integrative workflow for detecting large structural variations (SVs) such as deletions, duplications, inversions, fusions and translocations from standard DNA re-sequencing techniques, annotating and prioritising for clinically actionable events.
While established RNA-Seq fusion workflows exist to detect and filter fusion events in tumors detecting large structural changes from exome- and WGS data remains challenging. Current DNA-based SV callers predict a large percentage of false positive events, and the resulting event lists are not prioritised for validation. To streamline follow-up studies we automate running multiple structural variant callers (Manta, WHAM, Lumpy, MetaSV), identifying potentially disruptive large scale events. We evaluate the integrated workflow sensitivity and specificity against the ICGC-TCGA DREAM Mutation Calling Challenge data set, optimise filtering criteria based on quality and supporting information, and annotate the filtered calls using known cancer related alterations from CIViC and publicly available gene lists from AstraZeneca. This enables us to prioritise known and potentially interesting events over intergenic events or non-whole exon deletions.
We show validation results from test data and clinically actionable inversions, duplications and fusion events from cancer cell lines. Our approach is based on a two tier approach of first focusing on known events that yield fusion transcripts such as the TACC3-FGFR3 tandem duplication and ALK-EML4 inversion, and secondarily on events in oncogenes and tumor suppressors of interest. While whole genome sequencing is the preferred approach to detecting these events, we also show how by design or by the nature of the breakpoint being close enough to exons, hybrid capture data can also be surprisingly useful for SV inference.
Citation Format: Miika Ahdesmäki, Brad Chapman, Sally Luke, Hedley Carr, Daniel Stetson, Oliver Hofmann, Justin Johnson. Validated structural variant detection with prioritisation of known cancer related changes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3604.
Abstract 3608: Detection of somatic structural variants using nanopore sequencing
Authors: Norris Alexis L. , Workman Rachael E. , Fan Yunfan , Eshleman James R. , Timp Winston 
Published: July 2016

Abstract
Structural variants (SVs) are a hallmark of human cancer, but remain difficult to reliably and accurately detect with next generation sequencing (NGS). This is in part due to the difficult in mapping NGS's short reads (&lt;300bp) to repetitive elements, which often flank the genomic rearrangements of SVs. Nanopore sequencing, a 3rd generation sequencing technology, offers long sequencing reads (up to 20kb), that should allow for more reliable mapping of SVs. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Here, we have tested the ability of nanopore sequencing to detect a series of well-characterized SVs (including large deletions, inversions, and translocations), that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we show that nanopore sequencing on the MinION platform can detect large deletions, translocations, and inversions at dilutions as low as 1:100. Given the speed, small footprint (USB size), and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of somatic SVs, with clinical applications of molecular relapse, early detection, or therapeutic monitoring.
Citation Format: Alexis L. Norris, Rachael E. Workman, Yunfan Fan, James R. Eshleman, Winston Timp. Detection of somatic structural variants using nanopore sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3608.