bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3525: SOX2 promotes tumor growth via activation of the PI3K/Akt/mTORC1 signaling pathway in esophageal squamous cell carcinoma
Authors: Gen Yasuyuki , Yasui Kohichiroh , Kitaichi Tomoko , Tomie Akira , Ito Yoshito 
Published: May 2015

Abstract
Our previous study revealed that SOX2, a master regulator during embryogenesis, is an amplification target of 3q26.3 in esophageal squamous cell carcinoma (ESCC) and that SOX2 promotes ESCC cell proliferation. To identify the mechanisms by which SOX2 promotes proliferation of ESCC cells, we assayed multiple signaling pathways activated by SOX2 using a phosphoprotein array. We determined that SOX2 activated the AKT/mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. Immunoblotting confirmed that SOX2 elevated levels of p-AKT and levels of p-p70S6K and p-4E-BP1 which are direct targets of mTORC1. Effects of SOX2 knockdown, including reduced levels of p-AKT and decreased ESCC cell viability, were reversed with constitutive activation of AKT with PTEN knockdown. SOX2 also promoted in vivo tumor growth of ESCC with AKT/mTORC1 activation in mouse xenografts. LY294002, a PI3K inhibitor, suppressed the ability of SOX2 to enhance tumor growth of ESCC by reducing cell proliferation. Furthermore, tissue microarray analysis showed a positive correlation between expression levels of SOX2 and p-AKT in 61 primary ESCC tumors. Our results suggest that SOX2 promotes ESCC tumor growth via activation of the PI3K/AKT / mTORC1 signaling pathway, which enhances cell proliferation.
Citation Format: Yasuyuki Gen, Kohichiroh Yasui, Tomoko Kitaichi, Akira Tomie, Yoshito Ito. SOX2 promotes tumor growth via activation of the PI3K/Akt/mTORC1 signaling pathway in esophageal squamous cell carcinoma. [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 3525. doi:10.1158/1538-7445.AM2014-3525
Abstract 3531: MicroRNA delivery by bionanoparticles: regulation of the liver cancer susceptibility gene MICA expression in hepatocytes
Authors: Ohno Motoko , Otsuka Motoyuki , Kishikawa Takahiro , Yoshikawa Takeshi , Takata Akemi , Koike Kazuhiko 
Published: May 2015

Abstract
Hepatocellular carcinoma (HCC) is an important issue to public health of the world. We recently reported by genome wide association study (GWAS) analyses that a single nucleotide polymorphism (SNP) in the promoter region of the MHC class I polypeptide-related sequence A (MICA) gene that is significantly associated with the risk of hepatitis-virus-related HCC. Because there was a correlation between the expression levels of MICA in the serum depending on the different alleles at the SNP site and the risk of HCC, regulation of MICA expression levels may be useful in the prevention of HCC. Here we show that MICA protein expression in HCC cells can be regulated by the microRNA (miR) 25-93-106b cluster. By use of luciferase assay and FACS analyses, it was confirmed that forced expression of the miR 25-93-106b cluster significantly suppressed MICA expression, whereas inhibition of this miR cluster increased MICA expression in cells that stably express MICA. Furthermore, to deliver efficiently miRNAs into hepatocytes specifically, we developed bio-nanocapsules containing miR93 inside, utilizing hepatitis B virus envelope L-protein. MICA expression levels were indeed suppressed after the delivery of miR93 by these bionanoparticles into hepatocytes. Besides, the binding ability of NKG2D (a receptor of MICA) and in vivo cell-killing by NK cells were changed proportionally to miRNA-induced MICA expression levels. These results suggest that the modulation of MICA expression levels in hepatocytes by delivering miRNAs using these bionanocapsules may be a novel and effective approach to prevent hepatitis-virus-related HCC.
Citation Format: Motoko Ohno, Motoyuki Otsuka, Takahiro Kishikawa, Takeshi Yoshikawa, Akemi Takata, Kazuhiko Koike. MicroRNA delivery by bionanoparticles: regulation of the liver cancer susceptibility gene MICA expression in hepatocytes. [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 3531. doi:10.1158/1538-7445.AM2014-3531
Abstract 3535: Epigenetic regulation of miR-31 and miR-205 of apoptosis in prostate cancer
Authors: Zhang Qunshu 
Published: May 2015

Abstract
Prostate cancer is the second leading cause of cancer-related mortality among men in the United States. However, our understanding of the cause of prostate cancer remains elusive. Recent studies have implicated that epigenetics, heritable changes in gene expression caused by mechanisms other than classical genetic alterations, is an important mechanism in tumorigenesis. MicroRNAs function as epigenetic regulators to alter gene expression, and very limited information is available regarding the roles of microRNAs in prostate cancer. Evasion of apoptosis is the hallmark of cancer, and it plays an important role in the growth and development of prostate cancer. We have recently demonstrated that miR-31 and miR-205 are downregulated in advanced prostate cancer. In addition, anti-apoptotic protein E2F6 was identified as the target of miR-31 and contributed resistance to chemotherapy-induced apoptosis. While we found that miR-205 is silenced by gene promoter methylation, the mechanism of the downregulation of miR-31 in prostate cancer remains poorly defined. In this study, we report that EZH2 (Enhancer of zeste 2), a histone methyltransferase and component of the polycomb repressive complex 2 (PRC2), is responsible for miR-31 silencing in prostate cancer. EZH2 plays an essential role in the epigenetic maintenance of the H3K27me3 repressive chromatin mark. Our results have shown that siRNA knockdown of EZH2 and DZNep (3-deazaneplanocin) treatment (an EZH2 inhibitor) in prostate cancer cells increased miR-31 expression. Furthermore, EZH2 is responsible for histone methylation at the promoter of miR-31 gene. In addition, siRNA knockdown of EZH2 and the treatment with DZNep sensitized prostate cancer cells to apoptosis. In contrast, EZH2 overexpression confers resistance to chemotherapy-induced apoptosis in prostate cancer cells. Thus, polycomb protein EZH2 suppresses the expression of miR-31 and consequently contributes to apoptosis resistance in prostate cancer. The results will improve our understanding of the mechanism of drug resistance in prostate cancer cells. Novel strategies targeting EZH2 and miR-31 can be developed to increase drug-induced apoptosis and improve cancer response to chemotherapy.
Citation Format: Qunshu Zhang. Epigenetic regulation of miR-31 and miR-205 of apoptosis in prostate 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 3535. doi:10.1158/1538-7445.AM2014-3535
Abstract 3538: Obligate haploinsufficiency of the microRNA-processing molecule dicer1 in a murine colitis-associated tumorigenesis model
Authors: Yoshikawa Takeshi , Otsuka Motoyuki , Koike Kazuhiko 
Published: May 2015

Abstract
Background: A widespread downregulated expression of microRNAs (miRNAs) is commonly observed in human cancers. Similarly, deregulated expression of miRNA-processing pathway components, which results in the reduction of global miRNA expression, may also be associated with tumorigenesis. Thus, we hypothesized that the deregulation of microRNA-processing molecule Dicer1 in intestinal epithelial cells may accelerate intestinal inflammation-associated tumorigenesis.
Methods & Results: We constructed Dicer1 gene-disrupted mice with monoallelic and biallelic loss of its locus. Inflammation-associated colon tumors were induced by azoxymethane (AOM) injection with the treatment by three cycles of Dextran Sulfate Sodium (DSS). 1) Dicer1 protein expression and subsequent mature miRNA levels in the isolated intestinal epithelial cells were inversely correlated with the number of intact Dicer1 alleles. 2) Although the severity of inflammation after the induction in this model was comparable in control and Dicer1-mutant mice, the number of colon tumors was significantly higher in heterozygous mice but not in homozygous mice. 3) Because the expression levels of Dicer1 were retained in tumors and its surrounding tissues even after induction of colitis-associated tumors, the effects of Dicer1 deletion on tumorigenesis were considered as cell-autonomous. 4) While the expression levels of representative oncogenes and tumor suppressor genes were in most cases inversely correlated with the expression levels of Dicer1, some genes were not affected by Dicer1 deletion.
Conclusion: Specific ablation of Dicer1 in intestinal epithelial cells accelerates intestinal inflammation-associated tumorigenesis. However, this effect was apparent only when a single copy of Dicer1 was deleted, but not with complete Dicer1 gene ablation. Generally, complete loss of the function of most tumor suppressor genes is advantageous for tumor development. However, our results suggest that, in case of Dicer1 gene, complete loss is deleterious for cancer development, while its partial inactivation promotes tumor formation. This unique “obligate haploinsufficient role” colitis-associated colon tumor of Dicer and miRNAs needs further attention to elucidate the pathogenesis of tumorigenesis related with deregulated miRNAs.
Citation Format: Takeshi Yoshikawa, Motoyuki Otsuka, Kazuhiko Koike. Obligate haploinsufficiency of the microRNA-processing molecule dicer1 in a murine colitis-associated tumorigenesis 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 3538. doi:10.1158/1538-7445.AM2014-3538
Abstract 3572: Copy number detection using genomics technologies: A comparison between aCGH and NGS
Authors: Vasmatzis George , Feldman Andrew L. , Johnson Sarah H. , Thorland Erik C. , Fonseca Rafael , Braggio Esteban , Gliem Troy J. 
Published: May 2015

Abstract
Introduction: Identification of causal DNA copy number variations (CNVs) is critical to the understanding of cancer development and progression, and is important clinically for accurate prognosis and efficient treatment. T-cell lymphomas are replete with amplifications and deletions that result in over- and under-expression of genes. Array comparative genomic hybridization (aCGH) has been the technology of choice to detect CNVs but recently, it has been proposed that mate-pair Next Generation Sequencing (mpNGS) can produce similar results. Here, we report a comparison between the two techniques.
Methods: We have developed an algorithm based on extreme value theory to identify CNVs across the genome at high resolution from mate-pair NGS data. The algorithm is based on plotting the distribution of read-counts in windows across the genome, and detecting deletions and gains by finding the windows that differ significantly from the distribution of the normal part of the genome. We compared this algorithm with aCGH data to detect CNVs. We ran five cases of T-cell lymphoma with both techniques and compared the results using concordance statistics.
Results: With 50kb lower cutoff for a CNV, mpNGS detected 98% of the cumulative deleted genome and 94% of the amplified/gained genome that were called by aCGH. Most of the discordant CNVs that were detected by only aCGH were in regions of repetitive areas where mapping fails. Conversely, aCGH detected 75% of the cumulative deleted genome and 74% of the amplified/gained genome that were called by mpNGS.
Conclusion: A detailed comparison of these techniques showed that both have pros and cons. In general, mpNGS can detect most CNVs detected by aCGH, as long as they are more than 50KB. Additionally, mpNGS offers confirmatory data, particularly for deletions, based on detection of aberrant mate pairs that map to the rejoined ends of deleted regional. Finally, the mate-pair technology can also detect balanced translocations and can also predict fusion genes.
Citation Format: George Vasmatzis, Andrew L. Feldman, Sarah H. Johnson, Erik C. Thorland, Rafael Fonseca, Esteban Braggio, Troy J. Gliem. Copy number detection using genomics technologies: A comparison between aCGH and NGS. [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 3572. doi:10.1158/1538-7445.AM2014-3572
Abstract 3577: Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients
Authors: Ni Xiaohui , Zhuo Minglei , Su Zhe , Duan Jiachun , Gao Yan , Wang Zhijie , Zong Chenghang , Bai Fan , Wang Jie , Xie X. Sunney 
Published: May 2015

Abstract
Circulating tumor cells (CTCs) enter peripheral blood from primary tumors and seed metastases. The genome sequencing of CTCs could offer noninvasive prognosis or even diagnosis, but has been hampered by the low single-cell genome coverage of scarce CTCs. Here, we report the use of the recently developed multiple annealing and looping-based amplification cycles for whole genome amplification of single CTCs from lung cancer patients. We observed characteristic cancer-associated single-nucleotide variations and insertions/deletions in exomes of CTCs. These mutations provided information needed for individualized therapy, such as drug resistance and phenotypic transition, but were heterogeneous from cell to cell. In contrast, every CTC from an individual patient, regardless of the cancer subtypes, exhibited reproducible copy number variation (CNV) patterns, similar to those of the metastatic tumor of the same patient. Interestingly, different patients with the same lung cancer adenocarcinoma (ADC) shared similar CNV patterns in their CTCs. Even more interestingly, patients of small-cell lung cancer have CNV patterns distinctly different from those of ADC patients. Our finding suggests that CNVs at certain genomic loci are selected for the metastasis of cancer. The reproducibility of cancer-specific CNVs offers potential for CTC-based cancer diagnostics.
Citation Format: Xiaohui Ni, Minglei Zhuo, Zhe Su, Jiachun Duan, Yan Gao, Zhijie Wang, Chenghang Zong, Fan Bai, Jie Wang, X. Sunney Xie. Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. [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 3577. doi:10.1158/1538-7445.AM2014-3577
Abstract 3583: Reducing GC-bias and improving coverage distribution in Illumina sequencing using the Kapa Biosystems library construction method
Authors: Thorner Aaron R. , Sunkavalli Ashwini , Lin Ling , Jones Robert T. , Schubert Laura , Ducar Matthew D. , Adusumilli Ravali , Dolcen Deniz Nesli , Ziaugra Liuda , Lepine Jack , MacConaill Laura E. , Hahn William C. , Meyerson Matthew , Hummelen Paul Van 
Published: May 2015

Abstract
Next-generation sequencing (NGS) is increasingly used in the laboratory and clinic to identify genomic factors contributing to tumorigenesis, such as somatic mutations, DNA insertions and deletions, transcriptome and epigenetic changes, and chromosomal abnormalities. Because tumor specimen tissues are often quite limited or are from rare and precious samples, it is necessary to prepare sequencing libraries from minimal amounts of DNA. Consequently, limited DNA input necessitates amplification during NGS library preparation. Therefore, it is of great importance to amplify the library in an efficient and uniform manner to achieve reproducible amplification of the library fragments and limit GC content bias. Variable GC-bias among libraries is of particular importance for copy number variant (CNV) detection based on sequence coverage.
Here, we compare the TruSeq DNA Sample Preparation Kit (Illumina Inc., San Diego, CA) and the KAPA Library Preparation Kit (Kapa Biosystems, Wilmington, MA) to determine which technique achieves optimal library coverage. The major difference between the methods is the DNA polymerase used for library enrichment. The Kapa HiFi polymerase was engineered to have higher fidelity and increased DNA affinity relative to the Herculase II Fusion DNA Polymerase (Agilent Technologies, Inc., Santa Clara, CA) that we used for library enrichment with the TruSeq kit. Thus, the Kapa HiFi polymerase should more efficiently amplify targets across a larger GC content range and improve sequence coverage uniformity.
Relative to TruSeq-prepared libraries, the Kapa-prepared libraries had a larger mean insert size, more uniform coverage distribution, and better coverage of GC-rich regions of the genome. This was observed for DNA extracted from blood, cell lines, and formalin-fixed paraffin embedded (FFPE) tumor samples. More experiments are underway to determine the effect of the improved recovery of high-GC content DNA fragments on CNV detection.
Citation Format: Aaron R. Thorner, Ashwini Sunkavalli, Ling Lin, Robert T. Jones, Laura Schubert, Matthew D. Ducar, Ravali Adusumilli, Deniz Nesli Dolcen, Liuda Ziaugra, Jack Lepine, Laura E. MacConaill, William C. Hahn, Matthew Meyerson, Paul Van Hummelen. Reducing GC-bias and improving coverage distribution in Illumina sequencing using the Kapa Biosystems library construction method. [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 3583. doi:10.1158/1538-7445.AM2014-3583
Abstract 3586: HIF-1α from tumor-surround fibroblasts contributes to breast cancer malignant progression
Authors: Lu Yi , Zhang Jun 
Published: May 2015

Abstract
As tumor-surrounding stromal cells (such as fibroblasts) are integrate components of the tumor environment that together as an entity plays critical roles in the tumor progression, we investigated whether HIF-1α from tumor-surrounding fibroblasts plays a critical role in breast cancer (BCa) malignant progression. We co-cultured BCa 4T1/GFP cells with MEF fibroblasts that either expressed or lacked the HIF-1α gene in a 3D culture system established in our lab. The mixed cells (BCa:MEF) grew in a suspension manner and formed aggregates/spheroids. We found that HIF-1α plays a role under hypoxia in the 3D BCa cells' protrusion formation, an established marker for invasive, aggressively malignant tumor cells that start to invade the surrounding matrix. These protrusions (fluorescent) only appeared in mixed-cell aggregates containing HIF-1α wild-type MEF fibroblasts; but not appear in mixed-cell aggregates containing HIF-1α knockout MEF fibroblasts, implying HIF-1α from fibroblasts (MEF) plays a critical role in inducing surrounding epithelial BCa cells to form protrusions, an indicator that tumor cells have become invasive. Moreover, we performed transwell overnight invasion assay of BCa LM2 cells with and without cocultured MEF under both normoxia (21% O2) and hypoxia (1% O2). We found that MEF significantly promoted BCa invade through matrigel, and HIF-1α WT MEF promoted BCa invasion more than HIF-KO MEF did under hypoxia. Furthermore, by using Boyden's chamber-based cell migration assay, we found that migration of HIF-1α WT BCa (MMTC-PyT) cells increased more than two fold under hypoxia than normoxia. However, this hypoxia-induced increase in migration disappeared if HIF-1α KO counterparts were used. The loss of this hypoxia-induced migration in HIF-1α KO cells can be rescued by exogenous HIF-1α with Ad-HIF-1α transduction. A similar pattern of HIF-1α-dependent, hypoxia-stimulated cell migration was observed in fibroblasts when we analyzed HIF-1α WT and KO MEF cells, demonstrating that hypoxia stimulated a HIF-1α-dependent cell migration in both BCa and MEF cells. Together, these results indicate that HIF-1α from tumor-surrounding fibroblasts plays critical roles in promoting BCa malignant progression.
Citation Format: Yi Lu, Jun Zhang. HIF-1α from tumor-surround fibroblasts contributes to breast cancer malignant progression. [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 3586. doi:10.1158/1538-7445.AM2014-3586
Abstract 3588: Reactivation of dormant estrogen-dependent breast cancer micrometastases by bone marrow stromal injury in an in vitro model of dormancy
Authors: Tivari Samir , Lu Haiyan , Dasgupta Tanya , Wieder Robert 
Published: May 2015

Abstract
Estrogen-dependent (ER+) breast cancer can remain dormant in the bone marrow for more than a decade and continues to recur in a stochastic pattern at continuous, low rates. Mechanisms of dormancy in the bone marrow are mostly uncharacterized but data suggest that dormancy depends on close interactions of micrometastases with stromal elements and on effects by structural and soluble proteins. We have developed an extensive and well characterized in vitro model incorporating relevant elements of the bone marrow niche. We have demonstrated that FGF-2, abundantly deposited on bone marrow stroma, induces a partial re-differentiation of ER+ human breast cancer cell lines, manifested in part by cell cycle arrest in G1 and re-expression of integrins lost with dedifferentiation. Ligation of integrin α5β1 by incubation of cells on fibronectin completes the model. It specifically induces a dormant epithelial phenotype with RhoA inactivation through the Rho Gap GRAF, cortical actin rearrangement, omnidirectional focal complex activation and adhesion and activation of survival signaling. The signaling is dually initiated through FGF-2 receptors and fibronectin ligation, which activate PI3K/Akt, Erk and p38. The model is recapitulated on both human and murine bone stromal monolayer coincubations of human ER+ breast cancer cell lines, with the FGF-2 and fibronectin provided by the stroma. Mechanisms of breast cancer recurrence are also not understood, but data in other systems suggest that inflammatory cytokines can stimulate proliferation of breast cancer cells. We hypothesized that injury to bone marrow stroma can be the source of such cytokines. Towards this end, we injured human and murine bone marrow stromal monolayers by oxidation and hypoxia through one hour exposures to variable concentrations of H2O2 and a cyanide-containing analog, respectively, and by estrogen deprivation. These interventions induced secretion of IL-6 and IL-8, and induced activation TGFβ and TNFα under variable conditions. Incubation of human recombinant IL-6, IL-8 and TGFβ with dormant colonies in fibronectin culture induced dormant clones to proliferate into growing colonies. These data suggest a potential mechanism for reactivation of dormant breast cancer micrometastases and identify potential targets for suppression of the effect.
Citation Format: Samir Tivari, Haiyan Lu, Tanya Dasgupta, Robert Wieder. Reactivation of dormant estrogen-dependent breast cancer micrometastases by bone marrow stromal injury in an in vitro model of dormancy. [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 3588. doi:10.1158/1538-7445.AM2014-3588