bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 530: MicroRNA expression profiling in MMTV-neu breast cancer mouse model
Authors: Piovan Claudia , Leva Gianpiero D. , Cheung Douglas , Fassan Matteo , Kumar Arpan , Palmieri Dario , Iorio Marilena V. , Croce Carlo M.
Published: May 2015

In addition to mRNA gene expression profiling, miRNA expression analyses of human breast cancers have further demonstrated another layer of the molecular diversity of this disease and may potentially be a useful diagnostic and prognostic tool for breast cancer therapy and treatment. The development and use of relevant mouse models that closely reflect genetic alterations found in human breast cancers is critical to understand malignant progression in this disease and to test developmental therapeutics. The Mammary Tumour Virus (MMTV) Long Terminal Repeat (LTR) promoter-driven HER2/neu transgenic mouse model was developed to directly assess the effects of mammary gland specific expression of the neu protooncogene.

Global miRNA expression profiling was performed on tumours derived from the MMTV-HER2/neu model. Normal mammary glands from FVB wild-type mice, HER2 overexpressing mammary glands from MMTV-HER2/neu transgenic mice and tumours derived from this model at different stages of the tumourigenic process were collected and microRNA expression profiling performed on them by Nanostring analysis. Differential expression of selected miRNAs, obtained by Nanostring screening, was further confirmed by quantitative Real Time analysis.

By analyzing global miRNA expression profile on tissues collected from MMTV-HER2/neu mice at different stages of the tumourigenesis, we identified significant differences in miRNA expression patterns between tumours and normal mammary tissue and between non-metastatic and metastatic tumours. miRNA expression characterization of tumours at various stages of development along with gene expression in mouse models would profoundly enhance our knowledge of progressive genetic changes associated with oncogene-induced events in breast cancer.

Citation Format: Claudia Piovan, Gianpiero Di Leva, Douglas Cheung, Matteo Fassan, Arpan Kumar, Dario Palmieri, Marilena V. Iorio, Carlo M. Croce. MicroRNA expression profiling in MMTV-neu breast cancer mouse model. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 530. doi:10.1158/1538-7445.AM2014-530
Abstract 5303: Uptake and Efflux of 2-amino-1-methyl-6-phenylimidazo [4, 5-b] pyridine (PhIP) in human adipocytes
Authors: Yao-Borengasser Aiwei , Rogers Lora J. , Kadlubar Susan A.
Published: May 2015

Obesity has been linked to the development of numerous chronic diseases, including breast cancer. Although the association between obesity and breast cancer risk is clear in postmenopausal women, high body mass index (BMI) appears to protect against breast cancer in pre-menopausal women. The mechanistic basis of this “obesity paradox” is unknown. One hypothesis is that abundant adipose tissue in the mammary gland functions as a storage depot for lipid-soluble carcinogens of dietary origin, initially offering protection against exposures. Heterocyclic amines (HCAs) are pro-carcinogens that are formed from high-temperature cooked meats. Exposures to these compounds are ubiquitous in Western diets and 2-amino-1-methyl-6-phenylimidazo [4, 5-b] pyridine (PhIP), the most mass-abundant HCA, is classified as a “probable human carcinogen.” To determine rates of influx of PhIP into adipocytes, differentiated Simpson-Golabi-Behmel Syndrome (SGBS) adipocytes were treated with 5 µM plus 0.02 µCi 14C-PhIP for 0.5, 1, 2, 5, 10, 15, 30, 45, and 60 minutes, and media was removed at time points. Cells were re-suspended in scintillation fluid, and counted with a 1450 LSL & Luminescence Count (Perkin Elmer). Influx was rapid and PhIP continued to accumulate in the cells between 15 and 60 minutes. To determine efflux, SGBS cells were exposed to 5 µM plus 0.02 µCi 14C-PhIP and allowed to equilibrate for 30 minutes. Media was removed and the cells were washed with PBS. Radioactivity retained in SGBS cells was counted at 0.5, 1, 5, 10, 30, and 60 minutes. SGBS cells retained 50% of the radioactivity for more than 10 minutes, compared to other studies where PhIP efflux from pancreatic acinii and hepatocytes occurs within the first 15 seconds. Our data demonstrates that human adipocyte efflux is significantly slower than those in other type of cells reported in the literature, suggesting that human adipocytes can sequester PhIP, thereby protecting the breast from dietary exposure to carcinogens.

Citation Format: Aiwei Yao-Borengasser, Lora J. Rogers, Susan A. Kadlubar. Uptake and Efflux of 2-amino-1-methyl-6-phenylimidazo [4, 5-b] pyridine (PhIP) in human adipocytes. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5303. doi:10.1158/1538-7445.AM2014-5303
Abstract 5304: Inhibition of kallikrein-related peptidase-4 by SPINK1
Authors: Koistinen Hannu , Domanskyy Mykola , Stenman Ulf-Håkan
Published: May 2015

Serine protease inhibitor Kazal type-1 (SPINK1), also known as TATI (tumor-associated trypsin inhibitor), is a 56 amino acid trypsin inhibitor, whose levels are elevated in several cancers, including those of ovaries, prostate, bladder and colon. Some mutations in SPINK1, such as N34S, are associated with pancreatitis. Furthermore, SPINK1 was recently found to be associated with ETS rearrangement-negative prostate cancers and to stimulate the invasion of prostate cancer cells, perhaps by activating the EGF-receptor. Recently, SPINK3, the mouse ortholog of SPINK1, was identified as a potent inhibitor of human kallikrein-related peptidases (KLKs) -2, -3 (PSA) and -5. We studied the effect of human SPINK1 on KLK2, -3 and -4. Synthetic cDNAs encoding wild-type and mutant forms of 56 amino acid SPINK1 without signal peptide were expressed in E. coli. The SUMOstar E. coli Expression System was used for expression and purification of recombinant SPINK1. Final purification was done using an antibody affinity column and HPLC. Enzyme activities were measured using chromogenic substrates and recombinant human KLK2 and -4, and KLK3 purified from seminal fluid. SPINK1 was found to efficiently inhibit KLK4, while KLK2-inhibition was less pronounced. KLK3 was not inhibited at all. SPINK1 mutant (K41Y), which does not inhibit trypsins, did not inhibit KLK4 either, while pancreatitis associated mutant (N34S) showed strong inhibition. It is possible that SPINK1 has a dual role in cancer, i.e., it induces tumor growth by stimulating the EGF-receptor, while by inhibiting the activity of trypsin and KLKs it suppress metastasis and activation of protease-activated receptors (PARs), which promote tumor growth.

Citation Format: Hannu Koistinen, Mykola Domanskyy, Ulf-Håkan Stenman. Inhibition of kallikrein-related peptidase-4 by SPINK1. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5304. doi:10.1158/1538-7445.AM2014-5304
Abstract 5307: Development of pIMAGO for universal detection of protein phosphorylation
Authors: Iliuk Anton , Li Li , Pan Li , Tao Weiguo A.
Published: May 2015

Protein phosphorylation, as the most common covalent modification of proteins, plays a critical role in the regulation of many cellular functions. Irregularities in phosphorylation network are a major cause of onset and progression of many diseases, most notably cancer. Consequently, detection of protein phosphorylation is essential in further understanding of cellular signaling pathways and mechanisms of cell growth and proliferation. To assist in effective phosphorylation analyses, we introduce here a novel technique based on soluble nanopolymers with excellent solubility, compact spherical shape and chemical homogeneity. Soluble nanopolymers functionalized with Ti(IV) ions have shown highly versatility and allow for highly efficient analyses of phosphorylation and signaling pathways.

We devise here a novel strategy, termed pIMAGO (phospho-imaging), for effective detection of phosphoproteins on a membrane in Western Blot format. Unlike antibody-based strategies, the new method is capable of selectively binding a phosphorylated residue independent of amino acid microenvironment. It shows no preference for either of the phosphosites, and thus holds great promise in biological analyses where the site of phosphorylation is not known or its specific antibody is not available. Using this technique, the phosphorylation levels of proteins of interest under physiological conditions can be readily detected as part of a standard Western Blot procedure without the need for radioactivity or expensive phosphosite-specific antibodies. The utility of the approach has been demonstrated using standard mixtures of proteins and by in vitro kinase and phosphatase assays. In addition, multiplexing capabilities of pIMAGO are presented, a feature often unavailable during antibodies-based detection. Finally, we further confirmed that the technique is sensitive and specific enough to detect endogenous phosphorylation changes by analyzing physiological signaling in number of endogenous protein complexes isolated directly from cells.

Citation Format: Anton Iliuk, Li Li, Li Pan, Weiguo A. Tao. Development of pIMAGO for universal detection of protein phosphorylation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5307. doi:10.1158/1538-7445.AM2014-5307
Abstract 5313: Phosphoproteomic analysis with reverse phase protein array identifies N-myc downstream regulated gene 1 (NDRG1) as a biomarker of phosphatidylinositol-3-kinase (PI3K)α inhibitor activity in a PTEN-deficient glioma cell line
Authors: Inoue Takeomi , Iwata Naoko , Nishiwaki Eiji , Kirii Yasuyuki
Published: May 2015

Aberrant activation of phosphoinositide 3-kinase (PI3K) signaling is commonly reported in cancer, and leads to deregulation of several intracellular processes, including cell survival, growth, proliferation and migration. PI3K activates AKT, serum/glucocorticoid regulated kinase (SGK), phosphoinositide -dependent kinase 1 (PDK1), mammalian target of rapamycin (mTOR), and several other molecules involved in cell progression and survival. Reports have also indicated that the deletion of the gene encoding the tumor suppressor phosphatase and tensin homologue (PTEN) is one of the key factors controlling activation of the PI3K pathway. Glioblastoma (GBM), the most common malignant brain tumor in adults, represents a compelling disease for kinase inhibitor therapy. Although many therapies to target the Ras-PI3K-mTOR axis in GBM have been attempted, their efficacies have not been pronounced, presumably because of the complexity of PI3K mediated signaling. To elucidate the role of PTEN in PI3K signaling, the phosphorylation status of two glioma cell lines, LN229 (wild type PTEN) and U-87 MG (PTEN deficient) was investigated with phosphoproteomic reverse phase protein array (RPPA). When basal phosphorylation was compared between both cell lines, the phosphorylation of N-myc downstream regulated gene 1 (NDRG1) (Thr346), a physiological substrate of SGK1, was increased in U-87 MG cells compared with levels in LN229 cells. These data suggest that PTEN deletion affects the phosphorylation status of NDRG1 in U-87 MG cells. Following treatment with PIK-90, a PI3Kα inhibitor, phosphorylation of Akt (Ser473) and its direct substrate PRAS40 (Thr246) were decreased in both cell lines, however, NDRG1 (Thr346) phosphorylation was strongly inhibited only in U-87 MG cells. These results suggest that the differential effects of PIK-90 on LN229 and U-87 MG cells is PTEN dependent, and that detecting NDRG1 (Thr346) phosphorylation could be a biomarker for PI3Kα inhibitor treatment in PTEN deleted cancer cells. Ongoing studies are focusing on elucidating the mechanism of action of PIK-90 in glioma cell lines.

Citation Format: Takeomi Inoue, Naoko Iwata, Eiji Nishiwaki, Yasuyuki Kirii. Phosphoproteomic analysis with reverse phase protein array identifies N-myc downstream regulated gene 1 (NDRG1) as a biomarker of phosphatidylinositol-3-kinase (PI3K)α inhibitor activity in a PTEN-deficient glioma cell line. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5313. doi:10.1158/1538-7445.AM2014-5313
Abstract 5319: The role of ISBER (The International Society for Biological and Environmental Repositories) in cancer research
Authors: Garcia Debra L. , Sexton Katherine , Grizzle William E. , Betsou Fay
Published: May 2015

High quality biospecimen collections are essential for biomarker discovery in Cancer Research. Biomarker analytical and clinical performance depends heavily upon the pre-analytical variation of biospecimens used. For this reason, standardization of procedures is of utmost importancein the collection, preparation, and storageof biospecimens, making it possible to accurately associateprocessing methods withappropriate end-use applications. 

The International Society for Biological and Environmental Repositories (ISBER) is a professional society of organizations and individuals who share an interest in promoting consistent, high quality standards, ethical principles, and Best Practices in biospecimen banking. ISBER, with almost 500 individual and organizational members throughout the world, is the leading international forum for promoting innovation in the science and management of biospecimen collection, processing, storage, distribution, and use.

ISBER educational resources and meetings focus on a wide variety of topics from biorepository development, maintenance, and improvement, to technical concerns regarding equipment, quality assurance and control, regulation, human subject privacy, and confidentiality. Additional tools developed by ISBER, many of which are web-based, are available to assist researchers in ensuring biospecimen quality and biorepository compliance with Best Practices. ISBER routinely provides information about existing biorepositories and their biospecimen collections as well. For more information, please visit http://www.ISBER.org.

Citation Format: Debra L. Garcia, Katherine Sexton, William E. Grizzle, Fay Betsou. The role of ISBER (The International Society for Biological and Environmental Repositories) in cancer research. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5319. doi:10.1158/1538-7445.AM2014-5319
Abstract 5324: Pan-cancer identification of mutated pathways and protein complexes
Authors: Leiserson Mark D. , Vandin Fabio , Wu Hsin-Ta , Dobson Jason R. , Raphael Benjamin R.
Published: May 2015

Large-scale cancer sequencing efforts such as The Cancer Genome Atlas (TCGA) and others have shown that tumors exhibit extensive mutational heterogeneity with relatively few genes mutated at significant frequency and many genes mutated in only a small number of individuals. This long tail phenomenon complicates the identification of driver mutations by their observed frequency. The long tail is explained in part by the fact that driver mutations target genes in signaling and regulatory pathways, and these pathways may be perturbed by different mutations in different tumors.

We developed two complementary algorithms, HotNet2 and Dendrix++, to analyze combinations of mutations in known or novel pathways. HotNet2 uses prior knowledge of pathways and protein complexes represented in a genome-scale protein-protein interaction network, and identifies significantly mutated subnetworks using a heat diffusion model. HotNet2 simultaneously assesses both the significance of mutations in individual proteins and the local topology of protein interactions. Dendrix++ identifies combinations of mutations de novo, without prior knowledge of pathways or protein interactions, by finding sets of mutations that are mutually exclusive across the tumor cohort. There are numerous examples of mutually exclusive mutations between interacting proteins; e.g. BRAF and KRAS in colorectal cancer. Dendrix++ generalizes this idea to find larger groups of mutually exclusive mutations.

We applied HotNet2 and Dendrix++ to whole-exome sequencing and copy number aberration data from 3299 samples of twelve tumor types from TCGA Pan-Cancer project. Both algorithms identified gene sets that overlap well-known cancer pathways (e.g. TP53, MAPK, and RAS signaling pathways), as well as genes and complexes with less characterized roles in cancer (e.g. the cohesin and condensin complexes). HotNet2 subnetworks also contained novel candidate cancer genes that were rarely mutated in this cohort and thus not reported by single-gene tests of significance, including KDM5A, SHPRH, and ARID4A, each of which interacts with well-known cancer genes. Many of these gene sets have biological functions often perturbed in cancer, such as chromatin modification (e.g. the SWI/SNF and BAP1 complexes) and DNA damage repair (e.g. SHPRH). These results demonstrate the ability of HotNet2 and Dendrix++ to identify novel combinations of mutations in thousands of tumors, prioritizing genes and mutations in the long tail for further experimental studies.

Citation Format: Mark D. Leiserson, Fabio Vandin, Hsin-Ta Wu, Jason R. Dobson, Benjamin R. Raphael. Pan-cancer identification of mutated pathways and protein complexes. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5324. doi:10.1158/1538-7445.AM2014-5324
Abstract 5328: GIAB: Genome reference material development resources for clinical sequencing
Authors: Xiao Chunlin , Zook Justin , Trask Shane , Sherry Stephen ,   the Genome-in-a-Bottle Consortium
Published: May 2015

Reference materials play important roles in validating performance of sequencing platforms and enabling regulations of clinical applications. Genome-in-a-Bottle (GIAB) project is a collaboration between NIST, FDA, NCBI, academic sequencing groups, sequencing technology developers, and clinical laboratories to develop analytical-grade reference genome materials and accompanying performance metrics for the development of regulations and professional standards for clinical sequencing. NCBI is serving as the Data Coordination Center (DCC) and repository for the raw sequencing reads, mapped alignments, genotypes, and other details for each sample on a dedicated FTP site (ftp://ftp-trace.ncbi.nih.gov/giab/ftp). Here we describe the processes of data generations and data submissions, and how the community can access the data. We are also developing a genome browser for data visualization. GIAB consortium plans to release data to the public on a regular basis.

Citation Format: Chunlin Xiao, Justin Zook, Shane Trask, Stephen Sherry, the Genome-in-a-Bottle Consortium. GIAB: Genome reference material development resources for clinical sequencing. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5328. doi:10.1158/1538-7445.AM2014-5328
Abstract 5333: A mathematical model for the kinetics of metastasis formation based on SEER data
Authors: El-Kareh Ardith W. , Secomb Timothy W.
Published: May 2015

Metastasis is responsible for most cancer mortality, yet many questions remain about how best to describe the kinetics of metastasis formation mathematically. Because the initial step of metastasis is the detachment of cells from a tumor mass, the rate of formation of new metastases is assumed to depend on the size of the original tumor mass. A power-law dependence, rather than linear proportionality, has been assumed, since access to blood vessels and lymphatics becomes more limited as tumor mass increases. Under this assumption, the cumulative distribution of fraction of patients not showing detectable metastases at diagnosis should decrease monotonically as tumor size at detection increases. Using data from the NCI's SEER (Surveillance, Epidemiology, and End Results) 1973-2010 database, it is shown here that this relation in fact shows non-monotonic behavior at larger detection sizes. A mathematical model for tumor growth and metastasis kinetics is developed to show that this implies that proliferation rates and metastatic rates are not independently distributed across the patient population, but rather, show some correlation. The model is further applied to deduce quantitative information about the size-dependence of the rate of metastasis. Kaplan-Meier curves stratified by tumor size, also computed from SEER 1973-2010 data, provide an additional data source for determining model parameters. It is found that accounting for age dependence is necessary for fitting these curves. Two possible age-related effects: a lower lethal tumor burden threshold; and an increased coefficient of metastatic rate due to declining immunity; are considered in the model, and a comparison is made of their ability to describe the observed age-dependence. In sum, the model shows how SEER data can be used to deduce information about the kinetics of metastasis formation, and is expected to have application in optimization of the treatment of metastatic tumors as well as screening schedules.

Citation Format: Ardith W. El-Kareh, Timothy W. Secomb. A mathematical model for the kinetics of metastasis formation based on SEER data. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5333. doi:10.1158/1538-7445.AM2014-5333
Abstract 5347: DNA repair protein Rev7 is required for primordial germ cell maintenance in the mouse
Authors: Murakumo Yoshiki , Watanabe Naoki , Mii Shinji , Asai Masato , Asai Naoya , Niimi Kaoru , Kato Takuya , Enomoto Atsushi , Takahashi Masahide
Published: May 2015

REV7 is involved in DNA repair, cell cycle regulation, gene expression and carcinogenesis. In vitro studies show that REV7 interacts with several proteins and regulates their function, and that downregulation of REV7 expression in human cancer cells results in enhancement of sensitivity to DNA damaging agents. It has been reported that human REV7 is highly expressed in the adult testis by northern blot analysis. However, the significance of REV7 in mammalian development has not been elucidated. Here, we present analyses of Rev7-deficient (Rev7-/-) mice to clarify the significance of Rev7 in mouse development. In wild-type mice (Rev7+/+), Rev7 expression was ubiquitously observed in the embryo and confined to germ cells in the testes after birth. Rev7-/- mice exhibited growth retardation and a partial embryonic lethal phenotype. Mice that survived to adulthood were infertile in both sexes and showed germ cell aplasia in the testes and ovaries. Analyses of Rev7-/- embryos revealed that primordial germ cells (PGCs) were present at embryonic day 8.5 (E8.5). However, progressive loss of PGCs was observed during migration, and PGCs were absent in the genital ridges at E13.5. An increase of apoptotic cells was detected not only among PGCs but also in the forebrain of the Rev7-/- embryo, while cell proliferation was unaffected. Gene expression analysis of E8.5 embryos showed upregulation of Oct4 and Nanog and downregulation of c-Kit and Rev3 in Rev7-/- embryos compared with those in Rev7+/- embryos. These findings indicate that Rev7 is essential for PGC maintenance by prevention of apoptotic cell death in the mouse.

Note: This abstract was not presented at the meeting.

Citation Format: Yoshiki Murakumo, Naoki Watanabe, Shinji Mii, Masato Asai, Naoya Asai, Kaoru Niimi, Takuya Kato, Atsushi Enomoto, Masahide Takahashi. DNA repair protein Rev7 is required for primordial germ cell maintenance in the mouse. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5347. doi:10.1158/1538-7445.AM2014-5347
Abstract 535: Expression of miR-21 in cancer associated fibroblasts in lung adenocarcinoma
Authors: Kunita Akiko , Morita Shigeki , Fukayama Masashi
Published: May 2015

Lung cancer is the leading cause of cancer mortality worldwide, and novel therapeutic targets and molecular diagnostic markers are highly warranted. Micro RNAs (miRNAs) are a class of small non-coding RNAs associated with a variety of cancer. miRNA-21 is an “oncomiR” and upregulated in many cancers, including lung cancer, and high miR-21 levels have been associated with poor prognosis. To determine the localization of miR-21 and to compare its expression levels, we performed in situ hybridization of miR-21 on 89 mixed subtypes of lung adenocarcinoma. miR-21 was predominantly expressed in cancer associated fibroblasts (CAF)s expressing α-SMA, with no difference in expression between non-invasive and invasive component. In addition, stromal miR-21 expression was significantly associated with decreased overall survival (p=0.0021). In functional analyses of miR-21 in vitro, miR-21 was overexpressed in lung fibroblasts to assess migration and invasion. miR-21 expression in lung fibroblasts promoted migration and invasion. Moreover, the proliferation of lung cancer cells was accelerated by conditioned medium of miR-21-expressing lung fibroblasts. These results suggest that miR-21 overexpression in CAFs of lung adenocarcinoma might serve as a prognostic biomarker and be involved in cancer cell proliferation through interactions with cancer cells.

Citation Format: Akiko Kunita, Shigeki Morita, Masashi Fukayama. Expression of miR-21 in cancer associated fibroblasts in lung adenocarcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 535. doi:10.1158/1538-7445.AM2014-535
Abstract 5351: The carcinogenesis rate is increased in MAL knock-out mice
Authors: Chen Wantao , Wu Xiangbing , Cao Wei , Wang Xu
Published: May 2015

Background:

The MAL gene was originally identified by Alonso during a study for differentially expressed genes in T-cell development. The MAL protein, which spans the membrane four times, is involved in normal apical transport and accurate sorting in distinct epithelial cells. The recent study on MAL gene down-regulation in primary human epithelial malignancies suggest that the loss of the MAL gene may be closely linked with a variety of human epithelial malignancies. In our previous study, we revealed that MAL was remarkably down-regulated in human head and neck squamous cell carcinoma. Exogenous expression of MAL in HNSCC cell lines could inhibit the proliferation, invasion, and induce apoptosis of cancer cells in vitro and suppress tumor growth in vivo. These data support that MAL, as a candidate tumor suppressor, contributes to carcinogenesis and development of HNSCC.

Methods:

To further confirm the role of MAL gene in development of carcinoma, a MAL gene knockout mouse model was produced. And the genotype and phenotype was investigated by our study group. The genotypes of MAL-/- and MAL+/+ mice were identified by RT-PCR, Western blot and Immunohistochemistry. The histopathology of main organs and tissues (esophagus, stomach, small intestine, colon, oral mucosa, etc.) were analyzed with H & E staining. Chemical carcinogenesis agent (4-nitroquinoline-N-oxide, 4NQO) was used to induce oral mucosa carcinomas.

Results: MAL gene knockout mouse model was successfully established and passed on from generation to generation more than 3 years. The genotypes of MAL-/-, MAL+/-, MAL+/+ mice were identified. Phenotypic investigation found that MAL-/- mice raised no obvious spontaneous phenotype in 12 months and the incidence of spontaneous tumor was zero. Nevertheless, we found that there were significant differences between MAL-/- and MAL+/+ mice in the incidence rate, occurrence time and growth speed of tongue and esophageal squamous carcinoma which induced by a low dose of 4NQO water feeding for 16 weeks (P<0.01). We also found that the occurrence of esophageal squamous cell carcinoma performed the same changes as oral mucosa.

Conclusions: Our results suggest that MAL gene knockout mouse significantly increased the susceptibility of cancer. The molecular mechanism about the tumor susceptibility becomes more important, and will be significant for developing cancer prevention and treatment methods.

Citation Format: Wantao Chen, Xiangbing Wu, Wei Cao, Xu Wang. The carcinogenesis rate is increased in MAL knock-out mice. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5351. doi:10.1158/1538-7445.AM2014-5351
Abstract 5352: Ultraviolet radiation induces carcinogenesis in a novel transgenic mouse model of melanoma
Authors: Benaduce Ana Paula , Batista Deannys , Grilo Gabriel , Jorge Karen , Cardero Diana , Milikowski Clara , Kos Lidia
Published: May 2015

Melanomagenesis is caused by environmental factors, such as ultraviolet (UV) radiation, as well as genetic factors. The Nucleotide Excision Repair (NER) pathway repairs photoproducts induced by UV radiation. In humans, NER pathway disruption leads to the development of skin cancers, including melanoma. Upon UV exposure, mice deficient in Xpc, an important protein in the NER pathway, develop skin cancer; but not melanoma. The Endothelin 3 (Edn3) signaling pathway is essential for melanocyte precursor cell development. In humans, this pathway has also been associated with melanoma progression and its metastatic potential. The purpose of this study is the development of a UV-dependent melanoma mouse model that combines Xpc deficiency with the over-activation of the Edn3 pathway. Transgenic mice over-expressing Edn3 under the control of the keratin 5 promoter (K5-Edn3) and carrying a targeted mutation in Xpc were exposed to a single suberythemal neonatal dose of UV radiation. Immunostaining and histomorphology were used to confirm the melanocytic origin of primary skin tumors. Melanomas were only found in animals with the K5-Edn3 transgene. High penetrance was observed in Xpc null (67%, n=3) and Xpc heterozygous (67%, n=3) mice in comparison to Xpc wild type (33%, n=3) mice. RNA extracted from melanomas of Xpc null (n=2), Xpc heterozygous (n=1) and Xpc wild type (n=1) mice were screened for UV signature mutations in Hras, Kras and Nras. No mutations were found in any of these genes. These results indicate that UV radiation exposure, in conjunction with over-activation of the Edn3 pathway is sufficient to lead to melanomagenesis in mice independently of mutations in Hras, Kras or Nras.

Citation Format: Ana Paula Benaduce, Deannys Batista, Gabriel Grilo, Karen Jorge, Diana Cardero, Clara Milikowski, Lidia Kos. Ultraviolet radiation induces carcinogenesis in a novel transgenic mouse model of melanoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5352. doi:10.1158/1538-7445.AM2014-5352
Abstract 5354: Neuropeptide Y as a prognostic marker of colorectal cancer
Authors: Sarkar Chandrani , Chakroborty Debanjan
Published: May 2015

Introduction: Colorectal cancer affects a large population not only in the United States but worldwide and is one of the major causes of mortality due to cancer. Among the numerous risk factors that might lead to the incidence and development of this disease, inflammatory bowel diseases (IBD) have been identified as a very prominent factor and patients are at much higher risk of developing colorectal cancer in their lifetime.

Objective/Hypothesis: As chronic inflammation leads to colorectal cancer and among the various neuromediators, the neuropeptides, particularly neuropeptide Y (NPY) is associated with the development and progression of IBD and as NPY has the potential to augment inflammation and angiogenesis through its Y2 receptor we hypothesize that NPY is an important regulator of the process of development of colorectal cancer (CRC).

Results: Our results show that the expression of both NPY its Y2 receptor is upregulated in an axozymethane / dextran sodium sulphate (AOM/DSS) induced mouse model of inflammatory CRC. Upregulation of NPY in AOM/DSS induced CRC in mice is associated with increased angiogenesis. NPY Y2 receptors are expressed in these angiogenic vessels. Furthermore, this upregulation of NPY and Y2 receptor is also related to higher expression of the inflammatory cytokine, TNF-α, that has been shown to promote progression of carcinogenesis in AOM/DSS induced CRC mouse models. Our in vitro studies show that NPY can promote angiogenic potential of human umbilical vein endothelial cells (migration and permeability) through Y2 receptors present in these cells.

Conclusion: We here show for the first time that NPY might be associated with the progression of inflammatory colorectal cancer and hence may serve as a prognostic marker of the disease.

Citation Format: Chandrani Sarkar, Debanjan Chakroborty. Neuropeptide Y as a prognostic marker of colorectal cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5354. doi:10.1158/1538-7445.AM2014-5354
Abstract 536: Elucidating the role of miRNA-31 in retinoblastoma
Authors: Montoya Vanessa , Bryar Paul J. , Mets Marilyn , Weinstein Joanna , Laurie Nikia
Published: May 2015

Retinoblastoma is the most common pediatric ocular cancer. Although early detection of the disease may have a favorable outcome for the patient, retinoblastoma can aggressively develop and become fatal. Current treatment strategies include focal therapies, chemotherapy and in more severe cases, enucleation (removal of the eye) is necessary. This cancer may initiate from acquired or inherited mutations in the RB1 gene. As a result, the mutant retinal cell is conferred an unrestrained proliferative ability that is facilitated by multiple genetic events. Determining the mechanism(s) responsible for tumor growth, invasion, and metastasis may provide an alternative treatment strategy that may delay enucleation, prevent toxic side effects from chemotherapy, or even prevent metastatic spread altogether. Genetic factors that are highly involved in both carcinogenesis and homeostasis are often regulated by miRNAs. miRNAs are small, non-coding molecules that negatively regulate gene expression by mediating mRNA cleavage and/or disrupting protein synthesis. Our rationale for this study is that investigating aberrant miRNA regulation in retinoblastoma will enable us to identify key genetic factors that can be targeted therapeutically. Our miRNA array suggests that there is a significant number of miRNAs whose expression is significantly downregulated between retinoblastoma tumors and normal human retinae. From this data, we have identified candidate miRNAs, such as miRNA-31, that have been previously reported to have an important anti-metastatic role in different cancer types. We are currently investigating the role of these miRNAs in regulating retinoblastoma progression. These functional studies will allow us to determine how increasing miRNA expression in retinoblastoma models can disrupt important signaling pathways associated with retinoblastoma progression and invasion.

Citation Format: Vanessa Montoya, Paul J. Bryar, Marilyn Mets, Joanna Weinstein, Nikia Laurie. Elucidating the role of miRNA-31 in retinoblastoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 536. doi:10.1158/1538-7445.AM2014-536
Abstract 5360: Ethanol enhances arsenic-induced mutagenesis in colon
Authors: Wang Lei , Kuang Lisha , Son Young-Ok , Hitron John Andrew , Poyil Pratheeshkumar , Zhang Zhuo , Luo Jia , Wang Zhigang , Shi Xianglin
Published: May 2015

Health effects due to environmental exposure to arsenic are a major health concern world-wide. Arsenic has been known to induce carcinogenesis and enhance tumor development via complex and unclear mechanism. As one of the common nutritional factors, ethanol is also a well-documented risk factor for many malignancies. However, little is known on the effects of co-exposure to arsenic and ethanol in mutagenesis and carcinogenesis. In this study, we investigate the mutagenic effect of co-exposure to arsenic and ethanol in vivo and in vitro. Results show that ethanol could markedly enhance arsenic-induced mutagenesis in colon in Big Blue Mice. This response related to intracellular reactive oxygen species (ROS) generation, NAPDH oxidase activation, and DNA damage/repair functional changes.

We conclude that ethanol enhances arsenic-induced mutagenesis in colon in vivo. These results indicated that alcohol consumption should be taken into consideration in the investigation on arsenic-induced carcinogenesis in arsenic-exposure population.

Citation Format: Lei Wang, Lisha Kuang, Young-Ok Son, John Andrew Hitron, Pratheeshkumar Poyil, Zhuo Zhang, Jia Luo, Zhigang Wang, Xianglin Shi. Ethanol enhances arsenic-induced mutagenesis in colon. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5360. doi:10.1158/1538-7445.AM2014-5360
Abstract 5365: Cdt2-mediated XPG degradation promotes DNA repair synthesis following DNA damage excision in nucleotide excision repair
Authors: Han Chunhua , Zhao Ran , Qian Jiang , Sharma Nidhi , Wani Gulzar , He Jinshan , Zhu Qianzheng , Wang Qi-En , Wani Altaf A.
Published: May 2015

Xeroderma pigmentosum group G (XPG) protein is a structure-specific repair endonuclease, which cleaves DNA strands on the 3′ side of the DNA damage during nucleotide excision repair (NER). In addition, XPG plays a crucial role in initiating DNA repair synthesis through recruitment of PCNA to the repair sites. However, the fate of XPG protein subsequent to the excision of DNA damage has remained unresolved. Here, we show that XPG is degraded through proteasome-mediated proteolysis upon induction of bulky lesions from exposures to UV irradiation and cisplatin. NER process is required for XPG degradation because both UV and cisplatin treatment-induced XPG degradation is compromised in NER-deficient XP-A, XP-B, XP-C, and XP-F cells. In addition, the NER-related XPG degradation requires Cdt2, a component of an E3 ubiquitin ligase, CRL4Cdt2. Micropore local UV irradiation and in situ Proximity Ligation assays demonstrated that Cdt2 is recruited to the UV-damage sites and interacts with XPG in the presence of PCNA. Importantly, Cdt2-mediated XPG degradation is crucial to the subsequent recruitment of DNA polymerase δ and DNA repair synthesis. Collectively, our data supports the idea of PCNA recruitment to damage sites in conjunction with XPG, recognition of the PCNA-bound XPG by CRL4Cdt2 for specific ubiquitylation and protein degradation. Thus, XPG removal clears the space needed at the damage site for the subsequent recruitment of DNA pol δ and initiation of DNA synthesis. (This work was supported by grants from NIH).

Note: This abstract was not presented at the meeting.

Citation Format: Chunhua Han, Ran Zhao, Jiang Qian, Nidhi Sharma, Gulzar Wani, Jinshan He, Qianzheng Zhu, Qi-En Wang, Altaf A. Wani. Cdt2-mediated XPG degradation promotes DNA repair synthesis following DNA damage excision in nucleotide excision repair. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5365. doi:10.1158/1538-7445.AM2014-5365
Abstract 5367: DNA repair capacity, gene expression and epigenomic profiles in bladder cancer
Authors: Pardini Barbara , Allione Alessandra , Guarrera Simonetta , Turinetto Valentina , Fiorito Giovanni , Rosa Fabio , Russo Alessia , Modica Federica , Giachino Claudia , Vineis Paolo , Sacerdote Carlotta , Matullo Giuseppe
Published: May 2015

In Europe, bladder cancer (BC) is the sixth most commonly diagnosed tumor and the second most common cause of death among patients with genitourinary tract malignancies. The ability to repair DNA damage is strongly associated with the risk of cancer and inter-individual variation in DNA repair capacity (DRC) might account for different susceptibility of developing cancer. DRC represents a complex marker comprising the sum of several factors such as gene variants, gene expression, stability of gene products, and effect of inhibitors/stimulators. Individuals with low DRC will tend to accumulate more damage than those who have a better ability to repair such damage. This variability is modulated by the genetic background to which SNPs/haplotype combinations in DNA repair genes, as well as epigenetic regulation are likely to contribute. Phenotypic assays to evaluate DNA repair activity (in particular NER comet assay, H2AX phosphorylation and micronucleus assay) were performed on cryopreserved lymphocytes from 159 cases (collected before treatment) and 159 controls matched by age and smoking habits, enrolled in Turin Bladder Cancer Study (TBCS). We aimed at studying the relationship between DRC (evaluated by comet assay, micronuclei and H2AX phosphorylation assay) and bladder cancer integrating, gene expression and epigenetic profile data (methylation levels and microRNA expression). In particular, we performed an integrated analysis on the genotype/phenotype correlation in a population of bladder cancer cases and controls provided with detailed description of the follow-up for response to therapy/recurrence/survival. This integrated approach will help in elucidating the role of DRC (and its determinants) as predictive and prognostic marker and to identify combined biomarkers to be measured in blood cells as non-invasive predictive method.

Citation Format: Barbara Pardini, Alessandra Allione, Simonetta Guarrera, Valentina Turinetto, Giovanni Fiorito, Fabio Rosa, Alessia Russo, Federica Modica, Claudia Giachino, Paolo Vineis, Carlotta Sacerdote, Giuseppe Matullo. DNA repair capacity, gene expression and epigenomic profiles in bladder cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5367. doi:10.1158/1538-7445.AM2014-5367
Abstract 5371: Drug repositioning with a bioinformatics platform that integrates the TCGA, cMap and CCLE
Authors: Lucas Francis A. San , Fowler Jerry , Kopetz Scott , Vilar Eduardo , Scheet Paul
Published: May 2015

Cancer In silico Drug Discovery Tools (CIDD) is a drug discovery platform that enables researchers to generate hypotheses for the following three general problems: 1) to determine if clinical phenotypes or gene mutations for a cancer are functional, inducing unique gene expression alterations, 2) to find candidate drugs to treat, or repress, these expression changes, and 3) to identify cell lines that resemble the tumors being studied for subsequent in vitro experimentation. CIDD integrates clinical and experimental data from The Cancer Genome Atlas (TCGA), the Connectivity Map (cMap) and the Cancer Cell Line Encyclopedia (CCLE) to perform in silico drug discovery experiments. CIDD generates gene expression signatures representative of the phenotypes or mutations being studied, characterizes the signatures using MSigDB, identifies candidate drugs to repress these signatures using data from the cMap, and finds optimal cell lines for in vitro drug testing using experimental data from the CCLE. The primary results of a CIDD execution are a biologically interpretable candidate drug list and a list of cell lines for subsequent drug experimentation. We applied CIDD for the identification of candidate drugs to treat BRAF V600E colorectal cancer (CRC). CIDD identified EGFR and proteasome inhibitors as candidate drugs, while proposing 7 large intestine cell lines from the CCLE for potential in vitro testing. CIDD is a command-line based tool written in Python and depends on R. We have developed a companion Python-based data management utility, tcga_util, which provides automated downloading and querying of TCGA data from the command-line, which we feel will be of substantial and independent interest to researchers wishing to use data from the TCGA. CIDD and tcga_util are available for download at http://scheet.org/software.

Citation Format: Francis A. San Lucas, Jerry Fowler, Scott Kopetz, Eduardo Vilar, Paul Scheet. Drug repositioning with a bioinformatics platform that integrates the TCGA, cMap and CCLE. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5371. doi:10.1158/1538-7445.AM2014-5371
Abstract 5385: A novel cell-based kinase assay panel paired with high content phenotypic profiling to correlate kinase inhibitor specificity and cellular activity
Authors: Wehrman Tom S. , O'Donnell Erika A. , Lumpe M. Jared , Osetek Benjamin E. , Krutzik Peter O.
Published: May 2015

In many cancers, drugs that target a single kinase often lack efficacy due to the presence of alternate oncogenic signaling pathways that may compensate for the inhibition of the targeted kinase. Although completely non-selective kinase inhibitors are highly toxic, selective and simultaneous inhibition of a number of kinases can lead to greater responses. Here we describe the development of a multiplexed cellular kinase assay platform in which compounds are simultaneously profiled against more than 12 kinase targets in a single sample. Using this high-throughput platform, target activity and selectivity in cells can be optimized concurrently, enabling the selection of specific multi-targeted compounds. Using this platform, 300 kinase inhibitors were fully characterized for cellular activity and potency across a large panel of tyrosine kinases. These inhibitors were then tested across a panel of diverse cancer cell lines in a phenotypic screen for their ability to affect viability, cell cycle, and apoptosis under different growth conditions. The resulting comprehensive data set of existing in vitro data, cellular kinase data, and phenotypic screening results provided novel insights into the relationship between inhibitor selectivity, cell cycle effects, and the correlation to anti-cancer activity.

Citation Format: Tom S. Wehrman, Erika A. O'Donnell, M. Jared Lumpe, Benjamin E. Osetek, Peter O. Krutzik. A novel cell-based kinase assay panel paired with high content phenotypic profiling to correlate kinase inhibitor specificity and cellular activity. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5385. doi:10.1158/1538-7445.AM2014-5385