bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4815: Aberrant DNA hypermethylation of the ITIH5 tumor suppressor gene in acute myeloid leukemia
Authors: Oing Christoph , Jost Edgar , Dahl Edgar , Wilop Stefan , Osieka Rainhardt , Brümmendorf Tim H. , Galm Oliver 
Published: June 2012

Abstract
Acute myeloid leukemia (AML) is a clonal disorder resulting from uncontrolled proliferation of hematopoietic stem cells. Important genetic findings in AML comprise chromosomal translocations involving different transcription factors and activating point mutations in multiple signal transduction pathways. Hypermethylation of CpG islands within gene promoter regions in collaboration with deacetylation and other modifications of histone amino acids is associated with transcriptional inactivation and represents, in addition to genetic aberrations, an important mechanism of gene silencing in the pathogenesis of human cancer. Inter-alpha-trypsine inhibitors (ITIs) are proteases consisting of one light chain (bikunin) and two heavy chains (ITIHs), which stabilize the extracellular matrix (ECM). The putative tumor suppressor gene ITIH5 has previously been reported to be downregulated in association with aberrant DNA methylation in breast cancer. In this study, we determined the methylation status of the promoter-associated CpG island of ITIH5 in hematopoietic cell lines and primary AML patient samples. Methylation specific polymerase chain reaction (MSP) analysis revealed that the ITIH5 promoter region was hypermethylated in the AML cell lines HL60 and KG1a. Treatment of cell lines that carry a hypermethylated ITIH5 gene with the demethylating agent 5-aza-2’-deoxycytidine resulted in partial promoter demethylation. We then analyzed the ITIH5 methylation status in primary mononuclear cells obtained from 110 patients with newly diagnosed AML. The frequency of aberrant methylation among the primary patient samples was 14.5 % (16/110). Among clinical prognostic parameters, we found a significant positive correlation between hypermethylation of ITIH5 and elevated serum levels of lactate dehydrogenase (LDH, p=0.013) in univariate analysis, whereas no correlation was found for cytogenetics, FAB subtype, age, white blood cell count and overall survival. We conclude that promoter hypermethylation of ITIH5 is a novel epigenetic event in AML that may contribute to leukemogenesis by interfering with the interaction between the ECM and the leukemic clone. Further studies are warranted to elucidate the functional consequences of epigenetic dysregulation of ITIH5 in leukemogenesis.
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 4815. doi:10.1158/1538-7445.AM2011-4815
Abstract 4822: Nonsense mediated decay defines deleterious TP53 mutations and tumor aggressiveness in ovarian cancer
Authors: Ahmed Ahmed A. , Bast Robert C. , Bowtell David , Goldsmith Juliet 
Published: June 2012

Abstract
Genetic mutations leading to premature termination of protein translation, nonsense mutations, result in aberrant precursor mRNA processing and subsequent UPF1-dependent exosomal degradation of mRNA. The significance of this surveillance mechanism in controlling the expression of key mutated tumor suppressor genes in cancer in vivo has remained unclear. We have recently shown that TP53 mutations are almost invariably present in high-grade serous ovarian cancers (Ahmed at al., Journal of Pathology, 2010;221:49) and that about one third of such mutations are nonsense. We have now tested the hypothesis that nonsense mutations induce nonsense mediated decay resulting in TP53 mRNA depletion. We analyzed microarray expression profiling data from 136 epithelial ovarian cancers with known TP53 mutation status and found a strikingly statistically significant underexpression of TP53 mRNA transcript in cancers with truncating mutations (p&lt;0.0001) compared to other types of mutations. This effect allowed the identification of a class of TP53-non-expressing serous epithelial cancers that comprised all TP53 truncating mutations. We next conducted a systematic analysis of 18 publically available expression profiling ovarian cancer studies published at the Gene Expression Omnibus database. We validated the results by showing that cancers that had nonsense mutations had a significantly lower TP53 expression irrespective of stage. Importantly, this systematic analysis of multiple independent data set established that lack of TP53 expression was, almost exclusively, a feature of high grade serous cancers and invasion as opposed to low grade disease or tumors of low malignant potential (p&lt;0.0001 and p=0.002, respectively). Expression profiling analysis revealed that cancers with truncating mutations had a distinct gene expression signature compared to those with missense mutations. This signature was enriched for genes that regulated angiogenesis such as CSPG4 and metabolism. Surprisingly, however, the magnitude of expression differences was not high. Based on these results, we propose a model for the biogenesis of a subset of high-grade serous ovarian cancers that is defined by nonsense mediated decay of nonsense TP53 mutations.
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 4822. doi:10.1158/1538-7445.AM2011-4822
Abstract 4837: Integrated genome sequence, epigenome, and transcriptome map of bladder cancer development
Authors: Czerniak Bogdan , Majewski Taddeusz , Chung Woonbok , Limei Hu , Cogdell David , Bondaruk Jolanta , Zhang Shizhen , Lee Sangkyou , Lee Sooyong , Shen Li , Wei Caimiao , Yoo Suk Young , Choi Woonyoung , McConkey David , Weinstein John , Baggerly Keith , Issa Jean-Pierre , Zhang Wei , Scherer Steve E. 
Published: June 2012

Abstract
Genomic maps that track the development of human cancer from its in situ precursor conditions to invasive disease can facilitate the search for genes and genomic sequences involved in the development of cancer. The identification of those chromosomal regions and their positional target genes as well as non-coding sequences that provide growth advantage for the incipient preneoplastic conditions can provide novel insights on molecular mechanisms of cancer development. Such an approach is also critical for the identification of novel biomarkers as well as targets for preventive and therapeutic strategies.
We report on the construction of a high resolution whole-organ histologic and genetic map of bladder cancer development that tracks its progression from in situ precursor conditions to invasive clinically aggressive cancer using exome deep sequencing and 1M SNP-based Illumina genotyping combined with CpG island methylation and cDNA microarray technology platforms. This approach provided a high resolution integrated pattern of structural genome, epigenome, and transcriptome alterations that parallel the development of bladder cancer from early field effects to invasive disease.
By analyzing genome-wide patterns of structural genomic (copy loss or gain), epigenomic, and transcriptome changes, we found three major waves of alterations associated with growth advantage of successive clones reflecting a stepwise conversion of normal urothelial cells into cancer cells. In particular, this approach is significant for the identification of specific chromosomal regions as well as epigenetically and transcriptionally modified gene ontologies involved in early clonal expansion of intraurothelial neoplasia and their clonal evolution to carcinoma in situ progressing to invasive cancer. These studies suggest involvement of ras/raf gene network in early clonal expansion of intraurothelial neoplasia.
This map represents a prerequisite for specific studies on the mechanisms of incipient phases of bladder cancer development and should have a significant impact on the understanding of human carcinogenesis.
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 4837. doi:10.1158/1538-7445.AM2011-4837
Abstract 4855: Use of blocker locked nucleic acid (LNA™) oligonucleotides in cycle sequencing for improved limits of detection (BLOC-Sequencing)
Authors: Legendre Benjamin , Wu Grant , Stoddard Jason , Scott Jaclyn , Johnson Emily , Sommer Julie , Murphy Tammy , Echtenkamp Karissa , Richardson Katherine 
Published: June 2012

Abstract
Epidermal growth factor receptor (EGFR) antagonists, such as cetuximab and panitumumab, are therapeutic agents that can be effective in colorectal cancer (CRC) treatment. It has been shown that 40% of CRC tumors have activating K-RAS exon 2 codon 12 and 13 mutations and that these mutations may be associated with a poor response to EGFR antagonists. Very high sensitivity detection of such diagnostic biomarkers is necessary to determine the presence or emergence of drug resistant tumor cell populations.
The use of Locked Nucleic Acid (LNA™) containing oligonucleotides (oligos) have been used in microRNA (sample preparation), RNA (in situ hybridization), and DNA (SNP detection using allele specific PCR) applications. The advantage of using LNA-containing oligos is that the denaturation temperature of LNA-oligo:DNA duplex is increased as compared to the DNA:DNA duplex
To further the limit of detection of Sanger sequencing, a LNA-based approach has been developed to selectively block the sequencing of the wild-type DNA and allow the sequencing of DNA containing any mutation (BLOC-Sequencing). During cycle sequencing, an additional annealing step is added to hybridize the LNA containing oligo to the template DNA. Then, a denaturing step is performed at a temperature at which the LNA-containing oligo remains annealed to the wild-type sequence; however, the LNA oligo denatures from the mutant sequence. The sequencing primer then anneals to the mutant sequence and subsequently extended. Since LNA-containing oligos block amplification of the wild-type sequence, the mutant-containing DNA will be sequenced in a non-biased manner.
Preliminary results using two sequences in a 1:1 ratio differing in only 2 nucleotides within the range where the LNA blocking oligo anneals demonstrated complete blocking of one sequence (sequence 1) where the LNA containing oligo was 100% complementary. The unblocked sequence (sequence 2) sequenced successfully, with minimal background due to sequence 1. Straight Sanger sequencing results of the 1:1 mixture without the LNA blocking oligo gave equal proportion of the two sequences present.
To show applicability for use of this methodology in CRC samples, the limit of detection for multiple codon 12 and codon 13 K-RAS exon 2 mutations with and without the addition of the K-RAS exon 2 wild type specific LNA oligo in both the forward and reverse directions will be demonstrated. In addition, we will compare the results of 30 previously genotyped FFPE samples with this technique.
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 4855. doi:10.1158/1538-7445.AM2011-4855
Abstract 4870: High-throughput proteomics using stable isotope labelling with amino acids in cell culture (SILAC) reveals potential modulators of androgen-independent prostate cancers
Authors: Saraon Punit , Batruch Ihor , Smith Chris , Mizokami Atsushi , Jarvi Keith , Diamandis Eleftherios P. 
Published: June 2012

Abstract
Prostate cancer is the most common malignancy and the second leading cause of cancer related deaths in men. One common treatment is androgen-deprivation therapy, which reduces symptoms in most patients. However, over time patients develop tumours that are androgen-independent and ultimately fatal. The mechanisms that cause this transition remain largely unknown, and as a result, there are no effective treatments against androgen-independent prostate cancer. As a model for androgen-independence, we used the LNCaP cell line which is naturally androgen-dependent grown in androgen depleted conditions for a 6 month period to generate the androgen-independent cell line LNCaP-SF. Preliminary experiments showed that the LNCaP-SF cell line had higher proliferation/viability rates in androgen-depleted conditions, and had increased expression of the androgen receptor protein, a key modulator in prostate cancer progression. Our next goal was to assess to differential global protein expression as well as differential expression of secreted proteins from each of the two cell lines. To identify differentially expressed proteins, we utilized Stable Isotope Labelling with Amino Acids in Cell Culture (SILAC) coupled to mass spectrometry. LNCaP cells were labelled in growth media containing light-Arg/Lys whereas LNCaP-SF was labelled in heavy Arg-Lys media. After proteomic analysis, we were able to quantify 3355 proteins with at least one peptide hit. From these proteins, using stringent criteria, 99 and 82 proteins were found to be up-regulated and down-regulated respectively, in LNCaP-SF cells compared to LNCaP cells. Using various bioinformatics tool, we found that genes involved in fatty acid degradation and ketogenesis as important pathways that with over-expressed in LNCaP-SF cells. We performed qPCR validation of genes involved in each of these pathways and found that LNCaP-SF cells generally had an increase in the expression of many these genes, compared to LNCaP cells. These preliminary results show that genes involved in fatty acid degradation and ketogenesis pathways could serve as potential biomarkers for androgen-independent prostate cancer.
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 4870. doi:10.1158/1538-7445.AM2011-4870
Abstract 4878: Application of a novel nano-immunoassay platform to assess changes in cIAP1 in response to the SMAC-mimetic, LCL161
Authors: Yeleswarapu Lakshmi , Nuti Shanthy , Graber Armin , Gardner Humphrey , Barrett Carl , Ramkumar Thiruvamoor 
Published: June 2012

Abstract
Introduction: cIAP1 is member of a class of inhibitor of apoptosis proteins (IAP) that function in a regulatory role to prevent unintended cell death by apoptosis. LCL161 is a small molecule antagonist of IAPs that reverses cIAP1 inhibition of caspases, causing apoptosis. The present study explores the use of the Nano Pro 1000, a novel proteomic platform to measure the changes in cellular cIAP1 in response to treatment with LCL161. Methods: SKOV3 cells, peripheral blood mononuclear cells (PBMC) and hair follicles collected from healthy donors were treated with LCL161 for different times and subjected to capillary iso-electric focusing. Immunodetection was performed using antibodies directed against cIAP1 and the signal was quantified using HRP-labeled chemiluminescence reagents. Data from the Nano Pro were compared to results from western blots run in parallel. Results: We report that results from the nano-immunoassay are reproducible and correlate well with the western blotting data. Modulation in the cellular levels of cIAP1 in response to LCL161 treatment could be captured in samples containing as little as 1 ng of total protein. Similar modulation of cIAP1 was seen upon exposure to LCL161 in the studied test matrices. Conclusions: This novel proteomic tool is more sensitive, specific and quantitative compared to the currently available option of western blotting assays which are labor intensive, and have a relatively low throughput. Measurable signals corresponding to cIAP1 levels can be detected in matrices like PBMCs and hair follicles. The modulation of cIAP1 levels in these matrices mirror that seen in SKOV3 cells.
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 4878. doi:10.1158/1538-7445.AM2011-4878
Abstract 492: ALDH1A1 expression predicts for a tumorigenic subset in primary cultures of malignant pleural effusions (MPE)
Authors: Basak Saroj Kumar , Mysore Veena , Lai Chi , Oh Scott , Srivatsan Eri , Batra Raj 
Published: June 2012

Abstract
Aldehyde dehydrogenases (ALDHs) are a group of enzymes that are responsible for oxidation of a variety of aldehydes. ALDH isoforms (ALDH1A1 and ALDH3A1) are highly expressed in non-small cell lung cancer (NSCLC) cell lines. Recent evidence suggests that elevated levels of these enzymes may be associated with malignant behavioral properties of cell subsets in epithelial malignancies. It is not known whether cell subsets with high ALDH expression are present in advance stage lung cancer patients, or whether ALDH expression is associated with malignant behaviors (e.g. tumorigenicity) in lung cancer cell subsets. We hypothesized that the ALDH1A1-biomarker is present in advanced lung cancer, and that as in other epithelial malignancies, its expression predicts for lethal behavioral properties.
We isolated lung tumor cells from advanced stage lung cancer patients (MPE), and maintained them in primary culture in presence of MPE fluid (an “autologous tumor microenvironment”). ALDH labeling by immunohistological methods revealed high intratumoral variability with respect to biomarker expression. To live detect MPE-primary culture cells, the Aldefluor (StemCell Technologies Inc.) method of Fluorescence Activated Cell Sorting (FACS) was used. 4-8% of MPE-primary culture cells expressed high level of ALDH1A1, whereas the majority of the cultured cells expressed intermediate or low levels of ALDH1A1. Interestingly, the ALDH1A1hi cell subset also expressed high levels of the CD44 surface biomarker. CD44 is another widely studied biomarker that has been associated with “cancer stem cell” properties. The ALDH1A1hi subset co-expresses 2 to 20 times higher CD44 expression, as compared to the ALDH1A1lo subset. Importantly, the cells that dually label for CD44hi and ALDH1A1hi exhibit increased soft agar colony forming efficiency in vitro, and increased tumorigencity in vivo. Limiting dilution studies of xenotransplantation in NOD/SCID mice also provide experimental evidence that clinical (MPE) biospecimens of some lung cancers possess ALDH1A1hi/CD44hi “cancer stem cells” (as evidenced by tumorigenesis following less than 1000 implanted cells). The tumors that emerge from the implantation of these lung “cancer stem cells” display phenotypic heterogeneity with respect to both CD44 and ALDHA1 expression. Collectively, these data provide experimental evidence for tumorigenic subsets in clinical lung cancer biospecimens, and suggest that ALDHA1 and CD44 expression are jointly regulated by a common oncogenic program in lung cancer cells.
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 492. doi:10.1158/1538-7445.AM2011-492
Abstract 4938: Extracellular miRNAs have potential as minimally-invasive biomarkers for predicting response to HER2-targeted agents, including Trastuzumab, as used in breast cancer
Authors: Corcoran Claire , Rani Sweta , Browne Brigid , Crown John , O'Donovan Norma , O'Driscoll Lorraine 
Published: June 2012

Abstract
The identification of minimally-invasive biomarkers, in efforts to aid in patient-tailored disease management, has become a key focus of cancer research. Recent studies by ourselves and others have reported the existence of circulating miRNAs associated with breast cancer. Despite this progress, resistance to anti-cancer treatment remains a major obstacle in the treatment of this disease and unfortunately there are no reliable methods of predicting sensitivity/resistance to anti-cancer agents.
This study aimed both to (i) identify miRNAs differentially-expressed in the breast cancer cell line SKBR3 and its Trastuzumab-resistant variant, SKBR3-H, developed by exposure to Trastuzumab for 6 months; and to (ii) investigate if corresponding differential levels of miRNAs were detectable in conditioned media (CM) from these cells, reflecting the relative sensitive/resistance profile of the SKBR3-H comparing to age-matched control SKBR3 cells.
Global analysis of miRNAs was successfully performed on biological triplicate RNA specimens isolated from SKBR3 cells, SKBR3-H cells and on their respective CM, using TaqMan low density arrays representing 667 human miRNAs. 71.5% (477/667) miRNAs were detected in SKBR3; most (85%; 406/477) of which were detected in its CM. For SKBR3-H, 75.7% (505/667) miRNA analyzed were present in the cells, with 70% (354/505) of these also detected in corresponding CM. Of the 187 miRNAs up-regulated by at least 2-fold in SKBR3-H compared to SKBR3 cells, 6.42% (12/187) were up-regulated in corresponding CM. Of the 62 miRNAs down-regulated by at least 2 fold in SKBR3-H compared to SKBR3 cells, more than half (53.2%; 33/62) were down-regulated in corresponding CM. Several differentially regulated miRNAs were selected from TLDA results and subsequently validated in triplicate by qRT-PCR.
Overall, the many hundred (∼500) miRNAs detected in CM further supports the existence of extracellular miRNAs and so their potential as minimally-invasive biomarkers. Furthermore, we identified a number of miRNAs that may help predict response to Trastuzumab. Our current research involves investigating the relative expression of miRNAs in SKBR3 variants resistant to other HER2-targeted agents and also examining the potential target genes for miRNAs identified as of most relevance here. Exploring the occurrence of these miRNAs in relevant patients’ serum specimens is now warranted to investigate clinical application.
Acknowledgements: Science Foundation Ireland's SRC award to MTCI (08/SRC/B1410).
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 4938. doi:10.1158/1538-7445.AM2011-4938