bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-383: Towards automation of germline variant curation in cancer genetics
Authors: Ravichandran Vignesh , Shameer Zarina , Offit Kenneth , Joseph Vijai
Published: August 2018

Cancer care professionals are now increasingly asked to interpret multiplexed gene sequencing of patients at hereditary risk for cancer. Assessments for variant classification now require orthogonal data searches, requiring aggregation of multiple lines of evidence from diverse resources. The burden of evidence required for each variant to meet thresholds for pathogenicity or actionability now poses a growing challenge for those seeking to counsel patients and families following germline genetic testing. A computational tool that automates, provides uniformity and significantly accelerates this interpretive process is required. The automated tool described here, Pathogenicity of Mutation Analyzer (PathoMAN) automates germline genomic variant curation from clinical sequencing based on ACMG guidelines. PathoMAN aggregates multiple tracks of genomic, protein and disease specific information from public sources. When compared against expert curation aggregated from three groups - (i) Prostate Cancer Study; (ii) Breast Cancer Study and (iii) ClinVar. PathoMAN achieves high concordance (83.1% pathogenic, 75.5% benign) and negligible discordance (0.04% pathogenic, 0.9% benign) when contrasted against expert curation. Loss of resolution (8.6% pathogenic, 23.64% benign) and gain of resolution (6.6% pathogenic, 1.6% benign) are observed. We highlight the advantages and weaknesses related to the use of programmable automation of variant classification. PathoMAN provides a substantial advance in rapid classification of genetic variants by generation of robust models using a knowledge-base of diverse genetic data. It is an easily accessible, web-based resource that allows rapid pathogenicity assessment of a large number of variants. We also propose a new nosology for the five ACMG classes to facilitate more accurate reporting to ClinVar. The proposed refinements will better structure ClinVar to allow automation in cancer susceptibility reporting. Such bioinformatics tools are an essential prerequisite to reduce the manual workload of domain level experts.

Citation Format: Vignesh Ravichandran, Zarina Shameer, Kenneth Offit, Vijai Joseph. Towards automation of germline variant curation in cancer genetics [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 LB-383.
Abstract LB-394: Profiling of endogenous circular RNA molecules in formalin-fixed paraffin-embedded tissues from patients with B-cell malignancies using an enzyme-free digital counting method
Authors: Kristensen Lasse Sommer , Dahl Mette , Andersen Maria S. , Daugaard Iben , Hansen Thomas B. , Grønbæk Kirsten , Kjems Jørgen
Published: August 2018

Circular RNAs (circRNAs) are covalently closed endogenous RNA molecules with tissue- and disease specific expression patterns, which have potential as diagnostic and prognostic biomarkers in cancer. The landscape of circRNA expression has not been characterized in B-cell malignancies, and current methods for circRNA quantification have several limitations that prevent development of clinically applicable assays. Based on high-throughput RNA sequencing (RNA-seq) data, we designed assays for analyzing 52 unique circRNAs simultaneously, using a digital, enzyme-free technology termed NanoString, in cell lines and paired fresh frozen and formalin-fixed, paraffin-embedded (FFPE) patient samples (including mantle cell lymphoma, multiple myeloma, follicular lymphoma, diffuse large B-cell lymphoma, Burkitt lymphoma and chronic lymphocytic leukemia). The data obtained using NanoString were compared to RNA-seq and reverse transcription-qPCR (RT-qPCR) data obtained on the same samples. RNA-seq profiling revealed a high expression of circRNAs in B-cell malignancies and the NanoString circRNA expression profiles were able to distinguish different B-cell malignancies. We detected circRNAs known to be deregulated in other cancers, including ciRS-7, circHIPK3 circCCDC66, circCDYL, circZKSCAN1 and circFBXW7, and identified a novel circRNA from the IKZF3 oncogene. NanoString data were more reproducible and quantitatively accurate than RNA-seq data and the technology works in particular well for low quality RNA samples. Together, we demonstrate that the NanoString technology enables specific, sensitive and accurate quantification of circRNAs in FFPE samples and provide a map of circRNA expression in B-cell malignancies.

Citation Format: Lasse Sommer Kristensen, Mette Dahl, Maria S. Andersen, Iben Daugaard, Thomas B. Hansen, Kirsten Grønbæk, Jørgen Kjems. Profiling of endogenous circular RNA molecules in formalin-fixed paraffin-embedded tissues from patients with B-cell malignancies using an enzyme-free digital counting method [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 LB-394.
Abstract LB-398: DNA-PKcs protects irradiated cells from persistent DNA damage signaling and accelerated senescence
Authors: Liu Yue , Efimova Elena V. , Ramamurthy Aishwarya , Kron Stephen J.
Published: August 2018

The DNA-dependent protein kinase catalytic subunit DNA-PKcs has long been considered as a promising target in cancer, based on its roles in DNA damage response and the potential for inhibitors to enhance sensitivity to genotoxic therapy. Multiple investigational DNA-PK inhibitors remain under evaluation, though several have failed in development and none have reached the clinic. DNA-PKcs has been assigned diverse roles in DNA damage response that overlap with ATM including direct phosphorylation of H2AX to form γH2AX and promoting double-strand break (DSB) repair by conventional non-homologous end-joining (NHEJ). Nonetheless, a recent report implicated DNA-PKcs as a negative regulator of ATM. This may resolve the paradox that while ATM inhibitors block H2AX phosphorylation, prevent ionizing radiation induced foci (IRIF) formation and suppress terminal arrest and onset of cellular senescence, DNA-PK inhibitors induce persistent γH2AX, delay IRIF resolution and promote senescence. Toward better defining DNA-PKcs roles in radiation response, we examined MCF7 mammary carcinoma cells for effects of DNA-PKcs shRNA knockdown or treatment with specific inhibitors on DNA damage response and senescence after irradiation. We confirmed a requirement for DNA-PK in resolution of γH2AX and IRIF by 24 h after irradiation. Rather than return to proliferation, surviving cells with DNA-PK defects developed characteristic features of senescence within five days in culture. To examine if this effect of DNA-PKcs inhibition was mediated by blocking DSB repair, we irradiated MCF7 cell lines expressing shRNAs targeting NHEJ factors Ku70, Ku80, XLF, XRCC4, PAXX, and LIG4 as well as scrambled control in the presence or absence of DNA-PKcs inhibitor NU7441. Strikingly, IRIF resolution at 24 h was similar to control in cell lines lacking NHEJ factors while NU7441 increased IRIF persistence and enhanced senescence in all cell lines. These results suggest that a critical role for DNA-PKcs in radiation response is to attenuate DNA damage signaling and prevent cellular senescence. Treating irradiated DNA-PKcs knockdown cells with the ATM inhibitor KU55933 at 24 h resolved persistent γH2AX and IRIF and blocked senescence. Taken together, our data demonstrate that DNA-PKcs regulates IRIF resolution and cell senescence by targeting ATM functions rather than directly affecting DSB repair.

Citation Format: Yue Liu, Elena V. Efimova, Aishwarya Ramamurthy, Stephen J. Kron. DNA-PKcs protects irradiated cells from persistent DNA damage signaling and accelerated senescence [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 LB-398.
Abstract LB-401: Induction of DISE by tumor suppressive microRNAs
Authors: Gao Quan Q. , Putzbach William T. , Murmann Andrea E. , Chen Siquan , Sarshad Aishe A. , Ambrosini Giovanna , Bartom Elizabeth T. , Hafner Markus , Peter Marcus E.
Published: August 2018

Many siRNAs and shRNAs induce a form of cell death in all cancer cells that involves silencing a set of critical survival genes, a process called death induced by survival gene elimination (DISE). Mechanistically a 6mer seed sequence (position 2-7 of the guide strand) is sufficient to confer DISE-inducing activity. We have now performed a strand specific screen testing the toxicity of all 4096 possible 6mer seed sequences in a neutral double stranded siRNA backbone. We found an asymmetric preference for guanine in positions 1-3 of the 6mer seed in the most toxic siRNAs which target survival genes that are GC rich in their 3'UTR. During over 800 million years of evolution miRNAs have evolved to avoid guanine in their seed sequences. However, two tumor suppressive miRNAs were found to be killing cancer cells through DISE using G rich toxic seeds in cells exposed to genotoxic stress: 1) the p53 inducible miR-34 family and most of its cell death inducing activity comes from its 6mer seed; and 2) miR-320a, a noncanonical miRNA that is still expressed in cancer cells when miRNA processing genes are mutated. Ago bound upregulated miR-320a is converted from a poorly to a highly toxic miRNA by removal of two adenine nucleotides from its 5' end. Our data suggest that most miRNAs have evolved to avoid induction of DISE but certain tumor suppressive miRNAs utilize this mechanism to kill cancer cells.

Citation Format: Quan Q. Gao, William T. Putzbach, Andrea E. Murmann, Siquan Chen, Aishe A. Sarshad, Giovanna Ambrosini, Elizabeth T. Bartom, Markus Hafner, Marcus E. Peter. Induction of DISE by tumor suppressive microRNAs [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 LB-401.
Abstract NG02: NFS1 undergoes positive selection in lung tumors and protects cells from ferroptosis
Authors: Alvarez Samantha W. , Sviderskiy Vladislav O. , Terzi Erdem M. , Papagiannakopoulos Thales , Moreira Andre L. , Adams Sylvia , Sabatini David M. , Birsoy Kıvanç , Possemato Richard L.
Published: August 2018

Environmental nutrient levels impact cancer cell metabolism, resulting in context-dependent gene essentiality. Here, using RNAi-based loss of function screening, we identify environmental oxygen level as a major driver of differential essentiality between in vitro model systems and in vivo tumours. Above the 3-8% oxygen concentration typical of most tissues, we find that cancer cells depend on high levels of the iron-sulfur cluster (ISC) biosynthetic enzyme NFS1. Accordingly, mammary or subcutaneous tumours grow despite NFS1 suppression, while metastatic or primary lung tumours do not. Consistent with a role in surviving the high oxygen environment of incipient lung tumours, NFS1 lies in a region of genomic amplification present in lung adenocarcinoma and is most highly expressed in well-differentiated adenocarcinomas. NFS1 activity is particularly important for maintaining the ISC cofactors present in multiple cell-essential proteins upon exposure to O2 compared to other forms of oxidative damage. Additionally, insufficient ISC maintenance robustly activates the iron-starvation response and, in combination with glutathione biosynthesis inhibition, triggers ferroptosis, a non-apoptotic form of cell death. Suppression of NFS1 cooperates with inhibition of cysteine transport to trigger ferroptosis in vitro and slow tumour growth. Therefore, lung adenocarcinomas select for expression of a pathway that confers resistance to high oxygen tension and protects cells from undergoing ferroptosis in response to oxidative damage. These observations lead to the tantalizing hypothesis that one can trick cancer cells into taking up large quantities of iron and releasing intracellular iron stores via modulation of NFS1 or downstream effectors, such as IRPs, leaving them at increased risk for ROS-mediated cell death mechanisms such as ferroptosis.

Citation Format: Samantha W. Alvarez, Vladislav O. Sviderskiy, Erdem M. Terzi, Thales Papagiannakopoulos, Andre L. Moreira, Sylvia Adams, David M. Sabatini, Kıvanç Birsoy, Richard L. Possemato. NFS1 undergoes positive selection in lung tumors and protects cells from ferroptosis [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 NG02.
Abstract PL02-01: Advancing cancer diagnostics with artificial intelligence
Authors: Hipp Jason D. , Stumpe Martin
Published: August 2018

Rendering cancer diagnoses from tissues is a highly complex process that requires many years of expert training. It involves challenging tasks for pathologists, such as identifying rare events in very large images (e.g., micrometastases in lymph nodes) or classifying subtle differences between normal vs tumor or among similar-looking tumors that have very different treatment plans. These tasks are typically more challenging for human cognition, and, consequently, over- and underdiagnoses are not uncommon, resulting in nonoptimal treatment selection. Deep learning, a type of machine intelligence, has been successfully applied to solve similar identification and classification problems for Gmail, Google Maps, Google Photos, Google Translate, etc., and may have the potential to solve these similar challenges in the practice of pathology and help improve patient's diagnoses. This talk will begin by providing a brief background on deep learning and how it has been utilized at Google for health care and non-health care applications. The latter half of the talk will discuss the potential of deep learning to improve the accuracy and efficiency of the pathology workflow while highlighting recent advances towards that goal.

Citation Format: Jason D. Hipp, Martin Stumpe. Advancing cancer diagnostics with artificial intelligence [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 PL02-01.
Abstract PL02-04: Decoding patient genomes through the hierarchical pathway architecture of the cancer cell
Authors: Ideker Trey
Published: August 2018

Although cancer is governed by complex molecular systems, the composition and modular organization of these systems remains poorly understood. I will describe efforts by the Cancer Cell Map Initiative (CCMI) to generate large protein interaction maps of tumor cells, which we are integrating with existing molecular and structural data to assemble a comprehensive multiscale map of cancer cell biology. The current draft map contains a hierarchy of ~250 systems covering both known hallmarks and unexpected components. Integration with tumor mutation profiles suggests that the modules under strongest selective pressure in cancer are often not genes, but extend upwards in scale to include protein complexes, broad cellular processes, and organelles. This observation suggests a classification of cancer based on convergence of mutations at key bottlenecks in the hierarchy of cellular systems.

Citation Format: Trey Ideker. Decoding patient genomes through the hierarchical pathway architecture of the cancer cell [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr PL02-04.
Abstract PL04-04: Oncohistones in cancer: How to turn a cell's symphony into non harmonic rap
Authors: Jabado Nada
Published: August 2018

Recent studies have shown that chromatin-associated proteins and transcription factors have more somatic alterations than any other class of oncoproteins in childhood CNS tumors. Different Histone H3 genes (H3F3A, Hist3.1B) and variants (K27, G34, K36) can be affected with remarkable specific association between tumor location and type as well as the particular H3 residue or variant that is mutated. We have shown a high prevalence of H3 mutations in pediatric and young adult High Grade Astrocytoma, in sarcomas such as Giant Cell Tumors of the bone and chondroblastomas, and most recently, in Head and Neck Squamous Cell Carcinomas. These ground-breaking discoveries of oncohistones implicate a direct effect of epigenetic misregulation in oncogenesis. Here, we describe these epigenetic misfits and our knowledge of their effects, along with novel tools needed to study them. We will also discuss how we are harnessing synergies between the approaches of cancer genomics and chemical biology to help make sense of the pathogenesis of oncohistones and describe how oncohistones are promoting global redistribution of important epigenetic marks, seemingly hijacking our epigenome.

Citation Format: Nada Jabado. Oncohistones in cancer: How to turn a cell's symphony into non harmonic rap [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 PL04-04.
Abstract SY18-03: Cross-presenting DC in the TME
Authors: Krummel Matthew F.
Published: August 2018

The immune response to tumors is malleable as we have learned from the various success of immunotherapies, across a diversity of tumor types. What are the foundations for a solid immune response, particularly one executed by T cells? Imaging and single-cell approaches provide key insights into immune cell types that can be unleashed on tumors, identifying both their identity and the immune interactions that are to be fostered. In considering this, we consider the concepts of seeking "allies" for tumor therapies as well as for understanding the balance of push/pull signals that likely contribute to determine the consensus immune response.We discuss a few of these with particular emphasis on the diversity of the innate immune system and how its component parts can contribute toward antitumor immunity.

Citation Format: Matthew F. Krummel. Cross-presenting DC in the TME [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 SY18-03.
Abstract SY24-01: Genomic biomarkers for radiation resistance and targeted radiosensitizers
Authors: Willers Henning
Published: August 2018

Preclinical and clinical development of molecular targeted drugs with radiation therapy (RT) +/- chemotherapy is of critical importance to the field. However, a huge body of preclinical drug/RT studies has not translated into an adequate number of successful radiation oncology trials. Major contributing factors likely include poor reproducibility of preclinical data, over-reliance on tumor growth delay but not long-term local tumor control experiments, and insufficient preclinical modeling of genomic heterogeneity that influences the treatment sensitivity of tumors in the clinic. There exists an urgent need to overcome these barriers to successful clinical translation of targeted radiosensitizers. Our efforts to establish high-throughput screening of targeted radiosensitizers and identify genomic biomarkers of radiosensitization will be presented. The key underlying concept is that short-term, nonclonogenic assays are suitable for capturing the relative change in radiation sensitivity that is induced by a targeted drug, and thus can serve as surrogate endpoints for the “gold standard” clonogenic survival assay. Through the use of a large number of annotated cancer cell lines, high-throughput platforms can model clinically relevant genomic heterogeneity across and within different tumor types. Moreover, these platforms facilitate the inclusion of patient-derived organoid tumor model,s which are likely better suited to mimic in vivo growth conditions than historical 2D monolayer cultures. Examples of biomarker-correlated radiosensitization effects in 2D as well as 3D settings will be shown. In particular, novel therapeutic targets associated with mutated KRAS will be highlighted. To this end, our recent in vitro, in vivo, and clinical data have established KRAS mutation as a biomarker of radiation resistance, especially when accompanied by co-mutation in TP53. The radiation resistance of KRAS mutant cancers constitutes an unmet clinical need. Taken together, by leveraging large panels of genomically characterized preclinical tumor models (2D or 3D) for testing the radiosensitizing properties of novel or repurposed agents, we may ultimately identify biomarker-directed combinatorial approaches that have a higher likelihood of leading to successful radiation therapy clinical trials than past studies.

Citation Format: Henning Willers. Genomic biomarkers for radiation resistance and targeted radiosensitizers [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 SY24-01.
Abstract SY25-01: Genome regulation by long noncoding RNAs
Authors: Chang Howard Y.
Published: August 2018

The discovery of extensive transcription of long noncoding RNAs (lncRNAs) provides an important new perspective on the centrality of RNA in gene regulation. I will discuss genome-scale strategies to discover and characterize lncRNAs. An emerging theme from multiple model systems is that LncRNAs form extensive networks of ribonucleoprotein (RNP) complexes with numerous chromatin regulators, and target these enzymatic activities to appropriate locations in the genome. Consistent with this notion, long noncoding RNAs can function as modular scaffolds to specify higher-order organization in RNP complexes and in chromatin states. The importance of these modes of regulation is underscored by the newly recognized roles of long RNAs in human diseases.

Citation Format: Howard Y. Chang. Genome regulation by long noncoding RNAs [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 SY25-01.
Abstract SY26-03: Dual targeting of senescence and tumor immunity for cancer therapy
Authors: Alimonti Andrea
Published: August 2018

Senescence induction in cancer works as a potent weapon to eradicate tumorigenesis. Therapies that enhance senescence not only promote a stable cell growth arrest but also work as a strong stimulus for the activation of the tumor immune response. However, cancer cells bypass senescence by either acquiring new genetic alterations or by disrupting the tumor immune response. Here, I will discuss the identification of oncogenic pathways that bypass Pten-loss-induced cellular senescence, thereby promoting prostate cancer progression and metastasis. Next, I will present evidence demonstrating that both tumor-infiltrating myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) control senescence induction in chemotherapy-treated prostate cancers and that immunotherapies that interfere with either MDSCs' recruitment or the polarization of TAMs promote senescence in advanced PTEN-deficient prostate cancer.

Citation Format: Andrea Alimonti. Dual targeting of senescence and tumor immunity for cancer therapy [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 SY26-03.
Abstract SY29-01: Role of nitrogen metabolism in obesity-associated pancreatic cancer
Authors: Kalaany Nada Y.
Published: August 2018

Obesity is an established risk factor for pancreatic ductal adenocarcinoma (PDAC). Despite recent identification of metabolic alterations in this lethal malignancy, the metabolic dependencies of obesity-associated PDAC remain unknown. Here we show that obesity-driven PDAC exhibits accelerated growth and a striking transcriptional enrichment for pathways regulating nitrogen metabolism. We find that the mitochondrial form of arginase (ARG2), which hydrolyzes arginine into ornithine and urea, is induced upon obesity, and silencing or loss of ARG2 markedly suppresses PDAC. In vivo infusion of 15N-glutamine in obese mouse models of PDAC demonstrates enhanced nitrogen flux into the urea cycle, and infusion of 15N-arginine shows that Arg2 loss causes significant ammonia accumulation that results from the shunting of arginine catabolism into alternative nitrogen repositories. Furthermore, analysis of PDAC patient tumors indicates that ARG2 levels correlate with body mass index (BMI). The specific dependency of PDAC on ARG2 rather than the principal hepatic ureagenic enzyme ARG1 opens a therapeutic window for obesity-associated pancreatic cancer.

Citation Format: Nada Y. Kalaany. Role of nitrogen metabolism in obesity-associated 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 SY29-01.
Abstract A29: Investigation of RECQL variants in European and African American breast cancer cohorts
Authors: Chandler Madison R. , Bergstresser Sydney , Huskey Anna LW , Stallworth Elizabeth , Davis Amber , Dean Holly , Johnson Brandon , Merner Nancy D.
Published: August 2018

Although an average woman in the United States can have a 12.5% lifetime risk of developing breast cancer (BC), inherited genetic risk variants can greatly influence a woman’s overall lifetime risk. Genes that harbor BC risk variants are referred to as BC susceptibility genes. Unfortunately, mutations in known BC susceptibility genes only explain approximately 35% of hereditary BC cases, leaving a large portion, approximately 65%, genetically unexplained. With the introduction of next-generation sequencing, several attempts have been carried out to identify additional hereditary BC susceptibility genes using whole-exome sequencing. The majority of these studies were relatively unsuccessful; however, Cybulski et al. (2015) successfully associated two rare truncation variants in RECQL, p.K555delinsMYKLIHYSFR and p.R215*, in a Polish and French-Canadian cohort, respectively. Subsequently, two additional studies were carried out in northern and southern regions of China, which also confirmed that overtly deleterious coding mutations in RECQL are associated with familial BC. Herein, we investigated RECQL variants in BC-affected African Americans (AAs) and European Americans (EAs). To our knowledge, this study represents the first attempt to identify an association between RECQL variants and BC cases in the United States. We initially screened all RECQL coding exons using polymerase chain reaction and Sanger sequencing in 49 BC cases (19 AAs and 30 EAs) from Alabama. Primarily synonymous variants were detected in both ethnicities; thus, in order to further investigate the role of RECQL synonymous variants in BC risk, we analyzed RECQL in blood-derived exomes of 168 and 580 BC-affected AAs and EAs, respectively, from The Cancer Genome Atlas (TCGA) project using an in-house bioinformatics pipeline. A case-control analysis revealed that all rare synonymous variants detected in EA BC cases were associated with BC, and p.S64= was significantly associated in both ethnicities. Interestingly, only one truncation variant was detected (p.Y492*) in all 748 BC cases analyzed. Unlike previous findings, this preliminary analysis suggests that rare RECQL synonymous variants may also increase an individual’s lifetime risk of developing BC; further investigation is warranted.

Citation Format: Madison R. Chandler, Sydney Bergstresser, Anna LW Huskey, Elizabeth Stallworth, Amber Davis, Holly Dean, Brandon Johnson, Nancy D. Merner. Investigation of RECQL variants in European and African American breast cancer cohorts [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr A29.
Abstract 51: The eukaryotic translation initiation factor 4H regulates proliferation, migration, and invasion in cancer cells
Authors: Singh Manohar , Trivedi Rachana , Mishra Durga Prasad
Published: August 2018

Background: Dysregulated translation during protein synthesis is a hallmark of multiple human cancers. However, the precise mechanisms remain to be understood. Protein translation of oncogenic mRNAs is highly upregulated in cancer cells and these cells are very sensitive to therapeutic strategies/agents targeting translation inhibition. In this study we investigated the role of translation initiation factor eIF4H in proliferation and survival of cancer cells.

Methods: We selected the breast cancer cell line MDA-MB 231 and the CML cell line K562 for our study. We silenced eIF4H by shRNA and cell proliferation were analyzed by MTT assay and flowcytometry. Expression of antiapoptotic and proproliferative proteins were analyzed by Western blotting and for analysis of mRNA expression real-time PCR was used. Effect of eIF4H silencing on cell migration and invasion was analyzed by migration and invasion assays, respectively.

Results: Using 2D Gel based proteomics we targeted the translational machinery in chronic myeloid leukemia cell line K562 and identified eIF4H as a critical regulator of carcinogenesis. The eIF4H expression was found to be overexpressed in a variety of cancer cell line vis-à-vis the normal nontransformed cells. Similarly, the real-time PCR analysis showed eIF4H overexpression in chronic myeloid leukemia clinical samples compared to that of the healthy controls. The pharmacologic inhibition of eIF4H induced downregulation of its regulatory proteins cMYC, cyclin D1, and antiapoptotic proteins in breast cancer cell line MDAMB-231 and CML cell line K562 cells. The genomic inhibition of eIF4H decreased cell migration and invasion in vitro in MDA-MB 231 cell line and it also inhibits proliferation of both cell lines. Furthermore, the p65-dependent transcriptional activation of eIF4H was observed to be associated with this process.

Conclusion: Our results demonstrate that eIF4H plays an important role in the proliferation, migration, and invasion of cancer cells. Silencing of eIF4H markedly decreased expression of antiapoptotic and proproliferative proteins. Collectively, our findings suggest that eIF4H may have translational relevance as a therapeutic target in cancer therapy.

Citation Format: Manohar Singh, Rachana Trivedi, Durga Prasad Mishra. The eukaryotic translation initiation factor 4H regulates proliferation, migration, and invasion in cancer cells [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr 51.
Abstract IA12: The role of malignant RNA editing in leukemia stem cell generation
Authors: Jamieson Catriona H. M.
Published: August 2018

Deregulation of RNA processing contributes to cancer progression and drug resistance. As a major driver of coding and noncoding transcriptomic diversity, adenosine deaminase associated with RNA1 (ADAR1) induces hydrolytic deamination of adenosines (A) to inosines (I) in response to proinflammatory cytokines elicited by viral infection or malignant microenvironments. Recently, we and other groups demonstrated that enhanced A-to-I RNA editing promotes therapeutic resistance of many cancers, including myeloproliferative neoplasms (MPN). As a paradigm for dissecting the molecular evolution of cancer, MPNs are initiated in hematopoietic stem cells (HSCs) by BCR-ABL1, JAK2 V617F or CALR mutation expression and transform to acute myeloid leukemia (AML) as a result of malignant reprogramming of progenitors into self-renewing leukemia stem cells (LSCs). With regard to the role of noncoding RNA editing in LSC evolution, ADAR1 enhances self-renewal of preleukemic progenitors in CML by impairing let-7 microRNA (miRNA) biogenesis. Moreover, ADAR1 editase activity suppresses the expression of miRNAs that regulate cell cycle, cancer progression, p53 stabilization, and WNT signaling. In addition to noncoding transcript deregulation, A-to-I editing is also observed in coding regions of stem cell regulatory transcripts, such as the sonic hedgehog transcriptional activator GLI1, and induces mis-splicing of GSK3β, thereby enhancing β-catenin activation. In summary, RNA editing research will inform the development of clinically tractable strategies for predicting and preventing LSC generation.

Citation Format: Catriona H. M. Jamieson. The role of malignant RNA editing in leukemia stem cell generation [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr IA12.
Abstract IA25: Epigenetic regulation of cancer immune surveillance processes
Authors: Johnstone Ricky W.
Published: August 2018

Altered expression, function, or localization of epigenetic enzymes and/or their partner proteins can play a crucial role in cancer onset and progression. Histone writers and erasers that regulate histone acetylation or methylation, or histone readers that recognize specific histone marks, play important roles in tightly regulating gene expression through the remodeling of chromatin and these proteins are promising targets for therapeutic interventions intended to reverse aberrant epigenetic states associated with cancer. The effects of HDAC inhibitors (HDACi) and BET bromodomain inhibitors (BETi) on tumor cell growth and survival have been well documented. However, HDACi and BETi also have immunomodulatory properties that could be important for antitumor responses and could be harnessed to enhance the activities of other anticancer agents. I will present data showing that HDACi and BETi can activate different components of the innate and adaptive immune response through effects on both the target tumor cells and on immune cells. These properties are important for the antitumor effects of HDACi and BETi and can be exploited to devise novel combination regimes involving epigenetic regulators and immune modulators.

Citation Format: Ricky W. Johnstone. Epigenetic regulation of cancer immune surveillance processes [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr IA25.
Abstract IA26: Role of mutations in epigenetic regulators in pathogenesis of myeloid malignancies
Authors: Levine Ross
Published: August 2018

Clinical, cytogenetic, and gene-based studies have been used to inform biology and improve prognostication for patients with acute myeloid leukemia (AML), myelodysplasia (MDS), and myeloroliferative neoplasms (MPN). Most recently, a series of candidate gene and whole-genome studies have identified recurrent somatic mutations in AML patients including TET2, ASXL1, DNMT3A, and cohesin complex mutations. Moreover, these mutations can be used to improve risk stratification in AML independent of established clinical parameters. Integrating mutational data with dose-intensity revealed that high-dose daunorubicin improved survival in patients with DNMT3A/NPM1 mutations or MLL translocations relative to treatment with standard-dose daunorubicin, but not in patients wild-type for these alterations. These data provide important clinical implications of genetic alterations in AML by delineating mutation combination genotypes that predict outcome in AML and improve AML risk stratification. Of biologic importance, the TET family of proteins have been shown to place a hydroxyl mark on methylated DNA and lead to DNA demethylation. We and others have found that TET2/IDH mutations lead to loss of DNA hydroxymethylation and a hypermethylation phenotype in leukemia patients. In addition, in vitro and in vivo studies show that TET2 loss or neomorphic IDH1/2 mutations lead to impaired hematopoietic differentiation, increased stem cell self-renewal, and myeloid transformation in vivo. We have also investigated the role of mutant DNMT3A in AML pathogenesis, and shown that these mutations cooperate with other disease alleles to induce leukemic transformation and to confer chemoresistance due to impaired DNA damage sensing. We will present novel data showing how these mutations coopt the epigenetic state of hematopoietic stem/progenitor cells in order to contribute to transformation and that these mutations have biologic and prognostic relevance.

Citation Format: Ross Levine. Role of mutations in epigenetic regulators in pathogenesis of myeloid malignancies [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr IA26.
Abstract A50: EP4 receptor antagonism in paclitaxel-resistant ovarian clear cell carcinomas
Authors: Fan Cong , Reader Jocelyn , Rao Gautam , Staats Paul , Ching Mc Millan , Fulton Amy , Roque Dana
Published: August 2018

Advanced ovarian clear cell carcinoma (OCCC) is associated with a survival disadvantage relative to ovarian serous carcinoma following platinum/taxane-based chemotherapy and optimal cytoreduction. Prostaglandin E2 (PGE2) contributes to disease progression through modulation of several G-protein coupled receptors (EP1-4). Selective EP4 antagonism is preferred over global COX inhibition due to concerns over cardiotoxicity and compensatory upregulation of COX isoenzymes. Class III β-tubulin is a marker for paclitaxel resistance and is widely overexpressed in OCCC. The purpose of this study is to demonstrate that EP4 inhibition may overcome paclitaxel resistance in OCCC that overexpress class III β-tubulin. Expression of EP4 receptor and class III β-tubulin was quantified using immunohistochemistry and Western blot in solid tissues and cell lines. OCCC overexpress class IIIβ-tubulin/EP4 relative to normal ovary. EP4 staining intensity was 2+ in 100% OCCC using an ovarian cancer tissue microarray (62 cores, 13% OCCC); this rate was only 26-56% among other histologies. Standard metabolic growth and migration assays were employed to test the effects of drug treatment and EP4 inhibition. EP4 inhibition reduces growth of paclitaxel resistant cells. Likewise, treatment with EP inhibitors and silencing of EP4 resulted in reduced migration. Selective antagonism of PGE2 through EP4 receptor inhibition may represent a powerful targeted therapy for paclitaxel-resistant OCCC. Further study including simultaneous treatment (EP4 inhibitor + paclitaxel) and larger samples sizes is required.

Citation Format: Cong Fan, Jocelyn Reader, Gautam Rao, Paul Staats, Mc Millan Ching, Amy Fulton, Dana Roque. EP4 receptor antagonism in paclitaxel-resistant ovarian clear cell carcinomas. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr A50.
Abstract B07: Targeting DAB2IP in ovarian cancer stem cells
Authors: Zong Xingyue , Ozes Ali R. , Nephew Kenneth P.
Published: August 2018

Ovarian cancer is the leading cause of death from gynecologic malignancies. Failure to eliminate ovarian cancer stem cells (OCSCs) by the end of conventional chemotherapy contributes to tumor relapse and metastasis. Understanding the molecular features of OCSCs may allow for effective targeting and eradicating these cells and tumor remission. We reported tumor-initiation and expansion capacity by ALDH+ OCSCs after platinum-based treatment of ovarian cancer xenografts. In addition, loss of DAB2IP in prostate and colon cancer promoted CSC-like features, suggesting a critical role in modulating CSC maintenance. DAB2IP, a novel member of Ras GTPase-activating (GAP) protein family, was identified as a potent tumor suppressor that interfered with many aspects of cancer progression and was frequently downregulated in tumors. In the current study, we aimed to elucidate the tumor-suppressor role of DAB2IP in ovarian cancer in the context of OCSCs and explore epigenetic approaches to upregulate its expression. OCSCs and non-CSCs subpopulations were isolated from multiple high-grade serous ovarian cancer cell lines (Kuramochi, OVCAR3, and COV362). Reduced (p<0.05) DAB2IP expression in OCSCs compared to non-CSC counterparts was observed, suggesting that DAB2IP suppresses OCSC maintenance. Overexpression of DAB2IP in OCSCs derived from Kuramochi decreased (p<0.05) OCSC population, and DAB2IP overexpression inhibited stemness-related phenotypes, including reduced (P<0.05) spheroid formation ability after 14-day incubation under stem cell conditions and decreased (P<0.05) colony formation. Decreased expression of stem cell markers (Oct4, Nanog, and Twist) in DAB2IP-overexpressing cells was also observed, indicating potential key effectors downstream of DAB2IP. Furthermore, elevated DAB2IP expression in OCSCs decreased (p<0.05) cisplatin IC50 and cell migration capacity in transwell assay, suggesting DAB2IP plays a role in OCSC function. Aberrant DNA promoter methylation and histone modifications were previously shown to be two major mechanisms of DAB2IP inactivation in cancer. We treated OCSCs with next-generation DNMT inhibitor guadecitabine and EZH2 inhibitor GSK-126, either alone or in combination. Single-agent guadecitabine or GSK-126 decreased ALDH expression with greater (p<0.05) effect in combination. Single GSK-126 was sufficient to increase DAB2IP expression (p<0.05) with additional increase when combined with guadecitabine, correlating with decreased ALDH expression. Collectively, our data suggested a possible combination epigenetic therapy to eliminate OCSCs, potentially through targeting DAB2IP, an important OCSC regulator.

Citation Format: Xingyue Zong, Ali R. Ozes, Kenneth P. Nephew. Targeting DAB2IP in ovarian cancer stem cells. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B07.
Abstract B26: Immune-active microenvironment in SCCOHT: Rationale for therapy with immune checkpoint blockade
Authors: Oudenhove Elke Van , Jelinic Petar , Ricca Jacob , Olvera Narciso , Merghoub Taha , Levine Douglas A. , Dmitriy Zamarin
Published: August 2018

Introduction: Small cell carcinoma of the ovaries, hypercalcemic type (SCCOHT) is a rare and very aggressive malignancy with limited treatment options. SCCOHT is described as an epigenetically altered SMARCA4-mutated monogenic disease, but the exact mechanism of SCCOHT tumorigenesis is not clear. Immune checkpoint-targeting antibodies have not been considered as a suitable treatment option for SCCOHT, because this cancer is characterized by a small number of mutations. Anecdotal reports of patients with SCCOHT responding to PD-1 blockade have challenged this view. We aimed to characterize the immune microenvironment of SCCOHT in order to evaluate a rationale for therapy with PD-1/PD-L1 targeting antibodies.

Methods: To test whether SCCOHT tumors were identified by the immune system, we examined PD-L1 expression and T cell populations within tumor samples. The immune landscape was profiled using quantitative immunofluorescence and gene expression profiling.

Results: Most tumors showed PD-L1 expression and prominent T cell infiltration, with PD-L1 being primarily limited to tumor-infiltrating immune cells. Gene expression analyses revealed upregulation of genes related to T-cell infiltration and cytolytic function in the PD-L1-high tumors. We hypothesize that PD-L1 upregulation in SCCOHT is an adaptive immune response to T-cell infiltration, as has been previously reported for several other cancer types.

Conclusions: Our findings provide an impetus for further investigation of PD-1/PD-L1 as a potential therapy for patients with SCCOHT. More generally, these results challenge the prevailing view that tumor immunogenicity is primarily driven by mutational burden, calling for identification of additional immune pathways involved in tumor recognition.

Citation Format: Elke Van Oudenhove, Petar Jelinic, Jacob Ricca, Narciso Olvera, Taha Merghoub, Douglas A. Levine, Zamarin Dmitriy. Immune-active microenvironment in SCCOHT: Rationale for therapy with immune checkpoint blockade. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B26.
Abstract B38: Synergistic effects of SHP2 and PI3K inhibitors in GAB2-overexpressing ovarian cancer
Authors: Cheung Hiu Wing
Published: August 2018

We previously found that the scaffold/adaptor growth factor receptor bound 2 (GRB2)-associated binding protein 2 (GAB2) is frequently amplified and overexpressed in primary high-grade serous ovarian cancers (HGSOCs) and cell lines. Ovarian cancer cell lines overexpressing GAB2 are dependent on GAB2 for activation of ERK1/2 and AKT signaling, consistent with its role in regulating the protein tyrosine phosphatase SHP2 (encoded by the PTPN11 gene) and the p85 regulatory subunit of phosphoinositide 3-kinase (PI3K). In this study, we investigated whether ovarian cancer cell lines overexpressing GAB2 are sensitive to combinatorial SHP2 and PI3K inhibition. Analysis of gene expression profiles reveals that primary HGSOCs overexpressing GAB2 are associated with increased ERBB, RAS, and MAPK activity signatures. Inhibition of SHP2 by an allosteric inhibitor SHP099 selectively inhibits ERK1/2 activity, proliferation, and survival of ovarian cancer cell lines with GAB2 amplification/overexpression. Treatment with SHP099 has a synergistic effect with multiple PI3K pathway inhibitors such as BKM120, a pan-class I PI3K inhibitor, at suppressing proliferation and survival of ovarian cancer cells overexpressing GAB2 in part through induction of apoptosis. Combinatorial SHP2 and PI3K inhibition more effectively activates both pro-apoptotic proteins BIM and BAD and inhibits expression of transcription factor c-MYC, a master regulator of cancer stem cells, compared with individual inhibitor, and sensitized cancer cells to chemotherapeutic drugs paclitaxel and cisplatin. Combinatorial SHP2 and PI3K inhibition also suppresses spheroid formation of ALDH-positive ovarian cancer stem cells. Together, our findings identify a previously unrecognized role of SHP2 in promoting proliferation and survival of ovarian cancer cells in which GAB2 is amplified and/or overexpressed, and suggest that combinatorial SHP2 and PI3K inhibition may be a promising therapeutic approach for HGSOCs with GAB2 amplification/overexpression.

Citation Format: Hiu Wing Cheung. Synergistic effects of SHP2 and PI3K inhibitors in GAB2-overexpressing ovarian cancer. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B38.