bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2358: Uncovering novel mechanisms of resistance in AML using integrative functional genomics
Authors: Ramos Azucena , Barea Luis R. Millan , Puissant Alexandre , Fenouille Nina , Alexe Gabriela , Stegmaier Kimberly , Hemann Michael T.
Published: August 2018

Treatment options that effectively cure patients diagnosed with acute myeloid leukemia (AML) continue to represent an area of unmet need in oncology clinical care. While remission rates in AML patients can reach upwards of 90% under the current frontline therapy paradigm, nearly all patients relapse with treatment refractory disease less than 5 years after diagnosis. Relapse driven by therapy resistant cells that persist in the body after treatment (defined as minimal residual disease, or MRD) is the principal source of fatality in AML patients. Therefore, understanding how and where these leukemic cells survive treatment in vivo may help advance the rational development of highly synergistic combination therapies for the treatment of AML. Using a functional genomic approach (in vivo RNAi) and a new mouse model of AML chemoresistance (ChemoR) generated in our labs, we have identified several putative mediators of therapy resistance. Transcriptional profiling of the ChemoR model allowed us to generate a chemoresistance gene signature that we overlapped with the results of the shRNA screen to identify high-confidence genes of interest. The top genes from a ranked list of the most highly overexpressed (OE) genes in ChemoR cells and the top depleted genes from the shRNA screen in the context of therapy treatment were selected as high interest hits and subsequently tagged for individual follow-up experiments. Early validation studies suggest that some of our hits protect leukemic cells resident only at specific anatomical niches from therapy, while other proteins appear to be general chemosensitizers both in vivo and in vitro, and in both murine and human AML. Subsequent work will focus on elucidating the mechanisms by which these proteins promote resistance to frontline therapies in AML.

Citation Format: Azucena Ramos, Luis R. Millan Barea, Alexandre Puissant, Nina Fenouille, Gabriela Alexe, Kimberly Stegmaier, Michael T. Hemann. Uncovering novel mechanisms of resistance in AML using integrative functional genomics [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 2358.
Abstract 236: Identification of novel cancer target genes by combining data from the cancer genome-wide association studies (GWAS), regulatory DNA elements and The Cancer Genome Atlas (TCGA)
Authors: Kulkarni Diptee A. , Guo Karl , Jing Junping , Khaladkar Mugdha , Song Kijoung , Dong Coco , Cooper David , Schwartz Benjamin
Published: August 2018

Unlike tumors that develop because of somatic genetic alterations such as frequent coding mutations or chromosomal deletions, amplifications or translocations, some tumors are addicted to expression of certain genes for their sustained proliferation and survival - for example, LIM domain only 1 (LMO1) expression in neuroblastoma (NB). Numerous genome-wide association studies (GWAS) have identified significant associations between germline single-nucleotide polymorphisms (SNPs), many in the non-coding genome, and cancer. A robust genome-wide association has been reported previously between an intronic LMO1 SNP and NB susceptibility. By further sequencing and epigenetic fine mapping of the SNP locus, it was demonstrated that the causal SNP is part of a transcription factor binding site within an enhancer element, regulates expression of LMO1 and in turn increases the tumorigenic potential. To identify additional examples of regulatory SNPs as cancer drivers, we overlaid published genome-wide significant cancer associations with active chromatin marks from Encyclopedia of DNA Elements and searched for SNPs that resided within gene regulatory elements. To map these SNPs to candidate genes and determine direction of effect, we co-localized GWAS signals with expression quantitative trait (eQTL) signals from the Genotype-Tissue Expression (GTEx) Consortium database. Lastly, we checked for gene amplification and/or overexpression of the mapped genes in the Cancer Genome Atlas (TCGA) data to identify a set of target genes that not only exhibit significant cancer association in GWAS, but also have evidence for epigenetic regulation and propensity for amplification and/or overexpression in tumors. We identified more than 25 novel cancer-target pairs with strong germline, regulatory and somatic evidence. A look up through synthetic lethality screen data available in-house suggested that several of these targets are self-lethal, further underscoring their importance for cancer cell proliferation and survival. Additional in vitro experiments are being planned to further validate the targets.

Citation Format: Diptee A. Kulkarni, Karl Guo, Junping Jing, Mugdha Khaladkar, Kijoung Song, Coco Dong, David Cooper, Benjamin Schwartz. Identification of novel cancer target genes by combining data from the cancer genome-wide association studies (GWAS), regulatory DNA elements and The Cancer Genome Atlas (TCGA) [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 236.
Abstract 2360: Deregulated APA and cancer specific APA isoforms
Authors: Begik Oguzhan , Ercan Melda , Cingoz Harun , Can Tolga , Oyken Merve , Erson-Bensan Ayse Elif
Published: August 2018

Certain aspects of diagnosis, prognosis, and treatment of cancer patients are still important challenges to be addressed. We developed a pipeline to uncover patterns of alternative polyadenylation (APA), a hidden complexity in cancer transcriptomes, to further accelerate efforts to discover novel cancer genes and pathways. Here, we found a significant shift in usage of poly(A) signals in six common tumor types compared to normal tissues. We further defined specific subsets of APA events to efficiently classify cancer types/subtypes. Triple negative breast cancers, for example, have specific 3'UTR length alterations where the significant majority are shortening events (70%, 113 of 165) of mostly proliferation-related transcripts compared with normal breast tissue. Such shortening events correlate with increased protein levels and relapse free survival of patients, suggesting functional significance of isoform variability. In line with this isoform diversity, we also detected deregulated expression of mRNA polyadenylation complex proteins in breast cancer cells. Of note, APA proteins are responsive to proliferative signals including estrogen and epidermal growth factor, suggesting a potential explanation to 3'-end isoform diversity in cancer cells. Overall, our study offers a computational and experimental approach for use of APA in novel gene discovery and classification in common tumor types, with important implications in basic research, biomarker discovery, and precision medicine approaches.

Citation Format: Oguzhan Begik, Melda Ercan, Harun Cingoz, Tolga Can, Merve Oyken, Ayse Elif Erson-Bensan. Deregulated APA and cancer specific APA isoforms [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 2360.
Abstract 2361: Big data analysis allows the identification of long non-coding RNAs with therapeutic potential against hepatocellular carcinoma
Authors: Unfried Juan P. , Serrano Guillermo , Suárez Beatriz , Ferretti Valeria , Sangro Paloma , Prior Celia , Boix Loreto , Bruix Jordi , Sangro Bruno , Segura Victor , Fortes Puri
Published: August 2018

Hepatocellular carcinoma (HCC) is a disease associated with high morbidity and mortality for which there is currently no curative treatment and therapeutic targeting remains ineffective. To search for new therapeutic targets, we have evaluated the coding and non-coding transcriptome of all RNA-Seq data from TCGA, comprising over 10000 patients and 34 different tumors with HCC among them. To this, we have added the transcriptomes of additional 10000 samples from 53 human tissues from the GTEx project. Using neural networks and bioinformatics analyses we have identified coding and non-coding genes with preferential and differential expression and obtained a more precise location of HCC in the human transcriptional landscape. The analyses of tumor-deregulated gene expression indicated that coding genes have a high tumor promiscuity. Non-coding genes, on the contrary, showed higher tissue specificity and their expression was altered in a more tumor-specific manner, predictive of a therapeutic target with fewer secondary effects. We have identified 7321 long non-coding RNAs (lncRNAs) deregulated in at least one tumor type. In HCC, we found 1128 deregulated lncRNAs of which 138 were specific of HCC. Bioinformatic functional predictions indicated a positive relationship of deregulated lncRNAs with cell proliferation and motility while immune response was negatively associated. Ten lncRNAs with oncogenic potential were selected and their expression was validated in two independent cohorts of HCC patients. Most tumor samples showed high expression levels of these lncRNAs when compared to their paired peritumoral sample. Furthermore, several candidates were found to be expressed at very low levels in healthy liver. When expression of 2 of them was inhibited with antisense drugs in HCC cells, a drastic stall in proliferation was observed. Proliferation was recovered after restoring lncRNA expression. We think these candidates may play a key role in the proliferation and motility of cancer cells and show great potential as therapeutic targets. Our studies suggest that big data analyses can give a much-needed boost to HCC target search and to personalized medicine against cancer and other diseases.

Citation Format: Juan P. Unfried, Guillermo Serrano, Beatriz Suárez, Valeria Ferretti, Paloma Sangro, Celia Prior, Loreto Boix, Jordi Bruix, Bruno Sangro, Victor Segura, Puri Fortes. Big data analysis allows the identification of long non-coding RNAs with therapeutic potential against hepatocellular 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 2361.
Abstract 2365: A chemical genetics approach identifies PTP4A3 as a regulator of colon cancer cell adhesion
Authors: McQueeney Kelley E. , Salamoun Joseph M. , Ahn Jennifer , Pekic Paula , Blanco Isabella K. , Struckman Heather , Sharlow Elizabeth R. , Wipf Peter , Lazo John S.
Published: August 2018

Dysregulation of the tightly controlled protein phosphorylation networks that govern cellular behavior causes cancer. The membrane-associated, intracellular protein tyrosine phosphatase PTP4A3 is overexpressed in human colorectal cancer and contributes to cell migration and invasion. To interrogate further the role of PTP4A3 in colorectal cancer cell migration and invasion, we deleted the Ptp4a3 gene from murine colorectal tumor cells. The resulting PTP4A3-/- cells exhibited impaired colony formation, spheroid formation, migration, and adherence compared to the isogenic PTP4A3fl/fl cells. We replicated these phenotypic changes using the new small molecule allosteric PTP4A3 inhibitor, JMS-053. A related structure, JMS-038, which lacked phosphatase inhibition, displayed no cellular activity. Reduction in cell viability and colony formation by JMS-053 occurred in both mouse and human colorectal cell lines and required PTP4A3 expression. Ptp4a3 deletion increased the expression of extracellular matrix and adhesion genes, including the tumor suppressor Emilin 1. JMS-053 also increased Emilin 1 gene expression. Moreover, the human TCGA genomic database revealed colorectal tumors with high Ptp4a3 expression had low Emilin1 expression. These chemical and biological reagents reveal a previously unknown communication between the intracellular PTP4A3 phosphatase and the extracellular matrix and support efforts to pharmacologically target PTP4A3.

Citation Format: Kelley E. McQueeney, Joseph M. Salamoun, Jennifer Ahn, Paula Pekic, Isabella K. Blanco, Heather Struckman, Elizabeth R. Sharlow, Peter Wipf, John S. Lazo. A chemical genetics approach identifies PTP4A3 as a regulator of colon cancer cell adhesion [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 2365.
Abstract 2382: In silico/in vitro studies of novel hot spot mutations in BCR-ABL1: A multidisciplinary approach to shed a new light on TKI resistance
Authors: Laurini Erik , Aulic Suzana , Skoko Natasa , Polez Sulena , Baralle Marco , Romano Maurizio , Pricl Sabrina
Published: August 2018

Acquisition of mutations in the BCR-ABL1 kinase domain (KD) is frequently associated with tyrosine kinase inhibitor (TKI) failure in CML. Recently, we revealed a novel mutation “hot- spot” in the BCR-ABL1 KD region (residues 295 - 312), associated with high resistance and poor clinical outcomes [1]. Some of these new BCR-ABL1 variants locate in a protein region, which might not be directly involved in TKI interaction. Therefore, we hypothesized that some of these mutations might be linked to TKI resistance via a direct mechanism while others might exert an indirect effect on drug resistance. The present contribution integrates molecular, computational, and structural biology techniques to understand the eventual role of the newly reported hot-spot mutations of the BCR-ABL1 KD in TKI resistance observed in CML patients using a "two-tier level" investigation: isolated KDs and SH2-linker-SH3-KD BCR- ABL1 constructs. Molecular Modeling will assess in silico whether the clinically observed “hot-spot” BCR-ABL1 mutations might be directly related to a change in the thermodynamic stability and/or protein structure and how these modifications could be involved in the BCR-ABL1 binding profile to specific TKIs (e.g., imatinib, dasatinib, and ponatinib) compared with wild-type (WT) systems and “prototypical” BCR-ABL1 mutations (e.g. T315I). In parallel, in vitro analysis will evaluate the effects exerted by the selected mutations on the intrinsic activity of the kinase and to determine the inhibition activity of the selected drugs on these BCR-ABL1 variants. Specifically, direct drug binding to both KD and SSK constructs will be measured using isothermal titration calorimetry and in vitro kinase assays will monitor the ability of these mutant isoforms to auto-phosphorylate and to phosphorylate a substrate peptide. Finally, structural biology (e.g., SAXS and far-UV CD) evidences of WT and mutant isolated KDs and SH2-linker-SH3-KD (SSK) constructs (per se and in complex with TKIs) will be discussed to support in silico predictions. [1] Gibbons DL, Pricl S et al., Molecular dynamics reveal BCR-ABL1 polymutants as a unique mechanism of resistance to PAN-BCR-ABL1 kinase inhibitor therapy. Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3550-5. doi: 10.1073/pnas.1321173111.

Citation Format: Erik Laurini, Suzana Aulic, Natasa Skoko, Sulena Polez, Marco Baralle, Maurizio Romano, Sabrina Pricl. In silico/in vitro studies of novel hot spot mutations in BCR-ABL1: A multidisciplinary approach to shed a new light on TKI resistance [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 2382.
Abstract 2388: IC50 profiling against 320 protein kinases: Improving the accuracy of kinase inhibitor selectivity testing
Authors: Mueller Daniel , Totzke Frank , Weber Thomas , Pathe Marcel , Schaechtele Christoph , Kubbutat Michael H.
Published: August 2018

Protein kinases belong to one of the largest families of evolutionary related proteins. More than 500 distinct kinases are encoded by approximately 2% of all human genes. Over the past decades, numerous protein kinases have been described of which deregulation contributes to many human diseases. Today, more than 30 protein kinase inhibitors have been approved for the treatment of cancer emphasizing the significance of kinases as one of the most versatile drug targets.

Due to the structural similarity especially within the ATP-binding site, many kinase inhibitors show limited selectivity. Still, sufficient selectivity within the human kinases is of critical importance e.g. to reduce the risk of adverse side effects during treatment.

Therefore, measuring and improving selectivity of a compound within the kinome is of pivotal importance during drug discovery and optimization phase in the development of therapeutically relevant kinase inhibitors.

Broad profiling of kinase inhibitors in biochemical activity assays of several hundred kinases is nowadays well established. Commonly, kinase profiling is done using one or two concentrations of a test compound and measurement of the relative inhibition of the kinase activity compared to a high and low control.

However, due to the limited dynamic range of this approach, and the challenge to select the most appropriate compound concentration, this profiling approach gives often limited information with respect to the differences in the potency of compounds against On-target- and Off-target kinases.

We set up an IC50 kinase profiling approach that consists of measuring the effect of a compound on the activity of 320 human protein kinases at six different concentrations. We will present data showing the effect of compound concentration on the selectivity score in traditional profiling setting. IC50 kinase profiles of different approved and clinical stage kinase inhibitors will be presented demonstrating that an IC50 based profiling allows the accurate determination of selectivity of a compound based on the comparison of the IC50 values against the On-target- in relation to the IC50 values of the Off-target kinases providing significantly improved guidance in the further optimization of the test compound.

Citation Format: Daniel Mueller, Frank Totzke, Thomas Weber, Marcel Pathe, Christoph Schaechtele, Michael H. Kubbutat. IC50 profiling against 320 protein kinases: Improving the accuracy of kinase inhibitor selectivity testing [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 2388.
Abstract 239: Development of DNA chip for detection of predictive SNPs for gemcitabine-induced adverse events
Authors: Nakamura Noriaki , Hirayama Koichi , Yamano Hirofumi , Okamura Hiroshi , Zembutsu Hitoshi
Published: August 2018

[Introduction] Anticancer agent gemcitabine is one of the effective chemotherapies and has been widely used for the treatment of patients with various tumors. However, 13-35% of patients receiving gemcitabine experience severe leukopenia/neutropenia. In our previous studies, we identified four novel SNPs (rs11141915, rs1901440, rs11719165 and rs12046844) associated with this toxicity. To predict the risk of gemcitabine-induced myelosuppression, we developed a high accuracy DNA chip system for genotyping of these four SNPs.

[Methods] We used 17 and 170 germline DNA samples of patients who received gemcitabine therapy in the first stage and second stage respectively. For SNP genotyping using the DNA chip, we amplified target regions by PCR with 10 ng of DNA extracted from blood samples. The PCR product was hybridized with the probe on the DNA chip. Genotype was detected by genotyping score, which was calculated the ratio of risk allele fluorescence intensity to total fluorescence intensity. To confirm the accuracy and reliability of this method, TaqMan genotyping assay was performed for 187 samples.

[Results and Discussion] In the first stage, genotypes of 17 samples were clearly divided into 3 types (non-risk type homo, hetero type, risk type homo). We defined an appropriate cut off value of genotyping score for detection of genotype according to the results of first stage. In the second stage, 170 samples, whose genotype were unknown, were genotyped using the DNA chip. The genotype results were completely concordant (100%) with those using TaqMan genotyping assay. Our DNA chip system is extremely useful as a simple method that is capable of genotyping using DNAs extracted from small amount of blood samples in general hospitals. The development of our DNA chip system provides new insights into personalized anti-cancer drug therapy including gemcitabine for the patients with cancer.

Citation Format: Noriaki Nakamura, Koichi Hirayama, Hirofumi Yamano, Hiroshi Okamura, Hitoshi Zembutsu. Development of DNA chip for detection of predictive SNPs for gemcitabine-induced adverse events [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 239.
Abstract 240: SNP-mediated repression of DCBLD1 by YY1 may explain a GWAS finding on lung cancer
Authors: Wang Yu , Ma Rongna , Lin Hongyan , Yu Xiao , Yu Herbert , Qian Biyun
Published: August 2018

Genome-wide association studies (GWAS) have identified many cancer-associated single nucleotide polymorphisms (SNP) with limited understanding of their real implication in cancer. To study the biological relevance of a GWAS-discovered SNP, we performed linkage disequilibrium (LD) analysis on rs9387478 and identified four potentially functional SNPs. We found that SNP rs17079281 C>T was associated with lung cancer in 766 Chinese cases and 773 matched controls, and the association was validated by another independent study (558 cases and 534 controls). Luciferase assay and CRISP/Cas9-generated genotype experiments showed that transcription factor YY1 suppressed DCBLD1 expression in an allele-specific manner, higher inhibition to T than to C alleles. In vitro and in vivo experiments on gain and loss of function further demonstrated that DCBLD1 behaved like an oncogene for lung cancer. These findings suggest that rs17079281 genotype may differentially affect YY1's suppression on DCBLD1 which influences the risk of lung cancer as an oncogene.

Citation Format: Yu Wang, Rongna Ma, Hongyan Lin, Xiao Yu, Herbert Yu, Biyun Qian. SNP-mediated repression of DCBLD1 by YY1 may explain a GWAS finding on 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 240.
Abstract 2405: P53-dependent mitophagy controls glycolytic shift in radioresistant head and neck cancer cells
Authors: Chang Hyo Won , Kim Ji Won , Kim Mi Ra , Nam Hae Yun , Lee Myungjin , Lee Won Hyeok , Kim Song Hee , Seong Da Seul , Han Myung Woul , Lee Jong Cheol , Park Jung Je , Seo Ji-hyun , Kim Seong Who , Kim Sang Yoon
Published: August 2018

P53 is an important biomarker in response to genotoxic stress, but it is also known to plays a key role in the regulation of metabolic homeostasis. The loss of p53 is a well-established contributor to the malignant transformation and glycolytic phenotype acquisition of cells during cancer development. However, the role of p53 in genotoxic therapy-induced metabolic shift in cancers remains unclear. Here, we attempted to elucidate how p53 participates in the glycolytic shift of head and neck cancer cell lines following irradiation. We established a stable radioresistant head and neck cancer cells (HN30-R; p53 wild type and UMSCC1-R; p53 null type) through cumulative irradiation and then analyzed their glucose metabolic profiles and mitochondria respiration. As a result, the metabolic analysis revealed no changes glycolysis of HN30-R cells, but UMSCC1-R cells exhibited increased glycolysis through increased glucose uptake and lactate production and glycolytic intermediates as well as related glycolytic enzymes, compared to UMSCC1 cells. Also, we confirmed that the mitochondrial respiration was reduced by the maximal respiration parameters of oxygen consumption rate (OCR) and that abnormal mitochondria were accumulated by electron microscopy in UMSCC1-R cells. Thus, UMSCC1-R cells exhibited an increased sensitivity to glycolysis-targeting drugs such a hexokinases inhibitor (2-deoxy-D-glucoes; 2-DG) and a lactate dehydrogenase-A inhibitor (AT101), but HN30-R cells did not shown any changes. Moreover, we identified that mitophagy limits glycolytic shift through the p53-dependent clearance of abnormal mitochondria. Taken together, these results suggest that p53 null type cells increased aerobic glycolysis to overcome the accumulation of abnormal mitochondria in radioresistnat cells. Conversely, p53 wild type cells inhibited the glycolytic shift by regulating a integrity through p53-dependent mitophagy. Thus, glycolysis-targeted drugs could be an alternative strategy for overcoming recurrent cancers after radiotherapy, and p53 status could be a biomarker for selecting participants for clinical trials.

Citation Format: Hyo Won Chang, Ji Won Kim, Mi Ra Kim, Hae Yun Nam, Myungjin Lee, Won Hyeok Lee, Song Hee Kim, Da Seul Seong, Myung Woul Han, Jong Cheol Lee, Jung Je Park, Ji-hyun Seo, Seong Who Kim, Sang Yoon Kim. P53-dependent mitophagy controls glycolytic shift in radioresistant head and neck 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 2405.
Abstract 241: Contribution of female breast cancer predisposition SNPs to risk of male breast cancer
Authors: Orr Nick , Jones Michael , Maguire Sarah , Swerdlow Anthony
Published: August 2018

Genome-wide association studies have identified more than 170 loci that confer susceptibility to breast cancer. Male breast cancer accounts for approximately 1% off all newly diagnosed cases of breast cancer and several reports have implicated germline genetic factors as significant in the aetiology of the disease. Inherited germline mutations in the BRCA2 gene are thought to account for up to 10% of cases. Here we demonstrate that there are substantial overlaps between polygenic susceptibility to male and female breast cancer and that a subset of shared predisposition loci confer significantly larger risk effects in males than in females. Men in the highest quintile of the distribution of risk allele count have a 2.7-fold (2.17-3.30) increased risk of breast cancer compared to those in the lowest quintile. Furthermore, comparisons of the risk allele distributions in male and female cases suggests that the overall impact of genetic predisposition to breast cancer may be greater in a susceptible minority of males from the general population than in females.

Citation Format: Nick Orr, Michael Jones, Sarah Maguire, Anthony Swerdlow. Contribution of female breast cancer predisposition SNPs to risk of male breast 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 241.
Abstract 2412: The nuclear homeoprotein NKX3.1, has a novel function in the mitochondria in regulation of prostate cancer initiation
Authors: Dutta Aditya , Abate-Shen Cory
Published: August 2018

An emerging hallmark of cancer is reprograming of energy metabolism, in which mitochondrial plasticity plays a central role. Mitochondrial plasticity, particularly in response to oxidative stress, is coordinately orchestrated by both mitochondrial- and nuclear-encoded genes. Recent reports highlight the association of mitochondrial dysfunction and prostate cancer, one of the leading causes of cancer and cancer-related death for men. One of the earliest events in prostate cancer etiology is loss of functional NKX3.1, a homeoprotein that is known to play essential roles in prostate differentiation and prostate cancer by regulation of nuclear-encoded genes. We now show that in response to oxidative stress, NKX3.1 is localized to the mitochondria where it directly protects against reactive oxygen species (ROS). NKX3.1 regulates mitochondrial function by directly binding to the D-loop (mitochondrial DNA control region) to specifically regulate mitochondrial genes coding for the electron transport chain. Moreover, we show that aberrant NKX3.1 function in the mitochondria leads to enhanced reactive oxygen species and DNA damage, both of which are reversed by metformin, a biguanide class of anti-diabetic drug that targets the mitochondrial electron transport chain. This uncovers the potential for metformin administration to individuals with NKX3.1 loss as a precision prevention approach against prostate cancer initiation. These observations highlight novel functions for homeoproteins as direct regulators of mitochondrial DNA, and demonstrate the critical role of the mitochondrial stress response in enabling prostate cancer initiation with potential novel therapeutic implications. >

Citation Format: Aditya Dutta, Cory Abate-Shen. The nuclear homeoprotein NKX3.1, has a novel function in the mitochondria in regulation of prostate cancer initiation [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 2412.
Abstract 2418: PKM2 methylation by CARM1 activates aerobic glycolysis to promote tumorigenesis
Authors: Liu Fabao , Ma Fengfei , Wang Yuyuan , Hao Ling , Zeng Hao , Jia Chenxi , Wang Yidan , Liu Peng , Ong Irene M. , Li Baobin , Chen Guojun , Jiang Jiaoyang , Gong Shaoqin , Li Lingjun , Xu Wei
Published: August 2018

Metabolic reprogramming is a hallmark of cancer. Herein we discover that the key glycolytic enzyme pyruvate kinase M2 isoform (PKM2), but not the related isoform PKM1, is methylated by co-activator-associated arginine methyltransferase 1 (CARM1). PKM2 methylation reversibly shifts the balance of metabolism from oxidative phosphorylation to aerobic glycolysis in breast cancer cells. Oxidative phosphorylation depends on mitochondrial calcium concentration, which becomes critical for cancer cell survival when PKM2 methylation is blocked. By interacting with and suppressing the expression of inositol-1,4,5-trisphosphate receptors (InsP3Rs), methylated PKM2 inhibits the influx of calcium from the endoplasmic reticulum to mitochondria. Inhibiting PKM2 methylation with a competitive peptide delivered by nanoparticles perturbs the metabolic energy balance in cancer cells, leading to a decrease in cell proliferation, migration and metastasis. Collectively, the CARM1-PKM2 axis serves as a metabolic reprogramming mechanism in tumorigenesis, and inhibiting PKM2 methylation generates metabolic vulnerability to InsP3R-dependent mitochondrial functions

Citation Format: Fabao Liu, Fengfei Ma, Yuyuan Wang, Ling Hao, Hao Zeng, Chenxi Jia, Yidan Wang, Peng Liu, Irene M. Ong, Baobin Li, Guojun Chen, Jiaoyang Jiang, Shaoqin Gong, Lingjun Li, Wei Xu. PKM2 methylation by CARM1 activates aerobic glycolysis to promote tumorigenesis [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 2418.
Abstract 2420: Skp2-mediated stabilization of MTH1 promotes survival of melanoma cells upon oxidative stress
Authors: Jin Lei , Wang Jiayu , Liu Guangzhi , Wilmott James S. , Yan Xu Guang , Thorne Rick F. , Scolyer Richard A. , Zhang Xu Dong
Published: August 2018

MTH1 helps prevent misincorporation of ROS-damaged dNTPs into genomic DNA, however, there is little understanding of how MTH1 itself is regulated. Here we report that MTH1 is regulated by polyubiquitination mediated by the E3 ligase Skp2. In melanoma cells, MTH1 was upregulated commonly mainly due to its improved stability caused by K63-linked polyubiquitination. While Skp2 along with other components of the Skp1-cullin-F-box (SCF) ubiquitin ligase complex were physically associated with MTH1, blocking the SCF function ablated MTH1 ubiquitination and expression. Conversely, overexpressing Skp2 elevated levels of MTH1 associated with an increase in its K63-linked ubiquitination. In melanoma cell lines and patient specimens, we observed a positive correlation of Skp2 and MTH1 expression. Mechanistic investigations showed that Skp2 limited DNA damage and apoptosis triggered by oxidative stress and that MAPK upregulated Skp2 and MTH1 to render cells more resistant to such stress. Collectively, our findings identify Skp2-mediated K63-linked polyubiquitination as a critical regulatory mechanism responsible for MTH1 upregulation in melanoma, with potential implications to target the MAPK/Skp2/MTH1 pathway to improve its treatment.

Citation Format: Lei Jin, Jiayu Wang, Guangzhi Liu, James S. Wilmott, Xu Guang Yan, Rick F. Thorne, Richard A. Scolyer, Xu Dong Zhang. Skp2-mediated stabilization of MTH1 promotes survival of melanoma cells upon 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 2420.
Abstract 2435: ST6Gal-I sialylation potentiates hypoxia adaptation by enhancing HIF-1a signaling
Authors: Jones Robert B. , Dorsett Kaitlyn A. , Hjelmeland Anita B. , Bellis Susan L.
Published: August 2018

Aberrant surface glycosylation is a well-known hallmark of a tumor cell, however the functional role of glycans in cancer cell biology remains unclear. Tumor cells frequently display an increase in surface α2-6 sialylation, a modification added to N-glycosylated proteins by the ST6Gal-I sialyltransferase. ST6Gal-I sialylates a select cohort of surface receptors, which correspondingly modulates receptor-induced intracellular signaling cascades. Emerging evidence suggests that ST6Gal-I-mediated sialylation promotes the survival of tumor cells exposed to a variety of cell stressors. In the current study we identify a new function for ST6Gal-I in protecting against hypoxic stress. In response to low oxygen tension, the hypoxia inducible factor, HIF-1α, becomes stabilized in tumor cells. In turn, HIF-1α stimulates the transcription of genes important for cell survival. To interrogate a role for ST6Gal-I in hypoxic response, we evaluated HIF-1α accumulation in ovarian and pancreatic cancer cells with ST6Gal-I overexpression or knockdown. We find that ST6Gal-I activity augments HIF-1α accumulation in cells treated with chemical hypoxia mimetics (DFO and DMOG), or alternatively grown in a hypoxic environment. Furthermore, hypoxic cells with high ST6Gal-I expression have increased mRNA levels of HIF-1α transcriptional targets including the glucose transporters, GLUT1 GLUT3, and the glycolytic enzyme, PDHK1. Interestingly, cells with high ST6Gal-I expression also have an increased pool of HIF-1α mRNA, suggesting that ST6Gal-I may influence the biosynthesis of HIF-1α. Finally, cells grown in hypoxia for several weeks display an enrichment in ST6Gal-I expression, consistent with the concept that ST6Gal-I acts as a pro-survival factor. Taken together, these findings highlight a novel, glycosylation-dependent mechanism that facilitates tumor cell adaptation to a hypoxic milieu.

Citation Format: Robert B. Jones, Kaitlyn A. Dorsett, Anita B. Hjelmeland, Susan L. Bellis. ST6Gal-I sialylation potentiates hypoxia adaptation by enhancing HIF-1a 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 2435.
Abstract 2442: Detection of tissue hypoxia with EF5
Authors: Su Kevin , Noble Amy , Asbrock Nick , Koch Cameron , Chu Vi
Published: August 2018

Hypoxia, a condition of oxygen deprivation, is a salient feature of the tumor microenvironment. Hypoxia tumors are frequently resistant to conventional cancer therapies and are correlated with increased migratory and metastatic behavior. A number of detection modalities exist for the detection of hypoxia; however, only EF5 (2-[2-nitro-1H-imidazol-1-yl]-N-(2,2,3,3,3-pentafluoropropyl) acetamide) provides detailed information on the distribution of hypoxia in tissues at both the physiologic and pathologic levels. EF5 is a compound that, when injected into animal tissues, selectively binds to hypoxic cells and forms adducts. These adducts are detected by a mouse monoclonal antibody, clone ELK3-51, conjugated to fluorescent dyes including Cyanine 3, Alexa Fluor 488 and Cyanine 5. The use of EF5 and its specific fluorescent monoclonal antibody to selectively detect regions of hypoxia in mouse tissues is described. BALB/c mice between 7 to 10 weeks old and weighing between 18 to 30 g were used in the study. Mouse #1 was not treated with EF5 and its spleen was harvested as a negative control. Mouse #2 was injected with 10 mM EF5 (typically 1% of animal weight in mL) and allowed to run aerobically for 4 hours before euthanization. Mouse #3 was injected with EF5, euthanized after 10 minutes and kept warm at 37°C for 40 minutes to mimic the anaerobic hypoxic condition before the spleen was harvested (hypoxic control). Examination of spleen samples indicated highly specific binding of the EF5 adducts only in the anaerobic hypoxic mouse spleen. The use of EF5 with fluorescent conjugated antibodies provides a sensitive and quantitative method for the detection and measurement of tissue hypoxia in animal and human tumor tissues and cells.

Citation Format: Kevin Su, Amy Noble, Nick Asbrock, Cameron Koch, Vi Chu. Detection of tissue hypoxia with EF5 [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 2442.
Abstract 2450: The importance of a family of long noncoding RNAs from the Y chromosome in radiotherapy and chemotherapy response of male non-small cell lung cancer
Authors: Brownmiller Tayvia , Barr Jamie , Harold Abby , Bey Erik , Martinez Ivan
Published: August 2018

Lung cancer is the number one cause of cancer-related deaths in the United States. The 5-year overall survival rate for patients with non-small cell lung cancer (NSCLC) stands at 18%, with women having a twice better overall survival rate than men. Currently, there is no solid evidence to explain the disparity between gender survival rates. The protein coding genes of the X and Y chromosomes have been relatively well characterized, and previous studies have implicated phenomena such as the dysregulation of X inactivation and the loss of the Y chromosome in a number of cancers. However, the regions of these chromosomes responsible for producing noncoding RNAs (ncRNAs) are not well understood. One such class of ncRNAs are long noncoding RNAs (lncRNAs), which are primarily classified as larger than 200 nucleotides and carry out functions in nearly every cellular process via a variety of mechanisms. In this study, we have identified a novel family of Y chromosome-linked lncRNAs that we hypothesize play a role in NSCLC cell survival. Our preliminary data show a time- and dose-dependent response in expression of the Y chromosome lncRNA family after radiation in radiosensitive NSCLC cell lines but not in radioresistant NSCLC cell lines, and we see a similar trend in response to cisplatin. Additionally, upon knockdown of this family in a sensitive cell line using two different shRNAs, we immediately observed an increase in proliferation of the knockdown cells when compared to shCtrl as well as increased cell viability and resistance to apoptosis in response to radiation, and increased resistance to cisplatin. We plan to further characterize these lncRNAs using methods such as qRT-PCR, virtual Northern blotting, traditional Northern blotting, direct RNA sequencing, cellular fractionation, and fluorescent in situ hybridization and determine their function by shRNA knockdown and subsequent assays to measure cellular processes in response to radiation and chemotherapy. The Identification of a male-specific component of lung cancer would fill a knowledge gap that could provide potential therapeutic targets and new prognostic factors, thereby improving the response rate of men with NSCLC.

Citation Format: Tayvia Brownmiller, Jamie Barr, Abby Harold, Erik Bey, Ivan Martinez. The importance of a family of long noncoding RNAs from the Y chromosome in radiotherapy and chemotherapy response of male 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 2450.
Abstract 2454: Identification of a novel lncRNA family that is required for efficient cellular transformation by Bcr-Abl oncogene
Authors: Chen Jilong , Wang Xuefei
Published: August 2018

Human genome transcribes abundant long noncoding RNAs (lncRNAs) that are defined as the transcripts longer than 200 nt without protein-coding capacity. Recently, lncRNAs are being continuously recognized as critical regulators for various biological processes. Aberrant expression of lncRNAs has been shown to be a cornerstone in diverse human diseases and cancer development. Chronic myeloid leukemia (CML) is a hematological malignancy associated with a reciprocal translocation between chromosome 9 and 22 that generates the chimeric Bcr-Abl oncogene. About 10% of acute lymphoblastic leukemia (ALL) patients also contain Bcr-Abl oncogene. However, the functional relevance of lncRNAs in Bcr-Abl-mediated leukemia remains obscure. In this study, we perform a comprehensive analysis of lncRNAs in Bcr-Abl-positive K562 cells using a microarray of cDNAs encoding lncRNAs. This analysis revealed 987 upregulated lncRNAs and 1479 downregulated lncRNAs in response to treatment with imatinib, a Bcr-Abl inhibitor. Importantly, we identified a conserved, imatinib-inducible lncRNA (IIR) family, named lncRNA-IIR37. Upregulation of lncRNA-IIR37 has been detected in both human and mouse Abl-transformed cell lines after imatinib treatment. Interestingly, lncRNA-IIR37 levels are significantly lower in leukemic cells derived from Bcr-Abl-positive ALL patients than those in normal control group. Furthermore, altering lncRNA-IIR37 expression remarkably affects survival of Abl-transformed leukemic cells, and tumorigensis induced by leukemic cells in xenograft mouse model. Knockdown of lncRNA-IIR37 in transgenic mice significantly promotes Bcr-Abl-mediated primary bone marrow transformation. These results indicate that lncRNA-IIR37 functions as a suppressor gene in Bcr-Abl-induced tumorigenesis. In addition, we demonstrated that lncRNA-IIR37 directly bound and affected the phosphorylation of STAT5 to regulate leukemic cell survival. Together, our observations suggest that lncRNA-IIR37 is critically involved in Bcr-Abl-mediated leukemogenesis. These results provide novel insights into complicated mechanisms underlying cellular transformation by Bcr-Abl oncogene.

Citation Format: Jilong Chen, Xuefei Wang. Identification of a novel lncRNA family that is required for efficient cellular transformation by Bcr-Abl oncogene [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 2454.
Abstract 2470: Identification of long noncoding RNAs regulated by ZEB1 and epithelial-mesenchymal transition in lung cancer cells
Authors: Kim Jeong Seon , Ahn Young-Ho
Published: August 2018

Long non-coding RNA (lncRNA) are known to have various physiological and pathological functions. Some lncRNAs also show differential expression between cancer and normal tissues and play important roles in cancer development. In this study, we tried to identify novel lncRNAs that regulate epithelial-mesenchymal transition (EMT), invasion, tumorigenesis, and metastasis of lung cancer cells. We performed an NGS-based RNA sequencing analysis in murine lung cancer cells overexpressing ZEB1, an EMT-inducing transcription factor. ZEB1 overexpression changed the expression of total 194 lncRNAs: increased 80 and decreased 114 lncRNAs (fold change≥2, p≤0.01). We then selected 32 lncRNAs with high basal levels and confirmed their differential expression by qRT-PCR. In addition, we measured their expression changes after ZEB1-knockout in mesenchymal-like cells, TGFβ-treatment in epithelial-like cells, and ZEB1-overexpression in human lung cancer cells. Through these experiments, we found several lncRNAs regulated by ZEB1 or EMT in lung cancer cells. Expressions of these lncRNAs showed correlation with that of ZEB1 in human lung adenocarcinoma TCGA data. Further investigation will unveil the effects of these lncRNAs on EMT, cancer development, and metastasis of lung cancer cells.

Citation Format: Jeong Seon Kim, Young-Ho Ahn. Identification of long noncoding RNAs regulated by ZEB1 and epithelial-mesenchymal transition in lung 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 2470.
Abstract 2473: Association of functional genetic variants of long noncoding RNA HOTAIR with oral cancer susceptibility
Authors: Yang Shun-Fa , Su Shih-Chi , Lin Chiao-Wen
Published: August 2018

Genetic and acquired factors are thought to be interrelated and imperative to estimate the risk and prognosis of oral squamous cell carcinoma (OSCC). Polymorphisms in the HOX transcript antisense intergenic RNA (HOTAIR) have been recently linked to the predisposition to diverse malignancies. In the present study, we aimed to evaluate the influences of HOTAIR gene polymorphisms, combined with environmental triggers on the susceptibility to oral tumorigenesis. Four single-nucleotide polymorphisms (SNPs) of the HOTAIR gene, rs920778, rs1899663, rs4759314, and rs12427129 were tested in 1200 normal controls and 907 OSCC patients. We detected a significant association of rs1899663 with the risk of OSCC (AOR, 2.227; 95% CI, 1.197-4.146; p=0.012) after adjustment for three potential confounders, smoking, betel nut chewing, and alcohol consumption. In the further analyses where habitual exposure to each of three environmental factors was individually excluded, we found that, in addition to rs1899663, non-betel nut users who carried the polymorphic allele of rs920778 were more prone to develop OSCC than were those homozygous for wild-type allele (TC: OR, 1.472; 95% CI, 1.069-2.029; p=0.018; TC+CC: OR, 1.448; 95% CI, 1.060-1.977; p=0.020). This genetic association was not seen while comparing subjects who do not smoke or consume alcohol between the case and control cohort. Moreover, as exploring the relationship between HOTAIR gene polymorphisms and clinical status of only OSCC patients who were non-betel nut chewers, besides the association with the advanced clinical stage, rs920778 and rs4759314 were correlated with the development of large-size tumors (OR, 1.891; 95% CI, 1.027-3.484; p=0.04) and increased lymph node metastasis (OR, 4.140; 95% CI, 1.785-9.602; p=0.001), respectively. Further functional assessments link rs920778 to the regulation of HOTAIR expression and epigenetic status. Our results reveal an interactive effect of HOTAIR gene polymorphisms and betel nut chewing on the development and progression of oral cancer.

Citation Format: Shun-Fa Yang, Shih-Chi Su, Chiao-Wen Lin. Association of functional genetic variants of long noncoding RNA HOTAIR with oral cancer susceptibility [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 2473.