bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1994: Tobacco carcinogen-induced transformation of HBECs is associated with chromatin-mediated reprogramming of the epigenome
Authors: Tellez Carmen S. , Juri Daniel E. , Van Neste Leander , Hart Christopher , Liu Yushi , Do Kieu , Picchi Maria A. , Belinsky Steven A.
Published: August 2014

An in vitro model, hTERT/cdk4, immortalized human bronchial epithelial cells (HBECs), was used to identify key molecular changes driving cell transformation and the clonal outgrowth of preneoplastic lung epithelial cells. Low-dose weekly treatment (12 weeks) of HBECs with genotoxic, but not cytotoxic doses of the carcinogens methylnitrosourea (MNU), benzo(a)pyrene-diolepoxide 1 (BPDE), or both induced transformation. Transformation efficiency (0.2-3%) differed between HBECs and was associated with DNA repair capacity, increased levels of DNMT1 protein, promoter hypermethylation, EMT, and stem-like cell phenotype. Agilent 44K arrays were used to determine genome-wide changes in gene expression associated with transformation. Comparison of expression between HBEC1 and HBEC2 to cells transformed by BPDE, MNU, or the combination revealed 287-321 and 320-493 genes with increased or decreased (≥ 3-fold change) expression. Approximately 214 and 331 of the genes with decreased expression in HBEC1 and HBEC2 had CpG islands that extended through their transcriptional start site. HBEC2 MNU/BPDE transformed cells were treated with DAC or TSA to assess globally whether chromatin remodeling alone, or in combination with DNA methylation mediated gene silencing. Only 128 of 331 silenced genes in HBEC2 MNU/BPDE transformed cells responded to DAC alone. Promoter methylation arrays and genome-wide ChIP-chip for inactive chromatin marks were used to elucidate mechanisms of global gene silencing in HBEC2 MNU/BPDE transformed cells. Array analysis revealed 216 genes with reduced expression are enriched for H3K27me3 and 23 novel genes with reduced expression are hypermethylated in HBEC2 MNU/BPDE transformed cells. Our in vitro model suggests that the re-programming of the epigenome during carcinogen-induced transformation is initially mediated by chromatin remodeling with ensuing DNA methylation sustaining gene silencing. The authors’ work is supported by a research grant from National Institutes of Health (R01 ES008801).

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 1994. doi:10.1158/1538-7445.AM2011-1994
Abstract 1997: Changes in growth pattern and expression of epigenetic regulatory genes in human prostate epithelial cells exposed to arsenic and estrogen
Authors: Treas Justin , Singh Kamaleshwar P.
Published: August 2014

Chronic exposure to either arsenic or estrogen causes prostate cancer in animal model. However, the effects of co-exposure to estrogen and sodium arsenite on prostate epithelial cells are not known. Chromatin remodeling by epigenetic changes play important role in gene expression and carcinogenesis. Therefore, the objective of this study was to determine the effects of chronic exposure to 17-βestradiol and sodium arsenite on cell growth and the expression epigenetic regulatory genes in RWPE-1, a human prostate epithelial cell line. RWPE-1 cells were treated with estrogen and arsenic alone as well as in combination of these two chemicals for 4 months. The cell count and soft agar assay was performed to determine the growth and malignant transformation potential of arsenic and estrogen. The expression of genes that regulate DNA methylation and histone modifications was measured by quantitative real time PCR and was further confirmed at protein level by Western blot analysis. The result of this study revealed that exposure to arsenic causes increased growth and malignant transformation of RWPE-1 cells. Interestingly, co-exposure to arsenic and estrogen lead to a more dramatic and synergistic effects on alteration of gene expression than either of these two chemicals alone. The qRT-PCR data revealed that co-exposure causes a moderate to high decrease in expression of histone modifying genes HDAC1, 2, 3, and 7 as well as HAT1 and HMT1. The genes DNMT1, MBD1, and MeCP2 all showed slight downregulation, but MBD4 showed a dramatic downregulation. Western blot analysis further confirmed the arsenic and estrogen-induced changes in some of these genes as well as the changes in the level of acetylated and methylated histones. The findings of this study suggest that chronic co-exposure to arsenic and estrogen may cause synergistic effects on epigenetic reprogramming and consequently on carcinogenesis in human prostate epithelial 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 1997. doi:10.1158/1538-7445.AM2011-1997
Abstract 3926: Chronic inflammatory levels of nitric oxide/reactive nitrogen species downregulate BRCA1 protein expression
Authors: Yakovlev Vasily A.
Published: August 2014

The link between inflammation and cancer was proposed more than 150 years ago when Virchow suggested that malignancies tend to arise at sites of chronic inflammation. Recent studies have established that elevated levels of nitric oxide/reactive nitrogen species (NO/RNS) generated in the inflammatory microenvironment are associated with several conditions critical for initiation and promotion of cancer.

The BRCA1 protein contributes to cell viability in multiple ways, including DNA repair, cell cycle checkpoint control, transcription, and regulation of chromosome segregation. Hundreds of mutations in the BRCA1 gene have been identified and associated with an increased risk of cancer. Sporadic breast carcinomas, on the other hand, rarely show mutations of this gene. Instead, BRCA1 protein expression is frequently reduced in sporadic cases. As sporadic tumors account for >90% of the breast cancer, considerable research is directed towards the identification of mechanisms that down-regulate the function of the wild type BRCA1 and lead to genetic instability.

BRCA1 expression is negatively regulated at the transcriptional level by the repressive complex of retinoblastoma-like protein 2 (RBL2) and E2F4. Formation of the repression RBL2/E2F4 complex can be accelerated by, for example, RBL2 dephosphorylation. Recently, protein phosphatase 2A (PP2A), an enzyme responsible for RBL2 dephosphorylation, was shown to be nitrated and activated by NO/RNS (Ohama T., et al., JBC 285, 8711-18, 2010). In the present investigation I demonstrate that inflammatory levels of NO/RNS induce substantial dephosphorylation of RBL2. Normal human mammary epithelial cells (MCF-10A) were incubated with 0.1 mM of the NO-donor SNAP for 6 h. This concentration of NO-donor mimics the intracellular level of NO/RNS during chronic inflammation, hypoxia, and does not induce significant DNA damage and maintains the ATM/ATR-dependent pathways intact. After 6 h incubation with SNAP, significant decrease in total amount of BRCA1 protein was observed with no apparent changes in the levels of E2F1, E2F4, and the catalytic subunit of PP2A, all involved in the regulation of BRCA1. RBL2 dephosphorylation promotes a repressive RBL2/E2F4 complex formation, which inhibits expression of BRCA1. I hypothesize that NO/RNS generated by chronic inflammatory conditions posttranslationally modify proteins involved in the regulation of BRCA1 expression and downregulate BRCA1 expression, thereby constituting a critical role in genetic instability and ultimately 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 3926. doi:10.1158/1538-7445.AM2011-3926
Abstract 3928: Different characteristic features of mitochondrial microsatellite instability in keratoacanthomas and squamous cell carcinomas
Authors: Lee Jae-Ho , Kim Dae-Kwang , Kang Ju-Hwan
Published: August 2014

Keratoacanthoma (KA) as a common cutaneous neoplasm often resembles typical squamous cell carcinoma (SCC) clinically and historically. Several studies have attempted to find alternative methods to distinguish between KA and SCC, however, these did not appear to play a significant role in these tumors. To contribute to a better understanding of these tumors, we studied mitochondrial microsatellite instability (mtMSI) in KA and SCC. DNA was isolated from paired normal and tumoral tissues in 42 patients with KA and 43 patients with SCC. MtMSI was analyzed by using eight microsatellite markers. MtMSI was found in 8 (19%) of 42 KA patients and 7 (16.3%) of 43 SCC patients, respectively. MtMSI has been observed in different location depending on tumors. In KA patients, mtMSI has been detected mostly in the (CA)n of the D-loop region (7/42, 16.7%), in contrast, all of SCC patient had mtMSI in the (C)n of the D-loop region (7/43, 16.3%). Similar frequency of mtMSI was found in KA and SCC, however, their different characteristics support the current concept that KA and SCC have different pathogenetic pathways for their developments.

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 3928. doi:10.1158/1538-7445.AM2011-3928
Abstract 3930: Integrative genomic analysis reveals SWI/SNF chromatin remodeling complex to be a TGFβ-mediating tumor suppressor pathway in pancreatic cancer
Authors: Shain Alan H. , Matsukuma Karen , Giacomini Craig , Karikari Collins A. , Hidalgo Manuel , Maitra Anirban , Pollack Jonathan R.
Published: August 2014

Pancreatic ductal adenocarcinoma (PDAC) remains a leading cause of cancer deaths in the developed world. A more complete characterization of molecular alterations may suggest new avenues for targeted therapy. Here we report the high-resolution genomic and transcriptional profiling of seventy PDAC early-passage tumor xenografts and cell lines – the largest PDAC dataset currently available of this sample size and resolution. Notable among novel loci, genomic deletion/mutation frequently targeted components of the SWI/SNF chromatin remodeling complex, including ARID1A, ARID1B, PBRM1, SMARCA2 and SMARCA4. Overall, focal deletion/mutation of a SWI/SNF component occurred in at least one-third of all PDAC specimens. In cell culture, RNAi-mediated knockdown of SWI/SNF subunits enhanced cell growth, growth-factor independence, and resistance to TGFβ growth-inhibition. Previously, SWI/SNF was reported to mediate TGFβ signaling. Remarkably, we found that five of the top ten SWI/SNF-mediated TGFβ-downregulated genes were focally amplified (MYC, BIRC3, PARD6B, KLF5, and CEBPD), while two of the top ten upregulated genes were focally deleted (PPAP2B, TNC), implying that its role in TGFβ growth-inhibitory signaling drives SWI/SNF loss in PDAC. In summary, we report the SWI/SNF chromatin remodeling complex, likely through mediating TGFβ signaling, to be a major tumour suppressor pathway in PDAC.

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 3930. doi:10.1158/1538-7445.AM2011-3930
Abstract 3931: Whole genome and whole exome sequencing of head and neck cancer
Authors: Stransky Nicolas , Egloff Ann Marie , Tward Aaron , Auclair Daniel , Cibulskis Kristian , Lawrence Michael , Sivachenko Andrey , Berger Michael , Seethala Raja , Sougnez Carrie , Cortes Maria , Winckler Wendy , Gabriel Stacey , Getz Gad , Golub Todd , Grandis Jennifer , Garraway Levi
Published: August 2014

Head and neck cancer is responsible for an enormous cancer burden worldwide, with an estimated 500,000 new cases per year. However, knowledge of the spectrum of genetic alterations that drive this malignancy remains incomplete. Previous studies of this disease have identified recurrent somatic mutations in a few specific genes, but few systematic genome-scale studies have been performed. Accordingly, we have undertaken a pilot study of complete genome/exome characterization in this malignancy.

We obtained genomic DNA from 40 head and neck tumors together with matched normal DNA from whole blood. To date, we have obtained whole exome sequencing of 28 tumor/normal pairs and whole genome sequencing of two tumor/normal pairs. The average base mutation rate is 3.1 × 10-6 (range = 2.9 × 10-7 to 8.8 × 10-6), consistent with rates observed in lung cancer and other tobacco-related malignancies. We also identified 24 high-confidence somatic rearrangements in one sample and 120 in the other sample (including 7 and 44 inter-chromosomal rearrangements, respectively).

In addition to frequent mutations of TP53 (53%), HRAS, PIK3CA, and PTEN, we also observed other recurrently mutated genes that implicate several oncogenic pathways. Furthermore, layering of somatic mutation data onto known pathway information strengthens the evidence for several oncogenic processes not previously implicated in head and neck cancer. Altogether, these data should enhance our understanding of the mechanisms that drive head and neck carcinogenesis and progression and may also illuminate new therapeutic opportunities.

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 3931. doi:10.1158/1538-7445.AM2011-3931
Abstract 3934: Identification of novel cancer DNA sequence variants in human sarcomas
Authors: Abaan Ogan D. , Francis Princy , Pineda Marbin , Walker Robert , Bilke Sven , Davis Sean R. , Meltzer Paul S.
Published: August 2014

Understanding of the genetic basis of cancer initiation and progression is a fundamental goal of cancer research. Identification of cancer variants is of profound importance for both understanding disease mechanism and for developing novel therapies. Soft-tissue sarcomas are multiple uncommon histotypes with features of diverse connective tissue lineages. Although some of their underlying genetic changes have been elucidated, for example in those types which contain etiologic chromosome translocations, in general, the genetics of these tumors is incompletely described. Adult soft tissue sarcomas often exhibit highly complex genomic rearrangements. To search for novel variants in these tumors, we utilized a custom “targeted-resequencing” approach to sequence coding exons from over 1300 known cancer-related genes and candidate gene families in 65 soft-tissue sarcoma patient samples covering several subtypes and their matching normal tissues where available. We used the previously published method of “In-solution capture” to enrich for regions of interest and sequenced both the normals and the tumors using the Illumina GAII platform. The variant calls reveal the distribution of mutations affecting the exons of the targeted regions across histotypes, and reveal the role of critical functional pathways in sarcoma genesis. Preliminary data suggest that TP53 single nucleotide variants are mostly confined to one histotype. This work is an important step in cataloging novel cancer mutations in these cancers, with potential implications for understanding their biology and the development of new therapies.

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 3934. doi:10.1158/1538-7445.AM2011-3934
Abstract 3935: International Cancer Genome Consortium (ICGC)
Authors: Hudson Thomas J. , Jennings Jennifer L.
Published: August 2014

The International Cancer Genome Consortium (ICGC) is coordinating an extensive research effort to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in the major forms of cancer. This information will lead to better ways of diagnosing, treating and preventing cancer. The announcement of the ICGC Goals, Structure, Policies and Guidelines to the international scientific community in 2008 enabled funding agencies and research groups to plan their participation within the ICGC. Over 200 authors engaged in ICGC projects published a Nature paper in April 2010. The paper outlines the ethical framework, study design, use of common standards of data collection and analysis and describes how the projects will proceed. As of November 2010, the ICGC has received commitments from funding organizations in Asia, Australia, Europe and North America for the projects listed in the table (below). Over time, additional nations and organizations are anticipated to join the ICGC.

Each Cancer Genome Project is expected to involve specimens from approximately 500 patients. Over the next ten years, the ICGC expects to produce comprehensive catalogues of the full range of genetic mutations involved in 50 types of cancer, with key factors being the ability to detect all mutated cancer genes, data at the level of individual DNA bases, application of common standards for pathology and technology and comparison data from matched, non-tumour tissue.

The ICGC's informed consent and ethical oversight policies state that cancer patients enrolled in an ICGC-related study should be informed that their participation is voluntary, that their clinical care will not be affected by their participation and that data obtained from analyses using their samples will be made available to the international research community.

The genomic analyses of tumors conducted by ICGC members in the U.K. (breast, lung and skin cancer), Japan (liver cancer), and Australia and Canada (pancreatic cancer) are now available on the ICGC website at www.icgc.org.

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 3935. doi:10.1158/1538-7445.AM2011-3935
Abstract 3941: Amplifications of drug target genes in gastric cancer: Potential clinical implications
Authors: Labots Mariette , Haan Josien C. , Buffart Tineke E. , van Grieken Nicole CT , Tijssen Marianne , Ylstra Bauke , Carvalho Beatriz , van de Velde Cornelis JH , Grabsch Heike I. , Verheul Henk MW , Fijneman Remond JA , Meijer Gerrit A.
Published: August 2014

Background: The treatment of advanced gastric cancer remains a challenge for the clinical oncologist. Once distant metastases are present, median survival is around one year with the most active chemotherapeutic regimen. Besides the recent approval of trastuzumab in combination with chemotherapy, thus far no other molecular targeted agents have been approved for the treatment of this disease. There is an urgent need to improve selection of effective treatment for individual patients. A potentially promising approach for selecting active antitumor agents in individual patients could be the evaluation of tumor DNA for amplifications of genes coding for drug targets.

Material and Methods: 183 primary gastric adenocarcinomas were analyzed by genome wide array Comparative Genomic Hybridization (arrayCGH) using microarrays consisting of 5000 BAC clones. High level amplifications were defined as a minimum of 2 consecutive clones showing a log2 tumor to normal ratio of > 1. Amplification frequencies for each BAC clone were calculated among the 183 tumors, and genes located within the amplicons were identified by using the RefSeq genes in the UCSC genome browser, version hg16/NCBI34. Drug target genes were selected with Ingenuity Pathway Analysis (IPA) and the Pharmacogenomics Knowledge Base (PharmGKB). Genes amplified in at least 4 patients (2%) were classified according to the mechanism of action of the drug interacting with this specific gene.

Results: In 183 gastric cancers a mean number of 2.0 amplifications per tumor (range 0-21) was found. 167 genes out of more than 6000 at these loci were annotated as drug target genes by IPA, with 30 genes having an amplification frequency of at least 4 (2%). Most frequently amplified regions were located on chromosome 6, 8, 11, 16, 17 and 20. Genes for molecular targeting agents included VEGFA (6.5%), ERBB2 (6%), HSP90AB1 (5.5%) and EGFR (3.8%). Interestingly, also genes for non-anticancer agents, including HRH3 (10.4 %) and RARA (4.9%), and potential therapeutic targets such as TNFRSF4B (7.1%) were found. Conclusion: ArrayCGH analysis of a large series of gastric tumors revealed many non-randomly amplified gene loci, including substrates for targeted agents with potential antitumor activity in advanced gastric cancer. Moreover, targets of agents without established anticancer activity were identified as well. Our results provide a molecular rationale for the investigation of new treatment strategies in advanced gastric 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 3941. doi:10.1158/1538-7445.AM2011-3941
Abstract 3943: Affymetrix whole genome microarray analysis of 51 human tumor cell lines representative of 16 different tissues of origin: Unsupervised hierarchical clustering
Authors: Roberts Michael J. , Koratich Michael S. , May Richard D. , Waud William R. , Stackhouse Murray , Penman Andrew D. , Plaxco Meredith S. , Gamble Tommie A. , Berry Kristy L. , Rooney Robert J. , Maxuitenko Yulia Y.
Published: August 2014

The total mRNA for each sample of 51 human tumor cell lines representative of 16 different tissues of origin was split into 3 replicates, and analyzed against the entire human genome using standard Affx WT procedures. Approximately 50% of the samples (25 out of the 51 cell lines tested) exhibited low-level clustering related to their tissue of origin. The remaining 50% (26 out of the 51 cell lines tested) did not cluster with other samples of the same tissue of origin. These data reveal the importance of testing potential anticancer agents in multiple models representative of several different tumors of origin, as there is a 50% chance that the model chosen is not actually representative of the intended tissue of origin. This analysis also showed that the pancreatic cancer cell line CFPAC-1 did not cluster with any other cell line tested, revealing the unique genetic profile of this cell line. Interestingly, the reported lung cancer cell lines NCI-H69 and NCI-H82 clustered more closely with leukemic lines than with lung or any other solid tumor. This is particularly interesting as these lines are known to grow/behave more like a suspension culture than a monolayer. The NCI recently published its genetic analysis of their 60-panel, and they revealed that the MDA-MB-435 cell line, traditionally thought to be a breast cancer cell line, more closely resembled a melanoma line; hence, it was re-classified as a melanoma (likely a metastasized melanoma that was taken from the breast site). Our analysis reveals that another traditional breast cancer cell line, UISO-BCA-1, also clusters more closely with the melanomas (including the MDA-MB-435 cell line), suggesting that this cell line also may have been misclassified. Based on these data, we suggest that any potential anticancer agent showing activity in a particular cell line should be tested in other cell lines that cluster with the active line, and not merely in other lines supposedly representative of the same tissue of origin. Furthermore, in early stage testing, it would be more prudent to test several cell lines from different clusters, rather than several cell lines from different tissues of origin. It follows that by testing orphan drugs against several cell lines from each cluster, it would be possible to significantly narrow (and possibly identify), the likely drug target.

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 3943. doi:10.1158/1538-7445.AM2011-3943
Abstract 3944: PTEN is not directly regulated by miRNA-21 in non-small cell lung cancer
Authors: Sourvinou Ioanna S. , Markou Athina , Kaklamanis Loukas , Tsaroucha Emily G. , Lianidou Evi S.
Published: August 2014

Introduction: PTEN is a well known tumor suppressor gene that plays a crucial role in the regulation of many normal biological processes. Among the mechanisms taking part in its regulation has been demonstrated being miR-21 action, as it has been reported that PTEN consists one of miR-21 target genes. In this study, we speculated on the effect of miR-21 expression levels in non small cell lung cancer tissues towards: a) PTEN mRNA expression levels and b) PTEN protein levels.

Materials and Methods: Thirty pairs of NSCLC fresh-frozen tissues and their corresponding noncancerous tissues were analyzed for the expression of mature miR-21 as well as for the expression of PTEN transcript using RT-qPCR. PBGD was used as a reference gene and for the evaluation of RNA quality in our samples. In parallel, PTEN protein levels were evaluated by immunohistochemistry in the same samples. Deparaffinized sections cut from paraffin-embedded tissue samples were stained with a specific anti-PTEN antibody. Tumor types and stages were determined according to the WHO classification. All samples were analyzed histologically to access the amount of tumor component (at least 70% of tumor cells) and the quality of material.

Results: In 26/30 NSCLC tissues studied (86.7%), PTEN mRNA expression was decreased when compared to adjacent noncancerous tissues, while overexpression of PTEN transcript was perceived in only 4 samples (13.3%). Evaluation of PTEN protein level in these specimens revealed that in 28/30 samples (93.3%), PTEN protein was detected, while in only 2/30 samples (6.7%) PTEN protein loss was observed. The respective data for miR-21 expression levels indicated that PTEN mRNA as well as protein levels were independent of miR-21 expression status in non small cell lung cancer samples.

Conclusion: Our data indicate for the first time that in NSCLC miR-21 expression levels do not directly regulate PTEN protein levels. PTEN protein was detected by IHC in the vast majority of NSCLC tissues despite the fact that PTEN mRNA expression levels were lower in cancerous tissues than in the corresponding noncancerous tissues.

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 3944. doi:10.1158/1538-7445.AM2011-3944
Abstract 3947: MicroRNA-127 (miR127) promotes cell migration and invasion in lung adenocarcinoma cells
Authors: Ho Chiu-Yi , Lee Tai-Lin , Hsu Hui-Chen , Chen Jeremy Jian-Wei , Tsai Meng-Feng
Published: August 2014

MicroRNAs (miRNAs) are small non-coding RNAs, approximately 20-23 nucleotides in length. The specific functions of miRNAs involved in several cellular processes, including metabolism, development, differentiation, proliferation, apoptosis and tumorigenesis. In order to identify the invasion/metastasis related miRNA in lung cancer, the cell line model (lowly invasive lung cancer cells, CL1-0, and highly invasive lung cancer cells, CL1-5) and human miRNA microarray were carried out. In this study, we selected one of the invasion/metastasis related miRNAs, miR-127, derived from our microarray results for further functional characterization. Recently reports have indicated that human miR-127 was highly expressed in normal prostate and bladder tissues but was remarkably down-regulated in the corresponding tumors. miR-127 may function as a tumor suppressor in human bladder and prostate cancer cells. However, the role of the miR-127 in lung cancer cell proliferation, migration and invasion ability still remains unclear. The miR-127 expression level in various invasive capability lung cancer cell lines were also verified using stem-loop real time RT-PCR. We have constructed and established a miR-127 constitutive expression system in CL1-0 lung cancer cells using pSilencer3.1 vector, and we also knockdown the miR-127 expression in CL1-5 and A549 lung cancer cells using anti-miR127 modified oligonucleotide. Our results shown that over-expression of miR-127 can increase lung cancer cell proliferation, migration, and invasion ability. Finally, we suggest that miR-127 may be acting like an oncogene in lung adenocarcinoma cells. These results will provide important information and help us to understand the roles of miR127 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 3947. doi:10.1158/1538-7445.AM2011-3947
Abstract 3949: Micro-RNA regulated EGFR expression in head and neck squamous cell carcinoma
Authors: Hauser Belinda R. , Califano Joseph , Gu Xinbin , Hao Yubin
Published: August 2014

Purpose: Each year in the United States there are more than 65,000 Americans diagnosed with head and neck cancer and 25,000 die from this disease. Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with complex molecular abnormalities, including overexpression of epidermal growth factor receptor (EGFR). The overexpression of EGFR is seen in 80-90% of HNSCC cases and has been shown to be an indicator of poor prognosis and survival in oral cancer patients. The molecular mechanism of EGFR gene expression is poorly understood in HNSCC. MicroRNAs are a new class of posttranslational regulators of gene expression and are a useful target in understanding EGFR gene expression in HNSCC. We hypothesize that microRNAs may play an important role in EGFR gene overexpression during HNSCC processes. Design Methods: We generated stably expressing exogenous miRNA-7 or miRNA-128 in cell lines (JHU-06,-011,-013,-019, -022, and -029 using lentivirus infection, performed colony formation assays to determine cell growth and proliferation, QRT-PCR to analyze gene expression, and Western blot analysis to evaluate protein expression. Results: We found that the miR-7 and -128 transfection efficiency were quite different in these six cell lines. The transfected cell lines stably expressed exogenous miR-7 or -128. Compared with the control cells, the levels of EGFR protein and cell viability were significantly lower in miR-7, -128 transfected HNSCC cell lines. CONCLUSION: We successfully constructed the stably expressing exogenous miR-7, -128 HNSCC cell lines and validated that miR-7,-128 can down-regulate EGFR expression by specifically targeting the EGFR mRNA 3’UTR. MiR-7 and miR-128 have potential to serve as a therapeutic approach to specifically target EGFR in HNSCC. This work was supported in part by grants P20 CA118770 from National Cancer Institute.

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 3949. doi:10.1158/1538-7445.AM2011-3949
Abstract 395: Chemokine ligand 7 expression in liver metastasis of colorectal cancer
Authors: Cho Yong Beom , Hong Hye Kyung , Shin Hee Jung , Choi Hee-Jung , Kim Seok-Hyung , Choi Yoon-La , Choi So-Jung , Kim Jhingook , Kim Hee Cheol , Yun Seong Hyeon , Lee Woo Yong , Chun Ho-Kyung
Published: August 2014

The main cause of death for colorectal cancer (CRC) patients is the development of metastatic lesions at sites distant from the primary tumor. Therefore, it is important to find biomarkers that are related to the metastasis and to study the possible mechanism. Recent data have shown that soluble attractant molecules called chemokines support the metastasis of certain cancers to certain organs. To identify molecular regulators that are differentially expressed in liver metastasis of CRC, PCR array was performed and CCL7 showed remarkable overexpression in liver metastatic tumor tissues. To validate the result of PCR array, 30 patients with primary CRC and liver metastases were selected. Immunohistochemistry and real-time PCR analysis showed that CCL7 was expressed in normal colonic epithelium and the expression was higher in liver metastases than in primary CRC. CCR1, CCR2, and CCR3, receptors of CCL7, were not expressed in normal colonic epithelium nor colon and metastatic cancer, but expressed in normal hepatocytes and stroma by immunohistochemical staining. Real-time PCR showed that the expressions of CCR1, CCR2, and CCR3 were also higher in liver metastases than in primary CRC. There would be chemokine/chemokine receptors interactions between CCL7 and its receptors in liver, which supply the environment for metastatic colon cancer cells to survive and proliferate in liver.

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 395. doi:10.1158/1538-7445.AM2011-395
Abstract 3954: Identification of microRNAs epigenetically silenced in bladder cancer
Authors: Shimizu Takashi , Suzuki Hiromu , Kitamura Hiroshi , Yamamoto Eiichiro , Imai Kohzoh , Tsukamoto Taiji , Toyota Minoru
Published: August 2014

Purpose: Bladder cancer is the one of the most common malignancies in the urothelial tract. MicroRNAs (miRNAs) are small, non-coding RNAs that control gene expression post-transcriptionally, either by degradation of target mRNAs or by inhibition of protein translation. MiRNAs are involved in cancer development and progression, acting as tumor suppressors or oncogenes. Recent studies have demonstrated a role of DNA methylation in silencing miRNAs in bladder cancer. The aim of current study is to identify bladder cancer-related miRNAs by screening epigenetically silenced miRNAs in bladder cancer.

Materials & Methods: Two bladder cancer cell lines (T-24, UM-UC3) were treated with or without 5-aza-2’deoxycytidine (5-aza-dC) and 4-phenylbutyric acid (4-PBA), and expression of mature miRNAs was examined using a TaqMan Low Density Array System. We used UCSC genome browser to examine if CpG islands are located in the proximal upstream of the miRNAs upregulated after drug treatment. Methylation-specific PCR (MSP) and bisulfite pyrosequencing were carried out to analyze methylation status of the miRNA genes in bladder cancer cell lines and primary bladder cancer specimens.

Results: Of 664 miRNAs examined, 208 miRNAs were up-regulated (>5-fold) in T24 cells, and 200 miRNAs were up-regulated in UM-UC3 cells, respectively. Among the miRNAs, 146 were commonly up-regulated in both T-24 and UM-UC3 cells. Among those 146 miRNAs, 36 miRNAs contain CpG islands in their 5’ end of the genes, and further analyzed. Methylation-specific PCR (MSP) was carried out, and 12 miRNAs showed aberrant methylation in bladder cancer cell lines. Bisulfite pyrosequencing of these 12 miRNAs was carried out, and we identified hypermethylation of 12 miRNAs in cultured and primary bladder cancer specimens.

Conclusions: Our results suggest that DNA methylation is associated with miRNAs silencing in bladder cancer, and that these miRNAs may have a role in the development and progression of bladder 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 3954. doi:10.1158/1538-7445.AM2011-3954
Abstract 3957: Role of miRNA-211 in melanocyte and melanoma cells
Authors: Maddodi Nityanand D. , Madhavan Shajil , Devi Sulochana , Setaluri Vijayasaradhi
Published: August 2014

MicroRNAs (miRNAs) are regulatory RNAs that regulate gene expression. Evidence is accumulating that miRNAs are involved in almost all aspects of tumor biology including tumor cell survival, proliferation and migration. Here, we report that miRNA-221, which maps to the sixth intron of TRPM1 gene (a suppressor of melanoma metastasis), is highly expressed in melanocytes and its expression is reduced in primary and metastatic melanoma cell lines. Expression of miRNA-211 correlates with expression of TRPM1, a transient receptor potential family member calcium channel protein that we showed to be involved in regulation of melanocyte calcium homeostasis and melanin pigmentation. TRPM1and miRNA-211 expression are significantly lower in rapidly proliferative melanocytes compared to the slow growing, differentiated melanocytes. Expression of RAB22A (member of the RAS family of small GTPases), a predicted RNA target of miRNA-211is inversely correlated with the expression of miRNA-211and TRPM1 in melanocytes. Inhibition of miRNA-211 expression by anti-miR211 inhibited the growth of rapidly growing melanocytes. Ectopic expression of miRNA-211in melanoma cells inhibit growth and reduced their migration. We propose that activation of endogenous miRNA-211 expression or targeted delivery of miR-211 in melanoma is a potential therapeutic option for treatment of cutaneous melanoma.

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 3957. doi:10.1158/1538-7445.AM2011-3957
Abstract 3958: A miRNA inhibitor screen for synthetic lethal interactions in KRAS-driven NSCLC
Authors: Borkowski Robert , Du Liqin , Minna John D. , Gazdar Adi F. , Pertsemlidis Alexander
Published: August 2014

Lung cancer, especially non-small cell lung cancer (NSCLC), is currently the leading cause of cancer fatalities in the United States, accounting for 30% of the fatalities in males, and 26% in females. Additionally, the five-year survival rate for individuals affected by lung cancer has only improved by 3% in the past 35 years. As suggested by the survival data, very few effective treatment options are available for NSCLC, and many vary dramatically in efficacy depending on the genetic status of the tumor. In particular, the presence of mutant KRAS in NSCLC serves as a negative predictor for drug efficacy. KRAS mutations are found in ∼22% of NSCLC tumors, and tumors harboring these mutations are especially refractory to treatment.

We have identified synthetic lethal miRNAs in the background of KRAS-dependence through a four-armed miRNA inhibitor screen. A miRNA inhibitor screen can serve to not only identify miRNAs involved in context-dependent survival, but also genes and pathways that would be obscured by genomic redundancy in a conventional RNAi screen. Using a comprehensive library of miRNA inhibitors coupled with an endpoint assay for cell viability, we can identify miRNAs that modulate viability or paclitaxel sensitivity in KRAS-dependent NSCLC cell line NCI-H358 with minimal effect in the wild-type KRAS cell line NCI-H1993. Candidate miRNAs are validated in an expanded panel of ten cell lines including four KRAS mutant, four KRAS wild-type, and two immortalized human bronchial epithelial cell lines. The miRNAs identified here will allow us to elucidate vulnerable pathways in KRAS-dependent tumors that can be exploited for a therapeutic or predictive benefit in a typically difficult to manage class of tumor.

This research was supported by NIH R01 CA129632 from the National Cancer Institute and by P50 CA70907 from the UT Southwestern/MD Anderson Cancer Center Lung Specialized Program of Research Excellence.

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 3958. doi:10.1158/1538-7445.AM2011-3958
Abstract 3959: Growth suppression by TGF-β in responsive colon carcinoma is opposed by miR-20a through mechanisms altering p21WAF1 up-regulation
Authors: Sokolova Viktorija , Fiorino Antonio , Reid James F. , Crippa Elisabetta , Pierotti Marco A. , Gariboldi Manuela
Published: August 2014

Loss of response to TGF-β occurs in many cancers and disruption of its regulatory circuitry appears as a central event in the genesis of colorectal cancer (CRC) malignancy. Lack of inhibitory response to TGF-β is common to most colon cancer cell lines. However, inactivating mutations at receptors and transducers occur in less than a half of neoplastic colon tissues, which underscore the significance of additional mechanisms diverting TGF-β growth suppression. In this context, abrogation of TGF-β response by some miRNAs has been recently reported.

By searching for miRNAs in regions showing copy number changes and concordant gene expression in 36 sporadic CRCs compared to their normal counterpart, we identified the miR-17-92 cluster on the 13q31 locus, which is gained and highly expressed at early stages of CRC. MiR-20a from miR-17-92 cluster is a paralog of the miR-106b, which affects TGF-β sensitivity in gastric carcinoma. We hypothesized an involvement of miR-20a in the suppression of TGF-β response in CRCs and selected the TGF-β sensitive FET colon carcinoma, expressing low miR-20a levels, to investigate the relationship between enhanced expression of miR-20a and TGF-β sensitivity and address growth inhibition.

We report that miR-20a affects regulation of p21WAF1 expression, has a negative and significant effect on the cytostatic response mediated by TGF-β – evaluated by BrdU incorporation, MTT assay, and cell-cycle analysis – but shows little effect on TGF-β untreated cells. Although p21WAF1 transcript and protein are significantly decreased in cells treated or not with the cytokine, we could observe that the p21 up-regulation driven by TGF-β is strongly subverted by miR-20a. One potential mechanism of p21 down-modulation by miR-20a can be the targeting of its 3’UTR, as occurring for miR-106a. Moreover, we could observe that miR-20a is also able to block the transactivation of the 2.3-kb p21 promoter upon TGF-β stimulation, as assessed by luciferase-based assay, but not the activation of the Smad3/4-reponsive reporter. Down-modulation of c-Myc by TGF-β, crucial to regulation of p21 transcription, is also subverted by miR-20a delivery into cells.

Our experiments suggest for miR-20a an interference with the TGF-β homeostasis in colon addressing the up-regulation of p21 expression, through mechanisms involving more effectors of the TGF-β cascade. Overall, miR-20a seems to participate in the abrogation of this key regulatory response in colonic epithelium.

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 3959. doi:10.1158/1538-7445.AM2011-3959
Abstract 3963: MicroRNA-124 and microRNA-1, commonly lost in glioma, coordinately target sphingosine kinase-1 in glioma cells
Authors: Godlewski Jakub A. , Bronisz Agnieszka , Van Brocklyn James , Wang Yan , Lawler Sean , Chiocca E. Antonio
Published: August 2014

Glioma (Glioblastoma multiforme, GBM) is the most common and the most aggressive form of brain tumor. As its Latin name implies, glioma is characterized by enormous heterogeneity and many different genes and cellular pathways responsible for glioma genesis and progression have been described. One of them is Sphingosine Kinase-1 (SPHK-1), a bona fide oncogene in glioma, whose marked up-regulation of expression and activity is responsible for the poor patient outcome due to escalating proliferation and invasiveness of glioma cells.

MicroRNAs are short, non-coding regulators of the gene expression and deregulation of their expression is a frequent event in the formation and progression of many malignancies including glioma. Among these deregulated microRNAs, microRNA-124 is the most downregulated microRNA. It has been shown to promote neuronal differentiation and inhibit glioma cell proliferation and to target CDK6. Here we show that microRNA-1 is also severely downregulated in glioma patients and that it acts coordinately with microRNA-124 to target SPHK-1. We show that both microRNAs directly target the SPHK-1 3’UTR and that such targeting results in the decrease of both SPHK-1 expression and activity. We also demonstrate that overexpression of both microRNA-124 and microRNA-1 causes a significant increase in the frequency of apoptotic cells and marked decrease in glioma cell proliferation and invasiveness.

Additionally, we show that microRNA-1 directly targets another glioma oncogene – Annexin2A (ANXA2). Targeting of ANXA2 by microRNA-1 impairs glioma cell-cell adhesion and glioma spheroid formation, which effect can be partially rescued by the overexpression of ANXA2 with a mutated microRNA-1 target site but not by wild type ANXA2.

Our results provide another target of therapeutic importance for microRNA-124 in glioma cells. Here we show that microRNA-124, along with microRNA-1 can exert profound effect on glioma cells by inhibiting expression and activity of SPHK1 and that additional effects caused by microRNA-1 are likely mediated through targeting ANXA2.

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 3963. doi:10.1158/1538-7445.AM2011-3963