bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3375: The chromosomal instability in tumorigenesis of esophageal squamous cell carcinoma
Authors: Yan Ting , Cheng Xiaolong , Cui Yongping
Published: August 2018

Chromosomal instability (CIN) is the leading cause of the cell genome instability and is a common trait of more than 70% of human cancers, therefore is implicated as an initiator of tumorigenesis. More importantly, CIN may facilitate the adaptation of tumors to environmental or stromal stress and is implicated in determining tumor progression and associated with poor outcome, tumor relapse, and multi-drug resistance across a range of cancer types. The latest studies suggest that cancer is the result of micro-evolution altermate with macro-evolution. That means the cells get mutations through micro-evolution and expansion by the mutational accumulation; the cells begin to undergo macro-evolution instead of micro-evolution when encounter tumorigenic factors, and CIN will be the main driver for tumor evolution. However, studies focus on genomic signatures, especially for macro-evolutionary events, in esophageal squamous cell carcinoma (ESCC) are limited. We integrated 31 whole genomic sequencing data of ESCC samples from China to investigate underlying evolutionary characteristics in ESCC.

We combined copy number profiles of 1660 cancer specimens from 5 types of gestrointestinal tumors. Different from colorectal carcinoma, liver hepatocellular carcinoma, pancreatic adenocarcinoma and stomach adenocarcinoma, ESCC possesses largely copy number alterations, and frequent copy-number changes were not clustered in specific chromosome. In our cohort, we found whole genome doubling (WGD) that acts as one of mechanisms for polyploidy was predicted as a late event in the majority of ESCC genome. Moreover, loss of heterozygosity events was more likely to occur in chromosomes harboring tumor suppressor genes in ESCC. The 40% of neutral loss of heterozygosity events was not a result of genome doubling suggesting an alternative mechanism for neutral loss of heterozygosity formation. Importantly, deconstruction of copy number alterations extending to telomere revealed that telomere-bounded copy number alterations play a critical role for amplification/deletion of oncogenes/suppressor genes. For well-known genes SOX2, PIK3CA and TERT, almost all of their amplifications were telomere bounded, which was further confirmed in a Japanese ESCC cohort. Furthermore, we provide evidence that karyotype evolution was mostly punctuated in ESCC. Collectively, our data reveal the potential biological role of whole genome doubling, neutral loss of heterozygosity and telomere-bounded copy number alterations, and highlight macro-evolution in ESCC tumorigenesis.

Citation Format: Ting Yan, Xiaolong Cheng, Yongping Cui. The chromosomal instability in tumorigenesis of esophageal 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 3375.
Abstract 3398: Analysis of whole transcriptome RNA-seq of large numbers of clinical FFPE samples
Authors: Newton Yulia , Golovato Justin , Johnson Mark , Rabizadeh Shahrooz , Sanborn Zack , Benz Steve , Vaske Charles J.
Published: August 2018

Background: We evaluate the feasibility, quality, and analytical potential of whole-transcriptome RNA-seq on over one thousand clinical FFPE tumor samples. Transcriptional profiling of RNA is used for clinical decision making in many tumor types. Clinical analysis of RNA is complicated by the common use of formalin-fixed paraffin-embedded (FFPE) tissue storage, which can cause low yield and RNA degradation.

Methods: RNA was extracted from FFPE material using commercially available kits using an RNAseH based ribodeplete. Multiple libraries per sample are sequenced using standard Illumina sequencing. Bowtie2, RSEM, and custom software are used for alignment, transcript quantification, fusion detection, and variant expression analysis.

Results: We observe a >85% success rate on whole transcriptome RNA-seq on our cohort of more than 1000 samples. We find reliable transcript quantification upon successful sequencing, and on a subset of samples quantify differences between FFPE and fresh-frozen material when using ribodeplete. We also compare transcriptional profiles of clinical FFPE samples to an independent set of fresh frozen, poly-A capture samples from The Cancer Genome Atlas (TCGA) and show differences between poly-A capture and ribodeplete RNA isolation methods as well as FFPE vs. FF effects. We present a robust mapping methodology for comparison of public FF poly-A dataset to our FFPE ribodeplete samples. We demonstrate that we are able to utilize this joint gene expression space to perform site of origin prediction on FFPE samples. This is especially important for clinical application in analyzing Cancer of Unknown Primary (CUP) samples as well as detecting outlier samples whose molecular features may suggest additional therapeutic avenues. Finally, we show reliable detection of fusion transcripts from FFPE RNA-seq material from whole-transcriptome analysis and expression of somatic tumor variants detected from DNA sequencing.

Conclusions: Large scale sequencing of RNA from clinical FFPE materials provides reliable transcriptomic results comparable to existing public databases of RNA, enabling research on cohorts of tumors that are FFPE-banked and unavailable as frozen tissue.

Citation Format: Yulia Newton, Justin Golovato, Mark Johnson, Shahrooz Rabizadeh, Zack Sanborn, Steve Benz, Charles J. Vaske. Analysis of whole transcriptome RNA-seq of large numbers of clinical FFPE 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 3398.
Abstract 342: Strigolactone analogues show potential as new combination therapy agents against pancreatic cancer
Authors: Park Matthew D. , Haake Jefferson M. , Parasido Erika , Albanese Christopher , Yarden Ronit I.
Published: August 2018

There is an increasing appreciation for combination therapy of antineoplastic drugs that target key pathways often through a synergistic effect, reducing the chance for tumor growth, self-renewal of cancer stem cell (CSC), spread of metastasis and drug resistance. The combination of DNA repair impairment and DNA damage was shown to be a successful approach. Previously, we had shown that strigolactone (SLs; synthetic analogues, SLAs), a novel class of phytohormones, causes DNA double strand breaks (DSBs) and inhibits breast and osteosarcoma cancer cells and CSC viability. Here, we tested whether SLAs inhibit the growth of pancreatic ductal adenocarcinoma (PDAC) cells and stem cells and whether SLAs sensitize the effects of Gemcitabine (Gemzar), the most commonly prescribed drug for PDAC patients. We show that SLAs induce DSBs in different PDAC cells and the combination of SLAs with Gemcitabine significantly increases apoptosis when compared to PDAC cells treated with Gemcitabine alone. This additive effect is independent of BRCA2 expression, which suggests that SLAs are effective at impairing multiple repair mechanisms and is suitable in combination with multiple DNA damaging agents. Interestingly, we show that SLAs sensitize patient-derived Gemcitabine non-responsive, PDAC Conditionally-Reprogrammed Cells (CRCs) to Gemcitabine, reducing their overall viability by more than 30%. Accordingly, the SLA- Gemcitabine combination has a significant impact on tumorsphere (CSCs) growth outcome. These findings demonstrate the potential for a novel drug combination of SLAs and Gemcitabine and underscore the potential of SLAs for multiple highly valuable translational applications regarding alternative therapies to combat cancer.

Citation Format: Matthew D. Park, Jefferson M. Haake, Erika Parasido, Christopher Albanese, Ronit I. Yarden. Strigolactone analogues show potential as new combination therapy agents against pancreatic 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 342.
Abstract 3427: Gatekeeper inactivation drives glioma progression into secondary glioblastoma
Authors: Granberg Kirsi Johanna , Annala Matti , Jaatinen Serafiina , Haapasalo Joonas , Yli-Harja Olli , Haapasalo Hannu , Zhang Wei , Nykter Matti
Published: August 2018

<Glioblastoma (GBM) is the most common and lethal form of brain cancer in humans. Median survival is 15 months with best available treatment. Most GBMs arise de novo (primary GBM), but 5 - 10% progress from lower grade gliomas (secondary GBM). As progression of low grade glioma into secondary GBM significantly impacts prognosis, a better understanding of this process is paramount for treatment and monitoring of affected patients. In this study, we applied whole genome and transcriptome sequencing to primary glioma and relapsed secondary GBM tissue from seven patients with progression. All primary gliomas carried IDH1 mutations, and in all cases the mutation was inherited by the secondary GBM. ATRX alterations in all five astrocytomas and TERT promoter mutations in both 1p19q-codeleted oligoastrocytomas were also inherited in progressed tumors. In five patients, progression was associated with increased genomic instability, whereas mutation load was significantly increased in two other patients. One of them exhibited a hypermutation signature caused by a mutation in the proofreading domain of DNA polymerase epsilon, while the second had lost both copies of the DNA mismatch protein MSH2. In addition, both 1p19q-codeleted tumors had acquired focal inactivating deletions of the protein tyrosine phosphatase PTPRD at progression, suggesting a novel driver mechanism for GBM progression. The most common progression-related genomic alterations were CDKN2A deletions, TP53 mutations, RB1 deletions, PTEN deletions, and deletions of genes crucial to the double strand break repair pathway. Taken together, progression into secondary GBM was significantly related to deletions in tumor suppressor genes as well as TP53 mutations. Disruption of these gatekeepers appears to be a significant mechanism for glioma progression.>

Citation Format: Kirsi Johanna Granberg, Matti Annala, Serafiina Jaatinen, Joonas Haapasalo, Olli Yli-Harja, Hannu Haapasalo, Wei Zhang, Matti Nykter. Gatekeeper inactivation drives glioma progression into secondary glioblastoma [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 3427.
Abstract 3441: Genome-wide gene expression analysis in asbestos-related non-small cell lung cancer
Authors: Kettunen Eeva , Marwah Veer Singh , Wolff Henrik , Greco Dario , Husgafvel-Pursiainen Kirsti
Published: August 2018

Recently we examined genome-wide DNA methylation in lung cancer from patients occupationally exposed to asbestos (Kettunen et al 2017 Int J Cancer). Distinct methylation changes in lung tumors were shown in relation to asbestos exposure and tobacco smoking. Now we have performed genome-wide gene expression microarray experiments with Agilent SurePrint G3 Human GE 8x60K v3 Microarrays using same samples. Patients had been interviewed for work and smoking histories and their pulmonary asbestos fiber counts were measured by electron microscopy. Fresh-frozen lung cancer tissues (LC, n=42) and paired microscopically normal peripheral lung tissues (NT, n=21) were studied. After data processing and analyses for differential gene expression, data were filtered for adjusted p < 0.05 and fold change > 1.5. Principal component analysis showed distinct clusters of normal lung and cancer tissues. In lung cancers compared with their paired microscopically normal lung, 5931 genes such as those involved in neutrophil degranulation and immune system were differentially expressed, with the lowest adjusted p=6.71E-37. In our preliminary analyses, 34 genes in NT and 44 in LC, and 152 genes in NT and 12 in LC showed differential expression when the asbestos-exposed were compared to non-exposed and current smokers to ex-smokers, respectively. The genes differentially expressed in relation to smoking or to asbestos exposure had the lowest adjusted p=8.50E-06 and 9.83E-04, respectively. Within differential gene expression related to asbestos exposure, chemokine activity and regulation of cellular protein metabolic processes were implicated whereas microtubules and positive regulation of transcription were related with tobacco smoking burden. In conclusion, comparison of gene expression patterns between lung cancer tissue and paired normal lung showed distinct principal component analysis clusters. Our preliminary data suggest different major biological processes in gene expression for these exposures. Financial support from the Cancer Society of Finland (2014 and 2015) is gratefully acknowledged.

Citation Format: Eeva Kettunen, Veer Singh Marwah, Henrik Wolff, Dario Greco, Kirsti Husgafvel-Pursiainen. Genome-wide gene expression analysis in asbestos-related non-small cell lung 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 3441.
Abstract 3462: EGFRvIII-Stat5 signaling enhances glioblastoma cell invasion
Authors: Roos Alison , Dhruv Harshil D. , Peng Sen , Inge Landon J. , Tuncali Serdar , Pineda Michael , Millard Nghia , Winkles Jeffrey A. , Loftus Joseph C. , Tran Nhan L.
Published: August 2018

Glioblastoma Multiforme (GBM) is the most common malignant brain tumor in adults. Most GBM patients succumb to the disease less than one-year post diagnosis due to the highly invasive nature of the tumor, which prevents complete surgical resection and gives rise to tumor recurrence. The invasive phenotype also confers radio and chemoresistant properties to the tumor cells; therefore, there is a need to develop new therapeutics that target drivers of GBM invasion. Amplification of EGFR is observed in over 50% of GBM tumors, of which half concurrently overexpress the variant EGFRvIII, and expression of both receptors confers a worse prognosis. EGFR and EGFRvIII cooperate to promote tumor progression and invasion, in part, through activation of the Stat-signaling pathway. Here we report that EGFRvIII activates Stat5 and GBM invasion, in part, by inducing the expression of a previously established mediator of glioma cell invasion and survival, fibroblast growth factor-inducible 14 (Fn14). EGFRvIII-mediated induction of Fn14 expression is dependent upon Stat5 and requires activation of Src, whereas EGFR regulation of Fn14 is dependent upon MEK/ERK-Stat3 activation. Notably, treatment of EGFRvIII expressing GBM cells with the FDA approved Stat5 inhibitor pimozide blocked Stat5 phosphorylation, Fn14 expression, and cell migration. Since EGFR inhibitors display limited therapeutic efficacy in GBM patients, we hypothesize that the EGFRvIII-Stat5-Fn14 signaling pathway represents a node of vulnerability in the invasive GB cell population and that targeting critical effectors in this pathway will limit GBM tumor dispersion, mitigate therapeutic resistance, and increase survival.

Citation Format: Alison Roos, Harshil D. Dhruv, Sen Peng, Landon J. Inge, Serdar Tuncali, Michael Pineda, Nghia Millard, Jeffrey A. Winkles, Joseph C. Loftus, Nhan L. Tran. EGFRvIII-Stat5 signaling enhances glioblastoma cell invasion [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 3462.
Abstract 3467: Growth factor receptor trafficking in neuroblastoma differentiation
Authors: Lesperance Jacqueline , Subramonian Divya , Woodfield Sarah , Guo Rongjun , Bean Andrew , Lopez-Terrada Dolores , Ittmann Michael , Hakim Sara , Zage Peter E.
Published: August 2018

Background/Objectives: UBE4B is an E3/E4 ubiquitin ligase involved in growth factor receptor (GFR) trafficking. The UBE4B gene is located in the chromosome 1p36 region commonly deleted in high-risk neuroblastoma tumors. We have previously identified associations of UBE4B expression with neuroblastoma patient outcomes. However, the functional roles of UBE4B in neuroblastoma tumor differentiation are not known.

Design/Methods: We analyzed the association of UBE4B gene expression with expression of known markers of neuroblastoma tumor differentiation using publicly available databases and screened cell lines and neuroblastoma tumor samples for UBE4B protein expression using Western blot and quantitative immunohistochemistry. We measured UBE4B expression by Western blot in cell lines before and after induction of differentiation with 13-cis-retinoic acid treatment and determined the effects of UBE4B overexpression and depletion on retinoic acid-induced differentiation using continuous live-cell imaging of neurite morphology, immunohistochemistry, and Western blot for markers of differentiation. Effects on signaling through the Ras/MAPK pathway were measured using Western blots.

Results: UBE4B expression was associated with neuroblastoma differentiation in patient tumors, and UBE4B gene and protein expression were associated with expression levels of known markers of neuroblastoma differentiation. Retinoic acid treatment resulted in increased UBE4B expression in retinoic acid-sensitive, but not -resistant, neuroblastoma cells, and UBE4B depletion was associated with increased ERK phosphorylation, increased proliferation, and inhibition of retinoic acid-induced neuroblastoma differentiation.

Conclusion: We have demonstrated associations between UBE4B expression and tumor differentiation in gene expression databases and in neuroblastoma tumor samples, and our data suggests that UBE4B expression is required for retinoic acid-induced differentiation, potentially through effects on activation of the Ras/MAPK pathway. These associations between UBE4B and neuroblastoma differentiation combined with the established role of UBE4B in GFR trafficking suggest that UBE4B-mediated receptor trafficking may contribute to the responses of neuroblastoma tumors to therapy and to the outcomes of patients with neuroblastoma.

Citation Format: Jacqueline Lesperance, Divya Subramonian, Sarah Woodfield, Rongjun Guo, Andrew Bean, Dolores Lopez-Terrada, Michael Ittmann, Sara Hakim, Peter E. Zage. Growth factor receptor trafficking in neuroblastoma differentiation [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 3467.
Abstract 3475: Novel correlation-based network analysis of breast tumor metabolism identifies the glycerol channel protein Aquaporin-7 as a regulator of breast cancer metastasis
Authors: Dai Chen , Arceo Jennifer , Arnold James , Wu Junmin , Dovichi Norman J. , Sreekumar Arun , Li Jun , Littlepage Laurie E.
Published: August 2018

The complex yet interrelated connections between cancer metabolism, gene expression, and oncogenic driver genes have the potential to identify novel biomarkers and drug targets with prognostic and therapeutic value. Using GC-MS, LC-MS/MS, and capillary zone electrophoresis (CZE)-MS platforms, we quantified and compared the levels of 374 metabolites in breast tumor tissue from normal tissue and transgenic mouse breast cancer models overexpressing a panel of oncogenes (PyMT, PyMT-DB, Wnt1, Neu, and C3-TAg). Comparison of the metabolite profiles from the tumors identified oncogene-induced metabolic reprogramming of the tumor tissues. To develop a higher order understanding of the driver genes and metabolites in breast cancer, we next developed a discovery-based correlation network analysis that captured interactions between both metabolite and gene expression data. This analysis uniquely identified a metabolic network of metabolites and genes with prognostic value in breast cancer patients, identifying 35 metabolite and 33 gene hubs that are likely integral to breast tumor metabolism. Further MALDI-MS based imaging revealed heterogeneous distribution of hub metabolites between stromal and epithelial tissue in breast tumors from transgenic mouse models, as well as heterogeneity within the tumor epithelium, suggesting complex metabolic landscape even within the tumor epithelium. We initially focused on the gene hub aquaporin-7 (Aqp7), a water and glycerol channel protein, as a novel regulator of breast cancer. AQP7 deficiency in animal models is associated with adipocyte hypertrophy, increased glycerol and triglyceride accumulation, insulin resistance, and obesity. We discovered that AQP7 is a prognostic marker of overall survival and metastasis in breast cancer patients. Aqp7 is expressed in the epithelium and adipocytes in normal and tumor breast tissue. Reduced Aqp7 expression in mouse breast cancer cells decreased both proliferation and lung metastatic burden. These data suggest AQP7 promotes invasive phenotypes of breast cancer progression. Using an unbiased, discovery-based approach, this study shed light on important players in breast cancer metabolism from a new perspective that complements current guided network analyses.

Citation Format: Chen Dai, Jennifer Arceo, James Arnold, Junmin Wu, Norman J. Dovichi, Arun Sreekumar, Jun Li, Laurie E. Littlepage. Novel correlation-based network analysis of breast tumor metabolism identifies the glycerol channel protein Aquaporin-7 as a regulator of breast cancer metastasis [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 3475.
Abstract 3494: Downregulation of SREBPs inhibited colon cancer cell growth and tumor initiation by alteration of metabolism
Authors: Wen Yang-an , Xiong Xiaopeng , Zaytseva1 Yekaterina , Gao Tianyan
Published: August 2018

Sterol regulatory element binding proteins (SREBPs) belong to a family of transcription factors that regulate the expression of genes required for the synthesis of fatty acids and cholesterol. There are three SREBP isoforms, SREBP1a, SREBP1c and SREBP2, have been identified in mammalian cells. SREBP1a and SREBP1c are derived from a single gene through the use of alternative transcription start sites. Increasing evidence suggests that increased lipogenesis is needed for cancer cells to accommodate high rates of proliferation. Activation of SREBP1 and enhanced expression of its target genes have been observed in different types of human cancers. However, the functional importance of SREBPs in colon cancer remains to be fully elucidated. In this study, we investigated the role of SREBP-mediated lipid biosynthesis in promoting tumor growth and initiation by regulating cellular metabolism in colon cancer. Knockdown of SREBP-1 or SREBP-2 decreased the expression of target genes required for lipid biosynthesis and levels of fatty acids and triacylglycerides in colon cancer cells. Bioenergetic analysis using Seahorse XF96 Extracelluar Flux Analyzer revealed that silencing SREBP-1 or SREBP-2 expression reduced the mitochondrial respiration, glycolysis, as well as fatty acid oxidation suggesting an inhibition of cellular metabolism. As a result, the rate of cell proliferation and the ability of cancer cells to form tumor spheroids in suspension were decreased. Similar results were obtained in colon cancer cells in which SCAP, an upstream protease responsible for activating SREBP-1 and SREBP-2, was silenced. Mechanistically, downregulation of SREBPs inhibited the activation of AMPK and Akt signaling. Furthermore, knockdown of SREBP-1 or SREBP-2 inhibited xenograft tumor growth in vivo and significantly decreased the expression of genes associated cancer stem cells. Taken together, our findings establish the molecular basis of SREBPs-dependent metabolic regulation and provide a rationale for targeting fatty acid synthesis as a promising approach in colon cancer treatment.

Citation Format: Yang-an Wen, Xiaopeng Xiong, Yekaterina Zaytseva1, Tianyan Gao. Downregulation of SREBPs inhibited colon cancer cell growth and tumor initiation by alteration of 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 3494.
Abstract 3495: Trip13, a target of miR192, facilitates colorectal cancer progression through WNT/β-catenin signaling
Authors: Agarwal Sumit , Chakravarthi Balabhadrapatruni V. , Chandrashekar Darshan S. , Guo Rong Jun , Datta Pran , Varambally Sooryanarayana , Manne Upender
Published: August 2018

Most colorectal cancers (CRCs) exhibit genomic instability or chromosomal instability (CIN) in the form of aneuploidy. These aberrations are associated with chromosomal gains or losses. In human malignances, levels of a member of the AAA-ATPases family, TRIP13, correlate with CIN. In the present study, we investigated the expression and biological function of TRIP13 in CRC. In silico gene expression profiling using the UALCAN (http://ualcan.path.uab.edu/) web portal showed elevated TRIP13 expression in CRCs as compared to normal/benign colonic epithelial tissues. Studies employing immunoblot analyses confirmed elevated expression of the TRIP13 protein in CRC tissues compared to their matched normal/benign colorectal tissues. Concurrent immunohistochemical analysis of tissue microarrays, containing normal and tumor tissues, further validated cytoplasmic TRIP13 expression in CRCs as compared to their contiguous normal/benign epithelial components. To understand the functional significance of TRIP13 in CRCs, particularly in regard to progression of cancer cells, experiments were performed by utilizing lentivirus-mediated TRIP13 silencing in CRC cell lines that express high levels of TRIP13. Depletion of TRIP13 impeded cell proliferation, colony formation, invasion, cell motility, and spheroid-forming capacity. TRIP13 depletion also showed suppression of EGFR activation and WNT/β-catenin signaling. Furthermore, bioinformatic analysis revealed that TRIP13 is a predicted target of miR192. Dual-luciferase reporter assays showed that miR192 binds to the 3' UTR of TRIP13. Also, overexpression of miR192 in HCT116 cells lowered TRIP13 expression and reduced cell proliferation, colony formation, and invasion, suggesting that it is a tumor suppressor. Thus, these findings demonstrate a function of TRIP13 in the progression of CRCs and indicate that TRIP13 inhibition by small molecules is a possible strategy for treatment of CRC.

Citation Format: Sumit Agarwal, Balabhadrapatruni V. Chakravarthi, Darshan S. Chandrashekar, Rong Jun Guo, Pran Datta, Sooryanarayana Varambally, Upender Manne. Trip13, a target of miR192, facilitates colorectal cancer progression through WNT/β-catenin signaling [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 3495.
Abstract 3496: GC1118, a novel anti-EGFR andtibody, shows more potent antitumor activity regardless of KRAS mutation or high-affinity lignad stimulation compared with cetuximab in gastric cancer
Authors: Park Ji Eun , Jin Mei Hua , Nam Ah-Rong , Bang Ju-Hee , Oh Do-Youn , Bang Yung-Jue
Published: August 2018

Background: EGFR overexpression in gastric cancer (GC) has been reported in about 30% of patients. However, cetuximab and panitumulab, anti-EGFR antibodies, have failed to improve overall survival of GC patients compared with standard chemotherapy alone. GC1118 is a novel anti-EGFR antibody with distinct binding epitope compared to cetuximab or panitumumab, and has superior inhibitory activity against high-affinity EGFR ligands (Mol Cancer Ther 2016). In this study, GC1118 was tested to evaluate the antitumor effects in gastric cancer cells.

Methods: Using a total of 15 kinds of GC cell lines (SNU-1, SNU-5, SNU-16, SNU-216, SNU-484, SNU-601, SNU-620, SNU-638, SNU-668, SNU-719, AGS, MKN-28, MKN-45, NCI-N87, and KATO-), GC1118, cetuximab, cisplatin, and 5-FU were tested. Cells were treated with or without high-affinity EGFR ligands, EGF 20ng/mL or HB-EGF 100ng/mL.

Result: GC1118 exhibited more potent antigrowth effects in the majority of GC cells than cetuximab in colony forming assay and MTT assay, regardless of KRAS mutation status of cells. The synergistic efficacy was observed when cells were treated with GC1118 in combination with cytotoxic chemotherapeutic agents (cisplatin or 5FU) in colony formation assay and migration assay compared to each treatment alone, even under the EGFR-ligand stimulation condition. GC1118 significantly blocked the p-AKT or p-ERK signaling under the presence of ligand induced-EGFR activation. However, cetuximab failed to block p-AKT or p-ERK that was upregulated by EGF or HB-EGF. Moreover, this signal-blocking activity was more potent in case of GC1118 compared with cetuximab in the chemotherapy combination experiment.

Conclusion: GC1118 showed more potent antitumor effects in GC compared with cetuximab. In combination with cytotoxic chemotherapy, GC1118 also has more potent activity compared with cetuximab regardless of KRAS mutation status or high-affinity ligand stimulation condition. This study supports further clinical development of GC1118 in gastric cancer.

Citation Format: Ji Eun Park, Mei Hua Jin, Ah-Rong Nam, Ju-Hee Bang, Do-Youn Oh, Yung-Jue Bang. GC1118, a novel anti-EGFR andtibody, shows more potent antitumor activity regardless of KRAS mutation or high-affinity lignad stimulation compared with cetuximab in gastric 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 3496.
Abstract 3499: The mutational status of residue Y842 in FLT3 predicts the drug response in acute myeloid leukemia
Authors: Kazi Julhash U. , Rönnstrand Lars
Published: August 2018

The type III receptor tyrosine kinase FLT3 plays important roles in the development of early hematopoietic progenitor cells and is found to be mutated in around 35% of all cases of acute myeloid leukemia (AML). AML is a heterogeneous disease that affects the myeloid lineage of blood cells. Wild-type FLT3 needs its ligand, FL, for signal transduction. However, the oncogenic mutants are constitutively active even in the absence of ligand. Similar to the other type III receptor tyrosine kinases, such as KIT, CSF1R, PDGFRA and PDGFRB, ligand binding to the FLT3 induces dimerization, activation of the receptor and auto-phosphorylation. Tyrosine phosphorylation sites in FLT3 create docking sites for interacting proteins which transduce signals linked to survival and proliferation, among other things. Although the most common mutations in FLT3 includes the internal tandem duplication (ITD) mutations in the juxtamembrane domain of FLT3, point mutations in the kinase domain also occur. The so-called activation loop tyrosine residue is well conserved in all receptor tyrosine kinases and has long been known to be essential for the activity of some but not all receptor tyrosine kinases. Recently we have shown that activation loop tyrosine residue in KIT is not essential for its activation but plays an important role in regulating receptor stability and downstream signaling. The activation loop tyrosine residue in FLT3 (Y842) has been found to be mutated in some AML patients and acquired mutations of this residue results in drug resistance when combined with FLT3-ITD. We observed that different Y842 mutants (Y-to-F, Y-to-C and Y-to-H) display differential binding affinity for kinase inhibitors. Expression of Y-to-F mutant in myeloid cells resulted in impaired activation of ERK1/2 through reduced recruitment of SHP2 to the receptor. Furthermore, mice xenografted with myeloid cells expressing this Y-to-F mutant of FLT3, in FLT3-ITD background, resulted in delayed tumor formation. Gene set enrichment analysis (GESA) demonstrated that the Y-to-F mutation causes suppression of anti-apoptotic genes. Taken together, our data suggest that the activation loop tyrosine residue in FLT3 plays an important role in FLT3 downstream signaling and drug sensitivity.

Citation Format: Julhash U. Kazi, Lars Rönnstrand. The mutational status of residue Y842 in FLT3 predicts the drug response in acute myeloid leukemia [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 3499.
Abstract 3520: Targeting lipid metabolism eradicates peritoneal metastases of ovarian cancer
Authors: Chen Run , Chan David
Published: August 2018

Ovarian cancer is one of the deadliest women malignancies in the world. The chemoresistance accompanied with metastasis lead to high mortality of this disease. Different from other solid tumors, the advanced ovarian cancers prefer transcoelomic route in metastasis. Clinical observation indicates ovarian cancer patients with intraperitoneal metastases are closely association with poor prognosis. Emerging evidence has indicated that ascites fluids which acts as a reservoir providing plenty of growth factors, chemokines and importantly, free fatty acids etc. However, the significance of ascites microenvironment in governing ovarian cancer metastatic progression remain unclear. Herein, we report that the ascites microenvironment alters metabolism that in turn, enhances ovarian cancer cell aggressiveness. By mimicking the ascites microenvironment, we established omental conditioned medium (OCM). Ovarian cancer cells co-cultured in OCM showed enhanced ovarian cancer oncogenic capacities as observed in ascites. By RNA-Seq and proteomics analyses, we found the activities of lipid metabolism were elevated in ovarian cancer cells cultured in OCM. Depletion of Glut-1/-3/-4 by shRNAi approach or treatment of STF31, a glycolysis inhibitor, showed no or slight effect on ATP production and cell growth of ovarian cancer cells. In contrast, knockdown of Acetyl-CoA Carboxylase-α or -β (ACC1/2) or treatment of FASN inhibitor, Orlistat, significantly inhibited the ATP production and cell growth, suggesting ovarian cancer cells undergone a metabolic shift from aerobic glycolysis to β-oxidation when co-cultured in fatty acid enriched OCM. On the other hand, AMP-activated protein kinase (AMPK) is a key energy sensor and affects oncogenic capacities of many cancer cells. We found that its activity was induced initially for triggering fatty acid oxidation in ATP production. But the AMPK activity was gradually reduced due to the negative feedback loop of high ATP content. The lowered AMPK activity led to mTOR and TAK1/NF-κB signaling activation that result in the increased oncogenic capacities of ovarian cancer cells. Notably, inhibition of the above signaling pathways by a combined cocktails of AMPK activator, TAK1 and FASN inhibitors could remarkably impair OCM-mediated oncogenic properties of

ovarian cancer cells in vitro and in vivo. Taken together, these findings suggest that the ascites microenvironment induces metabolic reprogramming for ovarian cancer cells in production of energy supporting their aggressiveness, while targeting the lipid metabolism and associated signalings could impede peritoneal metastases of ovarian cancer.

Citation Format: Run Chen, David Chan. Targeting lipid metabolism eradicates peritoneal metastases of 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 3520.
Abstract 3526: Beta-oxidation inhibition as a novel therapy for cisplatin-resistant ovarian cancer
Authors: Rada Miran , Cha Jennifer , Sage Jessica , Zhou Bo , Yang Wei , Ashkavand Zahra , Norman Kenneth , Orsulic Sandra , Cheon Dong-Joo
Published: August 2018

Ovarian cancer is the most lethal gynecological cancer and affects one in 70 females in the United States during their lifetime. Cisplatin resistance is the major challenge in the treatment of ovarian cancer but the underlying mechanisms are not fully understood. The purpose of this study is to develop novel therapeutic strategies to treat cisplatin-resistant ovarian cancer. We identified collagen type XI alpha 1 (COL11A1) as a novel biomarker associated with cisplatin resistance in ovarian cancer. COL11A1 is highly expressed by cancer-associated fibroblasts adjacent to cancer cells as well as A2780CIS cisplatin-resistant ovarian cancer cell line. Our data show that COL11A1 binds to DDR2 in ovarian cancer cells and inhibits cisplatin-induced apoptosis in ovarian cancer cells. To obtain mechanistic insights underlying COL11A1-driven cisplatin resistance, we performed Tandem Mass Tag proteomic analysis of A2780CIS ovarian cancer cells before and after COL11A1 knockdown. Our proteomics data revealed that mitochondrial fatty acid β-oxidation was the most upregulated pathway by COL11A1 in ovarian cancer cells. Mitochondrial fatty acid β-oxidation is the major pathway that breaks down fatty acids to produce excess ATP and NADPH to support cell survival. Several studies suggested the association of β-oxidation with tumor cell proliferation in various cancers. However, the role of β-oxidation in ovarian cancer chemoresistance is largely unknown. Our results show that COL11A1 enhances the expression of not only fatty acid receptor CD36, but also key enzymes of fatty acid β-oxidation, such as CPT1A, HADHB, ACSL1 and ACAA2. Significantly, COL11A1-mediated overexpression of these proteins was diminished in the presence of shRNA against DDR2.We also confirmed that ovarian cancer cells increase both fatty acid uptake and oxygen consumption rate in response to palmitate in the presence of COL11A1. Importantly, inhibition of fatty acid β-oxidation using shRNA against CPT1A attenuated the function of COL11A1 in cisplatin resistance. Taken together, our results suggest that COL11A1 confers cisplatin resistance by increasing fatty acid β-oxidation in ovarian cancer cells. Our study uncovers fatty acid β-oxidation as a promising therapeutic target to treat cisplatin-resistant ovarian cancer, particularly cisplatin-resistant recurrent ovarian cancers which typically express high levels of COL11A1.

Citation Format: Miran Rada, Jennifer Cha, Jessica Sage, Bo Zhou, Wei Yang, Zahra Ashkavand, Kenneth Norman, Sandra Orsulic, Dong-Joo Cheon. Beta-oxidation inhibition as a novel therapy for cisplatin-resistant 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 3526.
Abstract 3527: Inhibition of mitochondrial pyruvate transport selectively sensitizes cancer cells to metabolic oxidative stress
Authors: Solst Shane R. , Rodman Samuel N. , Fath Melissa A. , Taylor Eric B. , Spitz Douglas R.
Published: August 2018

To determine if mitochondrial pyruvate transport could represent a therapeutic target for sensitizing cancer cells to oxidative stress, lung and breast cancer cells were treated with 5 µM UK5099 to inhibit the mitochondrial pyruvate carrier (MPC). Treatment with UK5099 selectively sensitized lung and breast cancer cells to clonogenic cell killing when combined with depletion of glutathione using 1 mM buthionine sulfoximine (BSO; a glutathione synthesis inhibitor) for 48 h and 72 h, relative to normal lung and breast epithelial cells. Furthermore, cancer cell killing mediated by UK5099 combined with BSO was inhibited by the thiol antioxidant, N-acetylcysteine (NAC; 20 mM), independent of GSH levels, indicating a mechanism of toxicity involving reduced thiols and metabolic oxidative stress. In addition, treatment with UK5099 alone for 48 h also decreased levels of total glutathione in cancer cells that could be reversed by NAC. Using oxidation-sensitive fluorescent dyes (CDCFH2 and MitoSOX), treatment of lung and breast cancer cells for 24 h and 48 h with UK5099 induced increases in steady state levels of pro-oxidants (presumably hydroperoxides and mitochondrial superoxide), which were further increased with BSO. Finally, treatment of breast cancer cells with UK5099 for 24 and 48 hours significantly sensitized breast cancer cells to clonogenic cell killing mediated by paclitaxel. These data support the hypothesis that inhibition of the MPC selectively causes an impairment of antioxidant capability in cancer cells that is enhanced by depletion of glutathione. Furthermore, these results also support the hypothesis that inhibition of the MPC represents a significant target for sensitizing human breast cancer cells to chemotherapy agents thought to induce oxidative stress.

Supported by R01CA182804.

Citation Format: Shane R. Solst, Samuel N. Rodman, Melissa A. Fath, Eric B. Taylor, Douglas R. Spitz. Inhibition of mitochondrial pyruvate transport selectively sensitizes cancer cells to metabolic oxidative stress [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 3527.
Abstract 3538: Targeting the E3 ubiquitin ligase RNF20 in ovarian cancer
Authors: Cole Alexander J. , Dickson Kristie-Ann , Clifton-Bligh Roderick , Marsh Deborah J.
Published: August 2018

E3 ubiquitin ligases are responsible for the final stage of the enzymatic ubiquitination cascade, where they transfer ubiquitin from an E2 conjugating enzyme to a lysine on the recognized substrate. The most common family of E3 ligases are RING (Really Interesting New Gene) domain proteins. Using immunohistochemistry, we have shown that the ring finger protein RNF20 is strongly expressed in 87% (379 of 424) of high-grade serous ovarian cancer (HGSOC) (1). In contrast, other tumors, including breast, metastatic prostate and colorectal cancer, have been reported to show a decrease in RNF20 transcript levels. The Cancer Genome Atlas has reported < 1% (3 of 316) HGSOCs with RNF20 missense variants of unknown pathogenicity. Given the high level of RNF20 expression in HGSOC, it is unlikely that RNF20 transcript levels are reduced in these tumors.

RNF20 functioning in a heterodimer with RNF40 is the main E3 ligase complex responsible for monoubiquitination of histone H2B at lysine 120 (H2Bub1) (2). This active histone mark leads to an open chromatin configuration favouring DNA access by transcriptional complexes and DNA repair proteins. The RNF20/RNF40 complex also monoubiquitinates and stabilizes the Eg5 motor protein that functions in spindle assembly during mitosis, preventing spindle assembly defects, cell cycle arrest and apoptosis. RNF20 has also been implicated in polyubiquitination of the tumor suppressor Ebp1, promoting its degradation via the 26S proteasome in malignant cells.

We have down-regulated RNF20 in ovarian cancer cell lines to investigate the potential of targeting this E3 ligase to overcome resistance to platinum therapies that is a major problem for the clinical management of women with ovarian cancer. Cell lines studied included the HGSOC lines; COV318, OVCAR-3, OVCAR-4, CaOV3, HEY and OVSAHO, as well as the endometrioid line A2780. Cells were studied as monolayers and spheroid cultures. We have shown that down-regulation of RNF20 leads to lower levels of H2Bub1, consistent with a more closed chromatin configuration. Clonogenic cell survival assays following the treatment of ovarian cancer cell lines with cisplatin showed an impaired ability of cells in which RNF20 had been down-regulated to form colonies. This work provides preliminary evidence that developing strategies to therapeutically down-regulate RNF20 may increase the efficacy of standard-of-care chemotherapy for women with ovarian cancer.

(1) Dickson KA et al., Hum Mol Genet (2016)

(2) Cole AJ et al., Endocr Relat Cancer (2015)

Citation Format: Alexander J. Cole, Kristie-Ann Dickson, Roderick Clifton-Bligh, Deborah J. Marsh. Targeting the E3 ubiquitin ligase RNF20 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 3538.
Abstract 3540: Ubiquitin code: Accelerating the discovery of poly-ubiquitylated proteins by novel chain-selective affinity matrices
Authors: Chaturvedi Apurva , Foote Peter , Julius Sarah , Abed Essam , Singh Rajesh K.
Published: August 2018

Ubiquitin (Ub) is attached via isopeptide bonds to lysine residues in the target protein or to another Ub to form poly-Ub chains. The reversibility, heterogeneity, and diversity of these modifications combined with the lack of suitable tools have made it difficult to properly isolate and characterize poly-ubiquitylated cellular proteins. However, in 2009, a novel technology called TUBEs (Tandem-repeated Ub-Binding Entities) was developed. TUBEs have revolutionized the Ub field by allowing poly-ubiquitylated proteins to be enriched/purified from cellular extracts. Development of TUBEs that selectively bind K48-, K63-, and M1-linked poly-ubiquitylated proteins has helped understand the role of modified proteins in cell physiology. However, the roles of other Ub-linkages remain obscured mainly due to the lack of tools that specifically recognize them. Structure-based approach to engineer unique high affinity Ub binding domains(UBDs) for rare Ub-linkages has been implemented to design highly selective affinity matrices. Biochemical and biophysical experiments demonstrate highly selective interactions of the matrices to distinct lysine-linked poly-Ub chains. Power of these highly selective affinity matrices has made it possible to perform Ub proteomics bypassing SILAC mass spectrometry. Application of these affinity matrices in Far Western detection, pull-down and imaging will be described in the poster. To conclude, we have identified unique binding partners for K6-, K11-, K27-, K29-, K33- and K48-linked poly-Ub chains. Development of chain selective affinity matrices (TUBEs) that selectively bind to poly-ubiquitylated proteins will dramatically accelerate the pace of discovery in this important area of biology.

Citation Format: Apurva Chaturvedi, Peter Foote, Sarah Julius, Essam Abed, Rajesh K. Singh. Ubiquitin code: Accelerating the discovery of poly-ubiquitylated proteins by novel chain-selective affinity matrices [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 3540.