bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1396: Pathway-directed DNA demethylation as an epithelial to mesenchymal targeting strategy
Authors: HUANG HAO , Yu Qing , Kandpal Maooj , Davuluri Ramana V. , Matei Daniela
Published: August 2018

It has been proposed that by silencing tumor suppressor genes, DNA methylation plays an important function in cancer initiation and progression. DNA hypomethylating agents are being developed as anti-cancer agents. However, this approach causes unrestricted hypomethylation, which could potentially activate tumor-promoting mechanisms. Therefore a strategy capable of inducing hypomethylation of selected genes is needed. Towards this goal, we designed a strategy to induce demethylation of a coordinated gene program by using Ten-eleven translocation (TET1) dioxygenase, which converts 5 -methylcytosine to 5-hydroxymethylcytosine. We constructed a fusion gene TET1-DBD containing the catalytic domain of TET1 and the DNA binding domain of Snail, the transcription factor that regulates epithelial-to-mesenchymal transition (EMT). We hypothesized that this fusion gene will bind to promoters targeted by Snail, induce hypomethylation, reactivate gene expression, and block EMT. To test this hypothesis, we used TET1-DBD and measured induction of EMT in an ovarian (SKOV3) and breast cancer (MCF10A) model driven by TGF-β. Genome-wide DNA methylation was assessed by Reduced Representation Bisulfite Sequencing (RRBS) to measure the downstream targets of TET1-DBD. TET1-DBD increased mRNA and protein expression levels of E-cadherin in transfected cells and prevented TGF-β induced expression of fibronectin and vimentin in MCF10A and SKOV3 cells. RRBS analysis demonstrated hypomethylation of genes targeted by Snail-DBD. Our results suggest that TET1-DBD selectively binds to and hypomethylates promoters of genes targeted by Snail, resulting in inhibition of the EMT program. We propose a novel approach to induce selective promoter hypomethylation and to block key oncogenic processes by using TET1 fused to a transcription factor “carrier”.

Citation Format: HAO HUANG, Qing Yu, Maooj Kandpal, Ramana V. Davuluri, Daniela Matei. Pathway-directed DNA demethylation as an epithelial to mesenchymal targeting strategy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1396.
Abstract 1402: Silencing of B4GALT1 inversely regulates malignant phenotypes of hepatocellular carcinoma cells
Authors: Chen Po-Da , Chang Ai-An , Wu Yao-Ming , Huang Min-Chuan
Published: August 2018

Identifying molecular targets for hepatocellular carcinoma (HCC) is an urgent need to overcome the treatment failure and death from cancer cell invasion and metastasis. Beta-1,4-galactosyltransferase 1 (B4GALT1) has been documented as the key enzyme in morphogenesis and cellular adhesion, for it adds galactose to N-acetylglucosamine residues of glycoprotein carbohydrate chains; whereas abnormal B4GALT1 expression is associated with tumor progress in many cancers. However, functional roles of B4GALT1 in HCC remains unclear. With clinical correlation, the immunohistochemistry confirmed that lower expression of B4GALT1 in cancer tissue is associated with higher ratio of vascular invasion and worse overall survival. Consistently, stable knockdown of B4GALT1 regarding HCC cell lines promoted cell migration, and invasion; as the overexpressed B4GALT1 inhibited cell migration and invasion of HCC cell lines. Moreover, our data suggested that down-regulated B4GALT1 modified LEL lectin, and interfered hepatocyte growth factor receptor (HGFR), Epidermal growth factor receptor (EGFR), and Axl signaling. Given that, B4GALT1 is sufficient to inversely regulate malignant behaviors of HCC cells with a significant correlation between gene expression and clinical prognosis, implying that B4GALT1 played a crucial role in cancer progress of HCC.

Citation Format: Po-Da Chen, Ai-An Chang, Yao-Ming Wu, Min-Chuan Huang. Silencing of B4GALT1 inversely regulates malignant phenotypes of hepatocellular carcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1402.
Abstract 1409: p53 negatively regulates keratin 17 expression in oral squamous cell carcinoma
Authors: Enaka Mayu , Nakanishi Masako , Muragaki Yasuteru
Published: August 2018

Background: Cytokeratin 17 (K17) has been shown to promote tumorigenesis and aggressiveness in oral squamous cell carcinomas (OSCCs) and other various carcinomas. Although p53 reportedly induces K17 transcription by irradiation, the correlation between p53 and K17 in OSCCs remains unknown. Methods: Human OSCC cell lines SAS and Ca9-22 were examined by Western blot, immunohistochemistry, ChIP assays, and overexpression of wild-type p53. Biopsy specimens from patients with OSCC were used for immunohistochemistry.Results: Western blot and immunohistochemistry showed that K17 expression negatively correlated with p53 expression. In biopsy specimens, positive staining for K17 was observed in OSCC cells that were negative for p53 in a mutually exclusive manner. SAS cells, which have higher K17 expression and almost negative p53 expression, showed more aggressive characteristics than Ca9-22 cells. A mutation to cause a premature stop codon was identified in the TP53 gene in SAS cells by DNA sequencing, whereas no mutation in the TP53 gene was identified in Ca9-22 cells. In addition, ChIP analysis showed that p53 bound specifically to the promoter region of the K17 gene. Furthermore, overexpression of wild-type p53 suppressed K17 expression in SAS cells. Conclusion: p53 acts as a direct transcriptional repressor of K17 in OSCCs. The interaction between p53 and K17 may regulate aggressiveness of the carcinoma cells.

Citation Format: Mayu Enaka, Masako Nakanishi, Yasuteru Muragaki. p53 negatively regulates keratin 17 expression in oral squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1409.
Abstract 141: HEY1-mediated inhibition of glioma stem cell proliferation is associated with restoration of glioma stem cell division asymmetry and transcriptional repression of PDGFRA
Authors: Bonnin Damian A. Almiron , Sullivan Jaclyn , Israel Mark A. , Havrda Matthew Havrda C.
Published: August 2018

Emerging evidence suggests that deregulation of cell-fate regulatory mechanisms in subpopulations of stem-like tumor cells can contribute to the initiation, progression, and recurrence of glioma. In this study, we report that Hey1 expression suppresses the expansion of oligodendroglial progenitor (OPC)-like glioma stem cells, which are a putative cell of origin for high-grade gliomas. We found that Hey1 expression reduced the proliferation of primary neural progenitor cells isolated from mice without the tumor suppressor Tp53, and OPC-like glioma stem cell cultures isolated from a mouse model of glioma driven by an EGFR gain-of-function mutation and Tp53 loss (v-ErbB/p53-/-). Further analysis of these cultures revealed that Hey1-mediated reductions in proliferation were associated with suppression of self-renewal and a reduced percentage of symmetric cell divisions. Mechanistically, we found that HEY1 directly bound to novel promoter elements and repressed the mRNA expression of a key marker and mitogenic driver of OPCs, the PDGF Receptor A (Pdgfra). Furthermore, Hey1-mediated of Pdgfra expression was associated with inactivation of the canonical PDGF/PDGFRA downstream target, extracellular signal-regulated kinases (ERK), in v-ErbB/p53-/- glioma stem-like cells. Key findings made in the murine system were validated in patient-derived glioma stem-like cells. Moreover, analyzing publicly available databases, we found that the subset of glioma patients with high levels of HEY1 expression had improved survival compared to patients with tumors expressing low levels of HEY1. Further supporting a role for HEY1 in the regulation of the oligodendroglial lineage, ontologic analysis revealed that the subset of patients with high levels of HEY1 expression were also characterized by the expression of gene sets associated with oligodendroglial differentiation. These cellular, molecular and genetic findings provide support for a model in which HEY1 functions to suppress glioma progression by inhibiting the expansion of glioma stem cells.

Citation Format: Damian A. Almiron Bonnin, Jaclyn Sullivan, Mark A. Israel, Matthew Havrda C. Havrda. HEY1-mediated inhibition of glioma stem cell proliferation is associated with restoration of glioma stem cell division asymmetry and transcriptional repression of PDGFRA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 141.
Abstract 1421: Flexible tools for the development and performance verification of customized target enrichment panels
Authors: Hendrickson Cynthia L. , Mauceli Evan , Barry Andrew , Patel Kruti , Huang Catherine , Adams Scott , Anekella Bharathi
Published: August 2018

Implementation of next generation sequencing for variant identification and discovery presents difficulties both in the selection of genomic loci for inclusion in a panel, as well as the ability to effectively verify the performance of the assay based on the content selected. Balancing the relevance of genomic content with the practical hurdles of developing specific assays necessitates new approaches for the application of next generation sequencing toward precision medicine that are aimed at providing the flexibility of content to efficiently provide data capable of testing fundamental biological hypotheses.

NEBNext Direct Custom Ready Panels overcome these obstacles by enabling the rapid development and deployment of customized target enrichment panels. This offering allows researchers to select from a large library of genes for which baits have been developed and optimized to produce sequencing data with extremely high specificity and coverage uniformity. These panels are effective in targeting a wide range of content, from highly focused, single-gene panels, to comprehensive panels comprised of hundreds of genes.

In a similar approach for the verification and validation of new panels, SeraCare has developed the VariantFlex™ system, which is comprised of a broad library of mutations to develop custom controls and reference materials for NGS-based assays. These biosynthetic constructs contain variants such as SNVs, indel, frameshift and fusion variants that can be used to formulate controls across a range of variant allele frequencies, providing the necessary content and flexibility to verify assay performance.

Here we will present data demonstrating the combined utility of these offerings to assess target enrichment panel performance with a range of genomic content, panel sizes and variant allele frequencies.

Citation Format: Cynthia L. Hendrickson, Evan Mauceli, Andrew Barry, Kruti Patel, Catherine Huang, Scott Adams, Bharathi Anekella. Flexible tools for the development and performance verification of customized target enrichment panels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1421.
Abstract 1425: A multi-enzyme DNA repair mix improves library quality and sequencing accuracy in FFPE tumor samples
Authors: Liu Pingfang , Heider Margaret , Song Chen , Chen Lixin , Ettwiller Laurence , Higgins Lauren , Dimalanta Eileen , Davis Theodore , Evans Thomas
Published: August 2018

Next-generation sequencing (NGS) methods are used extensively to profile mutations present in diseased human tissues. These genomic approaches hold great promise for personalized medicine but sequencing accuracy is essential for proper patient diagnosis and determining a treatment plan. A common source of DNA for genomic profiling is formalin-fixed, paraffin-embedded (FFPE) tissue samples obtained from patient biopsy. FFPE DNA poses important challenges for preparing NGS libraries including low input amounts and poor DNA quality, resulting from extensive fixation- and storage-induced DNA damage. Additionally, these damage-induced sequencing artifacts raise the background level of mutations, making it difficult to discern true, low frequency, disease-causing variants from noise. We previously showed that a major fraction of somatic mutations described in publicly available datasets are due to such sequencing artifacts (Chen et al., Science 2017). Furthermore, we showed that enzymatic repair of DNA before library preparation improves the library quality and reduces background noise. We developed a second-generation DNA repair enzyme mix (V2) that efficiently repairs the most prevalent damage types found in FFPE DNA and further improves the quality and yield of NGS libraries. Additionally, we tested the efficacy of the V2 repair mix in improving sequencing accuracy for FFPE DNA samples obtained from different cancer tissues. We performed target enrichment on a panel of 151 cancer genes, deep sequenced, and performed variant analysis. For a subset of variants, we further validated our results using a droplet digital PCR (ddPCR) assay. Both methods showed that the V2 repair mix did not alter the overall frequency of variants identified, thus it did not introduce bias, but significantly improved the sequencing accuracy by reducing the number of false variant calls. Therefore, enzymatic repair is a critical first step in preparing FFPE DNA sequencing libraries, allowing more sensitive and robust detection of low frequency, disease variants.

Citation Format: Pingfang Liu, Margaret Heider, Chen Song, Lixin Chen, Laurence Ettwiller, Lauren Higgins, Eileen Dimalanta, Theodore Davis, Thomas Evans. A multi-enzyme DNA repair mix improves library quality and sequencing accuracy in FFPE tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1425.
Abstract 1429: MYH8 R1292X: A novel mutation in relapsed AML induces EMT features and poor prognosis
Authors: Park Hyejoo , Kim Daeyoon , Kim Dongchan , Park Yungyeong , Koh Youngil , Yoon Sung-Soo
Published: August 2018

Introduction: Recent advances in tumor genomic analysis have led to the discovery of NPM1, FLT3, CEBPA, MLL, NRAS, and RUNX1 alterations as the cause of AML. Nevertheless, there is a limit to the treatment and clarification of AML, and research for the identification of novel genetic alterations that cause AML is actively underway.

Materials and methods: In this study, we performed Whole exome sequencing (WES) with 53 AML patient's samples and conducted targeted re-sequencing using 391 AML patient's samples based on locus of somatic mutation that were found by WES. For functional validation of novel oncogenic mutations, we used CRISPR-Cas9 system to generate knock-in (KI) cell line. For characterization of mutant cells, we performed proliferation assay, cell cycle assay, adhesion assay, and wound healing assay. Epithelial to mesenchymal transition (EMT) markers were checked by western blotting.

Results: Using WES and targeted resequencing, we could identify MYH8 R1292X novel mutation as recurrent potentially oncogenic mutation. Additional validation using separate AML cohort revealed MYH8 R1292X variants in four AML patients, suggesting that MYH8 R1292X is potential oncogenic mutation. In functional validation using KI cell line, we could not find change in morphology of KI cells. However, there was a difference in proliferation – the rate of proliferation was faster in KI cells than in cells without mutation. In the cell cycle assay, the mutant cells showed more S phase DNA than the non-mutant cells. Wound healing assay showed that the mutant cells had higher migration ability and lowered the ability of adhesion in comparison. PCR and western blot showed that EMT markers except vimentin increased in mutant cells.Survival analysis based on TCGA data showed that both the overall survival and the disease-free survival curves were significantly different according to MYH8 alterations.

Conclusion: Taken together, we conclude that the novel alteration MYH8 R1292X is associated with recurrent AML and poor prognosis by increasing migration, and inducing an increase in EMT markers.

Citation Format: Hyejoo Park, Daeyoon Kim, Dongchan Kim, Yungyeong Park, Youngil Koh, Sung-Soo Yoon. MYH8 R1292X: A novel mutation in relapsed AML induces EMT features and poor prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1429.
Abstract 1434: LSR promotes lipid metabolism via beta oxidation and contributes cell viability in epithelial ovarian cancer
Authors: Hiramatsu Kosuke , Serada Satoshi , Fujimoto Minoru , Matsuzaki Shinya , Ueda Yutaka , Yoshino Kiyoshi , Kimura Tadashi , Naka Tetsuji
Published: August 2018

Background:Previously, we identified lipolysis-stimulated lipoprotein receptor (LSR) as a new target of epithelial ovarian cancer (EOC), and we reported inhibitory effect of our newly developed monoclonal antibody (mAb) against LSR-positive ovarian cancer cells in vitro and in vivo. We also demonstrated that LSR took in triglyceride-rich protein and promoted cell proliferation, however, LSR function in EOC cells is not investigated enough. Therefore, we aimed to reveal the function of LSR in EOC cells focusing on lipid metabolism including beta oxidation and subsequent TCA cycle.

Material and Method: Using LSR-positive ovarian cancer cell lines (OVCAR3 and RMG-I), we investigated activation of beta-oxidation by LSR after administration of VLDL which is one of the triglyceride-rich protein. Moreover, we constructed LSR-knockdown EOC cells and investigated the effect of VLDL administration in these cells. In addition, we showed inhibitory effect of our anti-LSR mAb against lipid metabolism. Expression of beta-oxidation related proteins were analyzed by western blot analysis. Production of acetyl CoA and ATP were measured using each assay kit. Cell viability was analyzed by WST-8 assay and thymidine incorporation assay.

Results: In LSR-positive EOC cells, LSR promoted uptake of VLDL in glucose restricted environment compared with LSR-knockdown cells (p < 0.05) and VLDL administration promoted acetyl CoA and ATP production (p < 0.05), suggesting that beta-oxidation, TCA cycle and electron transport system were activated by fatty acid from VLDL in LSR-positive cells. Moreover, in LSR-positive EOC cells, VLDL administration increased viable cells compared with LSR-knockdown cells (p < 0.05), however, DNA synthesis was not promoted (p < 0.05). These results showed that VLDL uptake via LSR promoted lipid metabolism and contributed cell viability. Finally, our anti-LSR mAb inhibited these processes.

Conclusion: In glucose restricted environment, LSR takes in triglyceride-rich protein, activates lipid metabolism via beta-oxidation and contributes cell viability in LSR-positive EOC cells.

Citation Format: Kosuke Hiramatsu, Satoshi Serada, Minoru Fujimoto, Shinya Matsuzaki, Yutaka Ueda, Kiyoshi Yoshino, Tadashi Kimura, Tetsuji Naka. LSR promotes lipid metabolism via beta oxidation and contributes cell viability in epithelial ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1434.
Abstract 1442: Novel linkage of thymidine catabolism and the glycolytic pathway in human cancer cells
Authors: Tabata Sho , Yamamoto Masatatsu , Goto Hisatsugu , Nishioka Yasuhiko , Tomita Masaru , Soga Tomoyoshi , Furukawa Tatsuhiko , Akiyama Shin-ichi
Published: August 2018

Thymidine phosphorylase (TP), a rate-limiting enzyme in the thymidine catabolic pathway, catalyzes the reversible conversion of thymidine to thymine and 2-deoxy-D-ribose 1-phosphate (DR1P). We previously demonstrated that TP is identical to an anigogenic factor, platelet-derived endothelial cell growth factor (PD-ECGF). Although many reports indicate that TP has angiogenic activity and plays a pivotal role in tumor progression, the mechanism of the TP functions is not fully understood. Here, we find that TP-mediated thymidine catabolism can supply the carbon source in the glycolytic pathway and thus contribute to cell survival under conditions of nutrient deprivation. In certain procaryotes, phosphopentosemutase converts thymidine-derived DR1P to 2-deoxy-D-ribose 5-phosphate (DR5P), which is then converted to glyceraldehyde 3-phosphate (GAP) and acetaldehyde by deoxyriboaldorase (DERA). Given that GAP is an intermediate in the glycolytic pathway and the pentose phosphate pathway (PPP), we hypothesized that the activation of thymidine catabolism by TP could supply the carbon source for those pathways. However, the thymidine catabolic pathway in mammalian cells remains unclarified. We used 13C-labeled thymidine (13C5-thymidine) as a tracer and examined whether 13C5-thymidine-derived metabolites enter the glycolytic pathway and the PPP in TP-expressing cancer cells using capillary electrophoresis time-of-flight mass spectrometry. Thymidine was converted to metabolites, including glucose 6-phosphate, lactate, 5-phospho-α-ribose 1-diphosphate, and serine, via the glycolytic pathway both in vitro and in vivo. These thymidine-derived metabolites were required for the survival of cells under low-glucose conditions. Furthermore, enhanced thymidine catabolism was observed in human gastric cancer. These findings suggest that the thymidine catabolism plays an important role in the survival and growth of cancer cells in a microenvironment where glucose is insufficient.

Citation Format: Sho Tabata, Masatatsu Yamamoto, Hisatsugu Goto, Yasuhiko Nishioka, Masaru Tomita, Tomoyoshi Soga, Tatsuhiko Furukawa, Shin-ichi Akiyama. Novel linkage of thymidine catabolism and the glycolytic pathway in human cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1442.
Abstract 1444: RhoC regulation of inflammatory breast cancer metabolism
Authors: Goo Laura E. , Yates Joel A. , Bao Liwei , Wu Zhifen , Merajver Sofia D.
Published: August 2018

Inflammatory breast cancer (IBC) is an extremely aggressive and lethal type of cancer due to its ability to rapidly metastasize. Our previous reports have shown that the metabolic characteristics of IBC are altered from those of normal breast epithelial cells. Specifically, the levels of the metabolite N-acetylaspartate (NAA) are very high in the IBC-derived triple negative cell line SUM149 relative to the triple negative cancer cell line MDA-MB-231. Recent studies have also correlated high levels of tumoral NAA with significantly lower survival rates in ovarian cancer.

N-acetylaspartate (NAA) is the second most abundant metabolite in the brain, only exceeded by glutamate. NAA is synthesized from aspartate and acetyl-CoA by the enzyme Asp-NAT, which is encoded for by the gene NAT8L. The catabolism of NAA to aspartate and acetate is carried out by the enzyme aspartoacyclase (ASPA). In the central nervous system (CNS), altered levels of NAA have been historically used as a marker for neurodegenerative diseases such as Canavan disease, a fatal genetic disorder caused by a deleterious mutation in the ASPA gene. However, the fundamental role of NAA, especially in the context of cancer remains elusive.

We seek to understand and describe the role of NAA in the adapted metabolic pathways of inflammatory breast cancer that enable proliferation and metastasis of the disease. Our previous work revealed that the pro-metastatic small GTPase RhoC acts as a regulator of NAA metabolism in SUM149 cells. Knockdown of RhoC using shRNA significantly decreases NAT8L expression. RhoC and RhoA knockout cell lines have been generated using CRIPSR-Cas9 in both SUM149 and MDA-MB-231 cells to further distinguish the relationship between NAA and RhoC in these different cell lines. We have conducted metabolic studies to determine the relative abundance of common metabolites, including NAA, throughout glycolysis, the pentose-phosphate pathway, and the tricarboxylic acid cycle. We have performed similar metabolomics using xenograft mice implanted with these CRISPR knockout cell lines to determine in vivo recapitulation of the NAA phenotypes. Our work ultimately hopes to identify promising therapeutic pathways of NAA as well as further characterize NAA's role as a potential oncometabolite.

Citation Format: Laura E. Goo, Joel A. Yates, Liwei Bao, Zhifen Wu, Sofia D. Merajver. RhoC regulation of inflammatory breast cancer metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1444.
Abstract 1447: Aberrant tryptophan catabolism marked by high kynureninase expression contributes to immunosuppression and poor outcome in lung adenocarcinoma
Authors: Ostrin Edwin J. , Fahrmann Johannes F. , Tanaka Ichidai , Celiktas Muge , Aguilar Clemente , Aguilar Mitzi , Dennison Jennifer B. , Murage Eunice , Tripathi Satyendra C. , Delgado Oliver , Wang Hong , Rodriguez-Canales Jaime , Behrens Carmen , Wistuba Ignacio I. , Taguchi Ayumu , Hanash Samir M.
Published: August 2018

Low tryptophan levels promote tumor immune evasion by suppressing immune function. Elucidation of the immunomodulatory effects of altered tryptophan catabolism has relevance to cancer immunotherapy. Previous studies have largely focused on the role of the rate-limiting enzyme indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan depletion in the microenvironment. However, IDO1 levels are highly heterogeneous in different cancers, and numerous other downstream tryptophan catabolites have also been shown to have immunomodulatory activity. We surveyed the proteomes of 123 cancer cell lines for regulators of tryptophan metabolism which revealed overexpression of kynureninase (KYNU) in KEAP1 mutant lung adenocarcinomas. Functional analysis indicated that KYNU expression is regulated through nuclear factor, erythroid 2-like (Nrf2) activation. KYNU-high cell lines exhibited increased secretion of KYNU-derived anthranilate/3-hydroxyanthranilate. Ex-vivo studies using isolated PBMCs demonstrated that 3-hydroxyanthranilate reduced CD8+ T-cell viability. KYNU mRNA expression in three independent datasets of lung adenocarcinomas and additionally KYNU protein expression in lung adenocarcinoma tissue microarrays revealed that high KYNU expression predicts poor survival and disease recurrence. Our findings indicate that KYNU promotes immune suppression and is an independent prognostic marker for lung adenocarcinoma.

Citation Format: Edwin J. Ostrin, Johannes F. Fahrmann, Ichidai Tanaka, Muge Celiktas, Clemente Aguilar, Mitzi Aguilar, Jennifer B. Dennison, Eunice Murage, Satyendra C. Tripathi, Oliver Delgado, Hong Wang, Jaime Rodriguez-Canales, Carmen Behrens, Ignacio I. Wistuba, Ayumu Taguchi, Samir M. Hanash. Aberrant tryptophan catabolism marked by high kynureninase expression contributes to immunosuppression and poor outcome in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1447.
Abstract 1448: Integrated molecular analysis reveals novel SPARC-regulated metabolic programming in ovarian cancer
Authors: Naczki Christine , John Bincy , Patel Chirayu , Lafferty Ashlyn , Ghoneum Alia , Afify Hesham , Davis Amanda , Jin Guangxu , Said Neveen
Published: August 2018

We have reported a tumor suppressor effect of SPARC in ovarian cancer as both host and tumor SPARC are implicated in anti-proliferative, anti-adhesive effects as well as normalization of the peritoneal tumor microenvironment. Herein, we extend our studies using a syngeneic model of peritoneal ovarian carcinomatosis to gain comprehensive insight on the effect of SPARC on metabolic programming of the ovarian cancer ecosystem. We performed comprehensive metabolomic and transcriptomic profiling of micro-dissected ID8 omental tumors that developed after intra-peritoneal injection in SP-/- and SP+/+ mice. Integrated analysis revealed that the accelerated growth of ID8 tumors in SP-/- mice was associated with metabolic programming of cancer cells with up-regulation of the genes involved in glycolysis, fatty acid oxidation, and oxidative phosphorylation. Tumors also exhibited perturbed redox homeostasis, as well as mitochondrial and ribosomal biogenesis. Comparative analysis of the syngeneic tumors with human high grade serous ovarian cancer (HGSC) revealed upregulation of the same genes involved in metabolic programming with inverse correlation with SPARC transcript expression, implying a role of stromal-SPARC in the metabolic programming of HGSC. Bio-energetic studies revealed that SPARC inhibits basal glycolysis, glycolytic reserve, oxygen consumption rate and mitochondrial ATP synthesis. To the best of our knowledge this is the first study that characterizes the metabolic programming of the ovarian cancer ecosystem by host-SPARC.

Citation Format: Christine Naczki, Bincy John, Chirayu Patel, Ashlyn Lafferty, Alia Ghoneum, Hesham Afify, Amanda Davis, Guangxu Jin, Neveen Said. Integrated molecular analysis reveals novel SPARC-regulated metabolic programming in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1448.
Abstract 1457: SCAP/SREBP-1 regulates lipid metabolism reprogramming in cancer cell
Authors: cheng chunming , geng feng , cheng xiang , chakravarti arnab , guo deliang
Published: August 2018

Warburg initial observation shows tumorigenesis is associated with an increased glucose consumption. Recently, accumulating evidence show that lipid metabolism is reprogrammed in cancers. Elevated lipogenesis which contributes to the development of malignant phenotypes is known to meet requirements for cancer cell rapid growth. However, how they interact to promote cancer growth remain unclear.

Through biochemistry and molecular biology assays, we find that EGFR signaling, by increasing glucose uptake, promotes N-glycosylation of sterol regulatory element-binding protein (SREBP) cleavage-activating protein (SCAP) and consequent activation of SREBP-1, an ER-bound transcription factor with central roles in lipid metabolism. N-glycosylation promotes SCAP stabilization and dissociates from Insig-1, allowing movement of SCAP/SREBP to the Golgi and consequent SREBP activation. Blocking SCAP N-glycosylation ameliorates EGFRvIII-driven glioblastoma growth in xenograft mouse model.

These results show glucose consumption and lipogenesis are linked as reciprocal metabolic cross-talk in tumorigenesis, and targeting SCAP and its N-glycosylation may provide a promising means of more effective cancer therapy.

Citation Format: chunming cheng, feng geng, xiang cheng, arnab chakravarti, deliang guo. SCAP/SREBP-1 regulates lipid metabolism reprogramming in cancer cell [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1457.
Abstract 1461: Targeting mitotic kinases in breast cancers in Latinas
Authors: Rivera-Rivera Yainyrette , Marina Mihaela , King Jamie , Lee Miyoung , Saavedra Harold I.
Published: August 2018

African Americans and Latino women (Latinas) in the US have higher risks of developing molecular subtypes of breast cancer that associate with poor-prognosis, including hormone receptor-negative (HR-): triple-negative (ER-PR-Her2-), and Her2-positive breast cancer relative to whites. These women also present with higher-stage breast tumors relative to whites. We specifically study Puerto Rican women, a population in which breast cancers are the primary cause of cancer-related death, and who display a higher frequency of HR- breast tumors than other Latinas. We propose that chromosome instability (CIN) is a principal contributor to poor prognosis of breast cancers in African Americans and Latinas, since HR- breast cancers accumulate the highest CIN of all breast cancer subtypes. CIN in cancers correlates with poor clinical outcomes and centrosome amplification (CA) -defined as the presence of 3 or more centrosomes within a cell-, and defective mitosis are two principal drivers of CIN. Albeit CA correlates with invasion, metastasis, poor clinical outcomes, and HR- subtypes, molecular mechanisms responsible for CA in breast cancers are still unknown. We have identified MPS1 and NEK2 as centrosomes/mitotic kinases that drive CA/CIN in HR- breast cancer cells, and that can potentially be targeted to curb the malignant behavior of the most aggressive breast cancer subtypes affecting ethnic minorities. MPS1 and NEK2 are upregulated in HR- breast tumors and are co-overexpressed in several predictive signatures of poor prognosis subtypes and metastasis. Our preliminary data indicated that these kinases are overexpressed in over 60% breast cancers from Puerto Rican women and that they are exclusively co-upregulated in basal breast cancers. Our preliminary data also showed that these two mitotic kinases can significantly influence epithelial-to-mesenchymal transition (EMT) and invasion -activities never described for mitotic kinases. Also, although inactivating NEK2 suppresses S phase, inhibition of MPS1 reduces survival of breast cancer cells. Because inhibitors are available for MPS1 and NEK2, it would be feasible to target these kinases to combat metastatic HR- breast cancers. Our work will allow the identification of pathways influenced by mitotic regulators in breast cancer cells driving invasion and metastasis and will provide potential prognostic markers for high-risk breast tumors in various ethnic/racial groups, including African American and Latinas (including Puerto Rican women).

Citation Format: Yainyrette Rivera-Rivera, Mihaela Marina, Jamie King, Miyoung Lee, Harold I. Saavedra. Targeting mitotic kinases in breast cancers in Latinas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1461.
Abstract 1465: Clinicopathologic characteristics of TZAP mutation and expression in hepatocellular carcinomas
Authors: Lee Jae-Ho , Park Keon Uk
Published: August 2018

The zinc finger protein ZBTB48 is a telomere-associated factor and renamed it as telomeric zinc finger-associated protein (TZAP). It binds preferentially to long telomeres competing with TRF1 and TRF2. However, its expression in cancers has not been performed. Methods: In the present study, we analyzed TZAP mutation and expression in 123 hepatocellular carcinomas (HCC) and its association with telomere length and TERT expression was also investigated. TZAP mutations (c.1272G>A, L424L) was found in 10.6% (13/123) and TZAP expression level was not different between HCC and paired non-cancerous tissues. There was no association between TZAP mutation and TZAP expression (p = 0.53). TZAP mutation did not have any clinical and prognostic values in HCC. However, TZAP expression was positively associated with TERT expression (29.4% vs. 80.0%, P = 0.047). And, TZAP expression tended to induce poorer survival result (overall survival, χ2= 2.83, P = 0.092; disease-free survival, χ2= 3.59, p = 0.058). TCGA data also showed a positive correlation between TZAP and TERT expression levels (r = 0.839, p < 0.001). However, TCGA survival analysis showed no prognostic value of TZAP expression in HCC (p = 0.576). This result suggested that TZAP expression appears to be a possible prognosis marker dependently with TERT expression in HCC.

Citation Format: Jae-Ho Lee, Keon Uk Park. Clinicopathologic characteristics of TZAP mutation and expression in hepatocellular carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1465.
Abstract 1471: Genomic drivers differ across 33 tumor types, but factors regulating hallmarks of cancer are similar
Authors: Plaisier Christopher L.
Published: August 2018

The unique complement of genes expressed in a given cell type modifies the response to a specific somatic mutation. Thus, each tumor type would present with a different set of mutations that modulate the activity of common factors regulating genes which influence the cancer phenotypes (e.g. the hallmarks of cancer). We assessed the validity of this hypothesis by applying the SYstems Genetics Network AnaLysis (SYGNAL) pipeline to the ~10,000 multi-omic profiles across 33 tumor types from The Cancer Genome Atlas (TCGA). The SYGNAL pipeline synthesizes correlative approaches with mechanistic knowledge to construct a gene regulatory network. A basis of the SYGNAL approach is the discovery of biclusters: gene modules that are both co-expressed and co-regulated over subsets of tumors, by specific transcription factors (TFs) and miRNAs. On top of the biclusters we discover potential mechanistic influences of somatic mutations modulating the activity of these regulators. We discovered 284 somatically mutated genes modulating the activity of 187 transcriptional regulators (175 TFs and 12 miRNAs) which regulated 7,786 significantly co-expressed biclusters that were significantly associated with patient survival. The discovery of 1.5 fold more somatic mutations than transcriptional regulators is consistent with our hypothesis that mutations will be unique to tumor types while the regulation of the genes involved in the hallmarks of cancer will be common across tumor types. We also find that only 15% of causal flows (mutation->regulator->gene) are observed across multiple tumor types. We observed only four causal flows across three tumor types (NFE2L2->BCL6B->HSPG2 for BLCA, ESCA, and HNSC tumor types; TP53->ERG->MTX1 for BRCA, LUAD, and STAD tumor types; TP53->ZNF511->NAA38 for LUAD, PRAD, and READ tumor types; and TP53->AEBP2->THOC6 for COAD, KICH, and READ tumor types). There were no causal flows observed across more than three tumor types. Using our top-down systems approach we are able to catalog the impact of somatic mutations on the transcriptional regulatory network across 33 tumor types. We are working to replicate the co-expression and survival relationships we discovered in independent cohorts for each tumor type. In addition, we are working to identify potential therapeutic targets at both the regulator and gene level. Future studies will use predictive models based on our detailed transcriptional regulatory networks to identify transcriptional regulators driving cancer phenotypes that won't have general toxicity in normal cells.

Citation Format: Christopher L. Plaisier. Genomic drivers differ across 33 tumor types, but factors regulating hallmarks of cancer are similar [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1471.
Abstract 1472: The role of the BAF complex in Wnt signaling-mediated transcriptional regulation in colorectal cancer
Authors: Sen Madhobi , Hamdan Feda H. , Wang Xin , Rapp Jacobe , Johnsen Steven A.
Published: August 2018

Recent genome- and exome-wide sequencing studies have revealed a close association between the epigenome and the pathogenesis of cancer. Not only were chromatin regulators found to be commonly mutated in a wide range of cancers, but a class of these regulators, the ATP-dependent chromatin remodelers, especially subunits of the mammalian BAF complex, were among the most frequently mutated group of genes across cancer types, mutated in over 20% of cancers. Among these subunits, loss of function mutations in ARID1A (AT-rich interactive domain-containing protein 1A) are most frequent across cancer types including 10% of colorectal cancer (CRC). Very interestingly, a recent publication described the pivotal role of the loss of ARID1A in driving CRC wherein its inactivation alone led to the formation of invasive adenocarcinomas in mice. However, surprisingly, in contrast to the expected tumor suppressive role of ARID1A in CRC, we observe that the knockout (KO) of ARID1A in CRC cell lines leads to impaired proliferation. Moreover, subcutaneous xenografts in SCID/SHO mice using ARID1A KO CRC cells did not form more aggressive tumors than their wild type counterparts. One of the most commonly occurring mutations in CRC is in the APC gene, which leads to hyperactive Wnt signaling. Thus CRC progression is typically highly dependent on this pathway. Notably, it is reported that loss of ARID1A in the context of APC mutations results in diminished tumor formation in mice and increased differentiation. This led us to hypothesize that ARID1A is required for Wnt signaling-mediated transcriptional (de)regulation in CRC. To uncover this further, we utilized several publically available ChIP-seq, RNA-seq and ATAC-seq datasets as well as our own ChIP-seq data for ARID1A in the HCT116 cell line. We observe a substantial co-localization of the BAF complex with TCF7L2, a downstream effector of the Wnt signaling pathway, suggesting cooperation between these factors. Further, these sites are also co-occupied by AP1 transcription factors. A crosstalk between the TCF7L2 and AP1 factors has been reported in intestinal tumors. From data available in the ARID1A KO system, we observe a downregulation of potential target genes which are co-occupied at neighboring sites by these factors. Therefore, we suggest that ARID1A plays an important role in the regulation of colorectal cancer relevant genes that are targets of TCF7L2/AP1, thus facilitating a pathway that is most commonly hijacked in colorectal cancer.

Citation Format: Madhobi Sen, Feda H. Hamdan, Xin Wang, Jacobe Rapp, Steven A. Johnsen. The role of the BAF complex in Wnt signaling-mediated transcriptional regulation in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1472.
Abstract 1473: Role of acetyltransferases CBP and p300 in de novo fatty acid synthesis in colorectal cancer
Authors: Waddell Aaron , Mahmud Iqbal , Liao Daiqing
Published: August 2018

CBP/p300 are two paralogous lysine acetyltransferases that acetylate protein substrates including histones, and serve as transcriptional co-activators for numerous signaling pathways involved in tumorigenesis and cancer progression. Recently, evidence has emerged that p300 regulates the transcription of genes involved in lipogenesis in cancers. Dysregulated lipogenesis and increased de novo production of fatty acids (FA) represent a major metabolic shift in cancer. De novo FA synthesis in cancer is suggested to be a source of lipids for membrane biogenesis, a reservoir of energy, and a source of pro-survival signaling molecules. Therefore, de novo FA synthesis has been linked to survival and increased proliferation of cancer cells, representing a potential area for therapeutic intervention. While emerging evidence indicates CBP/p300 may play a key role in regulating lipogenesis, little is known about the mechanism of how these proteins control lipid production in different cancers. Colorectal cancer (CRC) is a commonly diagnosed human cancer and is a major cause of cancer-related mortality. Key regulators for de novo FA synthesis, such as FASN, have been reported to be elevated in colorectal cancer. We analyzed publically available data sets and report that in colon adenocarcinoma, the mRNA levels of CBP/p300 positively correlate with the expression of genes involved in lipogenesis, such as FASN, SREBP1 and SREBP2. Furthermore, our analysis shows that EP300 expression is negatively correlated with patient survival. Strikingly, our preliminary data suggests that HDAC inhibitors may regulate p300 activity and could serve as a therapeutic approach for suppressing lipogenesis. We are currently utilizing small molecule inhibitors, genetic manipulation of the CREBBP/EP300 genes, and biochemical experiments to investigate the role of CBP/p300 in de novo FA synthesis in colorectal cancer. We hypothesize that inhibition of CBP/p300 could be an attractive therapeutic option for inhibiting tumor growth through downregulating de novo FA synthesis in colorectal cancer. (Supported by grants from James and Esther King Biomedical Research Program and Bankhead-Coly Cancer Research Program, Florida Department of Health.)

Citation Format: Aaron Waddell, Iqbal Mahmud, Daiqing Liao. Role of acetyltransferases CBP and p300 in de novo fatty acid synthesis in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1473.
Abstract 1474: Identifying novel chromatin binding sites of nucleolin protein in cancer cells
Authors: Wu Guanhui , Onel Buket , Yang Danzhou
Published: August 2018

Nucleolin is an important regulator of cell proliferation and has been reported to play a role in c-Myc transcriptional regulation. Elevated expression levels of nucleolin have been shown in a number of malignant cells, but how nucleolin contributes to cancer development and progression remains unknown. Recently, G-quadruplexes (G4s) have been shown in vivo to form in G-rich sequences with biological importance. Nucleolin has been reported to bind to G-quadruplexes for its biological functions. In particular, G4s have been shown to form in the MYC promoter and inhibit MYC transcription; nucleolin was found to display a remarkable binding affinity to the c-Myc promoter G4 over its best-known RNA target. CX-3543, the first-in-class G-quadruplex-targeting small molecule, was shown to induce nucleolin redistribution from the cell nucleolus to the cell nucleoplasm and apoptosis in cancer cells, which was suggested to act through the c-Myc promoter G-quadruplex. Therefore, unbiased analysis of the genomic binding sites of nucleolin in human chromatin is pivotal in understanding nucleolin's biological functions. Using chromatin immunoprecipitation (ChIP) assay, we demonstrated that nucleolin binds to the c-Myc NHE III1 region in vivo. Using an anti-nucleolin antibody, the isolated DNA from the immunoprecipitated DNA-protein complexes from HeLa cells yielded numerous c-Myc promoter sequences that were determined by real-time PCR, suggesting the direct interaction between nucleolin and the c-Myc promoter G4-forming region in vivo. G4-interactive ligands have been shown to facilitate the formation of G4 structures in cells. To elucidate the association of nucleolin with G-quadruplexes in vivo, we monitored cellular localization of nucleolin before and after G4 ligand treatments and observed a rapid cellular translocation of nucleolin from the cell nucleolus to the cell nucleoplasm. Using ChIP coupled with next-generation sequencing analysis (ChIP-seq), we identified several binding sites of nucleolin in human chromatin. The determined chromatin binding sites of nucleolin will provide insights into the biological functions of nucleolin and its relationship with G-quadruplexes in cancer cells.

Citation Format: Guanhui Wu, Buket Onel, Danzhou Yang. Identifying novel chromatin binding sites of nucleolin protein in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1474.