bluuebunny/crossref_metadata_2025 huggingface dataset:
How preprocessor annotations (do not) affect maintainability: a case study on change-proneness
Authors: Fenske Wolfram , Schulze Sandro , Saake Gunter
Published: December 2017

Preprocessor annotations (e.g., #ifdef in C) enable the development of similar, but distinct software variants from a common code base. One particularly popular preprocessor is the C preprocessor, cpp. But the cpp is also widely criticized for impeding software maintenance by making code hard to understand and change. Yet, evidence to support this criticism is scarce. In this paper, we investigate the relation between cpp usage and maintenance effort, which we approximate with the frequency and extent of source code changes. To this end, we mined the version control repositories of eight open- source systems written in C. For each system, we measured if and how individual functions use cpp annotations and how they were changed. We found that functions containing cpp annotations are generally changed more frequently and more profoundly than other functions. However, when accounting for function size, the differences disappear or are greatly diminished. In summary, with respect to the frequency and extent of changes, our findings do not support the criticism of the cpp regarding maintainability.
The landscape of refactoring research in the last decade (keynote)
Authors: Dig Danny
Published: December 2017

In the last decade refactoring research has seen an exponential growth. I will attempt to map this vast landscape and the advances that the community has made by answering questions such as who does what, when, where, with who, why, and how. I will muse on some of the factors contributing to the growth of the field, the adoption of research into industry, and the lessons that we learned along this journey. This will inspire and equip you so that you can make a difference, with people who make a difference, at a time when it makes a difference.
The Power Behind the Throne: Senescence and the Hallmarks of Cancer
Authors: Hoare Matthew , Narita Masashi
Published: December 2017

Cellular senescence is a state of stable proliferative arrest triggered by various stimuli, including oncogenic and other cellular stress. Senescent cells are highly metabolically active and have diverse and profound nonautonomous effects through the senescence-associated secretory phenotype (SASP). It has become increasingly evident that senescent cells can have tumour suppressive or pro-oncogenic effects on adjacent cancer cells and other players in the tumor microenvironment such as the stroma, vasculature, and immune system. Thus, the last decade or so has witnessed a huge leap forward in our understanding of the biology of senescence, promoting it from an autonomous tumor suppressor to a complex, dynamic, and interactive phenotype. It is perhaps not a coincidence that the concept of the “hallmarks of cancer” has also evolved during this period, with the latest iteration ( Hanahan & Weinberg 2011 ) focusing more on the microenvironment. Here, we suggest that cellular senescence could underpin the biology of many of the hallmarks of cancer, making it the true power behind the throne.
The Key Ingredients of the Electronic Structure of FeSe
Authors: Coldea Amalia I. , Watson Matthew D.
Published: December 2017

FeSe is a fascinating superconducting material at the frontier of research in condensed matter physics. Here, we provide an overview of the current understanding of the electronic structure of FeSe, focusing in particular on its low-energy electronic structure as determined from angle-resolved photoemission spectroscopy, quantum oscillations, and magnetotransport measurements of single-crystal samples. We discuss the unique place of FeSe among iron-based superconductors, as it is a multiband system exhibiting strong orbitally dependent electronic correlations and unusually small Fermi surfaces and is prone to different electronic instabilities. We pay particular attention to the evolution of the electronic structure that accompanies the tetragonal-orthorhombic structural distortion of the lattice around 90 K, which stabilizes a unique nematic electronic state. Finally, we discuss how the multiband multiorbital nematic electronic structure impacts our understanding of the superconductivity, and show that the tunability of the nematic state with chemical and physical pressure helps to disentangle the role of different competing interactions relevant for enhancing superconductivity.
Abstract A01: Mechanisms of breast cancer risk in shift workers: Epigenetic changes in the circadian pathway
Authors: Zienolddiny Shan
Published: December 2017

Occupational factors such as shiftwork and especially night work that involves disruption of the circadian rhythm can increase breast cancer risk. Circadian disruption may also affect epigenetic factors such as 5-methyl cytosine methylation in DNA. DNA hypermethylation generally is associated with increased cancer risk, if it occurs in tumor suppressor genes. Some of the circadian genes are known to function as tumor suppressor genes. DNA methylation in cirdavdian genes and its association with breast cancer risk in shiftworkers is little investigated and the limited available data are inconclusive. We here investigated DNA methyalation at 5-meC sites in the promoter regions of core circadian and melatonin receptor genes as a potential mechanism for night work-related breast cancer risk. A nested breast cancer case-control study of nurses working night shifts comprising of seven-hundred breast cancer cases and matched controls was conducted. Methylation at 5-meC sites in a number of core circadian and melatonin receptor genes was in DNA from sputum samples obtained from cases and controls. Changes in methylation status of the 5-meC in DNA (methylation index) and the odds of breast cancer associated with DNA methylation was calculated in relation to the duration and intensity of night shiftwork. We demonstrate that generally the methylation of 5-meC is low for all the genes that were analyzed. However, we will present analyses of the effects of work schedules and duration, as number of consecutive night shifts, on epigenetic changes. The hypothesis is that increased breast cancer risk in workers with long periods of consecutive night shifts may be associated with changes in methylation status of the genes regulation the circadian rhythm.

Citation Format: Shan Zienolddiny. Mechanisms of breast cancer risk in shift workers: Epigenetic changes in the circadian pathway [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr A01.
Abstract B08: Differential regulation of Protein Kinase D isoforms in oxidative stress conditions via tyrosine phosphorylation in the activation segment
Authors: Cobbaut Mathias , Derua Rita , Waelkens Etienne , Störz Peter , Janssens Veerle , Lint Johan Van
Published: December 2017

The protein kinase D (PKD) family of kinases belongs to the CAMK group and consists of three highly homologous enzymes. They play a versatile role in cancer cell signaling, primarily downstream of PKC isoforms. Classically PKDs are activated upon co-localization with PKC at DAG containing membranes, where PKC phosphorylates the PKD activation loop, generating active PKD. Besides this, PKDs are also activated in oxidative stress conditions, where PKD1 protects against cellular damage via signaling to NF-kB. While the three isoforms are highly homologous, they are not redundant in their biological function and oncogenic potential. A picture has emerged which associates PKD1 expression and activity with decreased migration and inhibition of epithelial mesenchymal transition (EMT). PKD2 and PKD3 on the other hand are upregulated in various cancers, and show oncogenic potential e.g. via enhanced ECM breakdown and potentiation of angiogenesis. While non-redundant biological roles continue to surface, the biochemical mechanisms behind these discrepant functions remain mostly elusive. Here, we identify an isoform specific regulation of PKD2 in oxidative stress conditions via the phosphorylation of a key Tyrosine residue in the substrate binding loop of the activation segment which is highly conserved in most Ser/Thr kinases. Phosphorylation of this residue selectively occurs in PKD2 (and not in PKD1). While wild-type PKD1 signals to NF-kB in oxidative stress, we could show that wild-type PKD2 signaling to NF-kB is impeded in these conditions. Substitution of the activation segment Tyr-717 in PKD2 with a non-phosphorylatable Phe restores signaling to NF-kB, indicating that Tyr-717 phosphorylation is a key determinant for the signaling outcome of PKDs in oxidative stress.

Note: This abstract was not presented at the conference.

Citation Format: Mathias Cobbaut, Rita Derua, Etienne Waelkens, Peter Störz, Veerle Janssens, Johan Van Lint. Differential regulation of Protein Kinase D isoforms in oxidative stress conditions via tyrosine phosphorylation in the activation segment [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr B08.
Abstract B33: The role of WWOX in HNSCC through Wnt/beta-catenin pathway
Authors: Buyru Ayse Nur , Celebi Asuman , Seyhan Betul
Published: December 2017

The second most common fragile site in the human genome is the FRA16D region where the WWOX gene is localized which codes for a 414 amino acid protein. WWOX is a member of the WW-domain containing protein family consisting of 2000 members. It is a partner of several transcription factors and therefore functions in multiple physiological and pathological processes such as cell growth, differentiation and tumor suppression. Genomic alterations within the WWOX gene and its differential expression have been found in a variety of human tumors. Although some transcription factor partners of the WWOX protein have been identified its exact mechanism of action is not known. A recent study indicated that WWOX inhibits the Wnt/β-catenin pathway by preventing the nuclear import of the Dishvelled (Dvl) proteins. Dvl proteins are the main down-stream target of Wnt receptors (Frizzled- FRZ). Following binding of Wnt to its receptor alterations of β-catenin degradation lead to β-catenin accumulation in the cytoplasm. Accumulated β-catenin translocates into the nucleus and activates expression of target genes. Therefore dysregulation of the Wnt signaling pathway is a key oncogenic mechanism in many different cancers. Although Wnt and its receptor FRZ have been analyzed in head and neck squamous cell carcinoma (HNSCC) the intracellular components of the pathway have not been investigated. This is the first study in the literature reporting a role for β-catenin and Dvl mRNA level alterations in HNSCC. In our previous study we have identified that the WWOX gene is inactivated in HNSCC as a result of genetic and epigenetic alterations. To identify the mechanism of action of WWOX in HNSCC in this study we investigated its expression in association with Dvl-1, Dvl-2, Dvl-3 and β-catenin expression in 98 HNSCC samples. We observed down-regulation of the WWOX mRNA in 73.5% of the HNSCC tumor samples compared to their non-cancerous counterparts. Up-regulation of the Dvl-1, Dvl-2, Dvl-3 and β-catenin mRNAs were detected in 32.7%, 36%, 38.8% and 24.5% of the same tumor samples, respectively. We also detected a statistically significant correlation between the WWOX gene expression and mRNA levels of the intracellular components of the Wnt pathway genes. Our results indicate that WWOX acts as a tumor suppressor in the HNSCC development and progression by inhibiting the expression of the Dvl proteins.

Citation Format: Ayse Nur Buyru, Asuman Celebi, Betul Seyhan. The role of WWOX in HNSCC through Wnt/beta-catenin pathway [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr B33.
Abstract B36: Contrasting views on the role of mesenchymal stem cells in tumor progression: A systematic review
Authors: Oloyo Ahmed Kolade , Pepper Michael Sean
Published: December 2017

The role of mesenchymal stem cells (MSCs) in the progression of tumor remains controversial. Strong experimental evidences support both inhibitory and stimulatory roles of MSCs on tumor growth. To assess factors responsible for contrasting effects of MSCs on tumor growth, we did a systematic review of existing literature on the effect of MSCs on tumor growth from 01/01/00 - 01/05/16. A total of 168 original research articles with 315 experiments were assessed. Factors considered in the complex relationship between MSCs and tumor growth include: type of experiments (in-vivo, in-vitro), experimental models for the in-vivo studies (syngeneic or xenogeneic), immune status of the experimental animal (competent or deficient), sources and types of cancer and MSCs, status of the MSCs (naïve or engineered), methods of inducing cancer as well as methods of administering the MSCs in vivo and methods used in the in vitro experiments (co-culture or conditioned media). 55% of the studies favor the stimulatory effect of MSCs on tumor growth. The type of experiment is divided almost evenly, as about 53% of all the experiments were conducted in-vitro with 60% of the cancer cells exposed to the MSCs via co-culture methods. 78% of the in-vivo experiments were xenogeneic and 63% of these were carried out in immunocompetent animals. About 80% of both MSCs and cancer cells were sourced from human and 86% of these MSCs were used in their naïve form while 14% were engineered to produce factors that could alter the activity of the MSC itself or that of the cancer cells. About 61% of the MSCs were derived from bone marrow while 15% each were derived from adipose tissues and umbilical cord the remaining 8% MSCs were derived from other various tissues. Tumor growth was inhibited in 86% of experiments that used engineered MSCs. Tumor growth was inhibited in 82% of experiment that used umbilical cord MSCs while tumor growth was promoted in 62% of experiment that employed bone marrow MSCs, but the effect of MSCs on tumor growth was about 57% and 43% stimulatory and inhibitory respectively when adipose tissue derived MSCs were used. Thus several factors determine what effect MSCs would have on the progression of tumor growth.

Note: This abstract was not presented at the conference.

Citation Format: Ahmed Kolade Oloyo, Michael Sean Pepper. Contrasting views on the role of mesenchymal stem cells in tumor progression: A systematic review [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr B36.
Abstract IA1: Progress in scaling up cervical cancer prevention in health services of developing countries
Authors: Sankaranarayanan Rengaswamy
Published: December 2017

Cervical cancer is a major threat to women's health accounting for 528,000 new cases and 266,000 deaths annually around 2012, of which 85% occurred in low- and middle-income (LMICs). Substantial declines in cervical cancer incidence and mortality rates can be achieved by integrating HPV vaccination and cervical screening in public health services in LMICs. Since 2007, HPV vaccination has been introduced in national immunization programs in 73 countries, of which 33 are LMICs; in addition it has been introduced in pilot programs in another 17 countries, mostly in sub-Saharan Africa. It is particularly impressive that 7 out of 8 girls have access to HPV vaccination in Latin Region. So far, more than 270 million doses have been administered globally with excellent safety profile and high acceptance, despite the negative publicity surrounding HPV vaccination. The falling vaccine prices, possibility of new vaccines from China and India and the currently recommended two-dose schedule will make HPV vaccination more feasible. Screening is yet to be widely implemented in many LMICs and many of these countries lack the health care infrastructure and resources to introduce efficient screening programs. Screening has been sub-optimally performing in some LMICs for lack of adequate coverage, follow-up and quality assurance. A number of countries have introduced visual inspection (VIA) screening in their health services as opportunistic or pilot programs. HPV testing is the most effective cervical screening tool and HPV negative women are at very low risk for cervical cancer. Currently Mexico and Argentina have introduced HPV screening. The eventual availability of a simple, affordable, faster and accurate HPV tests will facilitate wider HPV screening in LMICs. Planned investments to implement HPV vaccination of single year cohorts of 9-13 year old girls and at least a single HPV screening of women between 30-59 will save many precious lives in developing countries.

Citation Format: Rengaswamy Sankaranarayanan. Progress in scaling up cervical cancer prevention in health services of developing countries [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr IA1.
Abstract IA14: Targeting human endogenous retroviruses for epigenetic therapy
Authors: Jones Peter A.
Published: December 2017

Vitamin C deficiency is found in patients with cancer and might complicate various therapy paradigms. Here we show how this deficiency may influence the use of DNA methyltransferase inhibitors (DNMTis) for treatment of hematological neoplasias. In vitro, when vitamin C is added at physiological levels to low doses of the DNMTi 5-aza-2'-deoxycytidine (5-aza-CdR), there is a synergistic inhibition of cancer-cell proliferation and increased apoptosis. These effects are associated with enhanced immune signals including increased expression of bidirectionally transcribed endogenous retrovirus (ERV) transcripts, increased cytosolic dsRNA, and activation of an IFN-inducing cellular response. This synergistic effect is likely the result of both passive DNA demethylation by DNMTi and active conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) enzymes at LTR regions of ERVs, because vitamin C acts as a cofactor for TET proteins. In addition, TET2 knockout reduces the synergy between the two compounds. Furthermore, we show that many patients with hematological neoplasia are markedly vitamin C deficient. Thus, our data suggest that correction of vitamin C deficiency in patients with hematological and other cancers may improve responses to epigenetic therapy with DNMTis.

Citation Format: Peter A. Jones. Targeting human endogenous retroviruses for epigenetic therapy [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr IA14.
Abstract IA17: New ways of targeting Ras
Authors: McCormick Frank
Published: December 2017

Activating K-Ras mutations occur frequently in many cancers, and account for about one million cancer deaths per year worldwide. Currently, no therapies exist that target K-Ras directly, and K-Ras cancers are very difficult to treat. Indeed, they are excluded from treatment with targeted agents such as tarceva and vemurafenib. The K-Ras protein is a member of a large family of related proteins, of which H-Ras and N-Ras are the closest relatives. Ablation of all three Ras genes is likely to be toxic, as these proteins are essential in most signaling transduction pathways. We therefore need to target the mutant oncoprotein itself, or target K-Ras, without affecting H-Ras or N-Ras. The striking similarity of these proteins makes this task challenging, together with the fact that the K-Ras gene expresses two splice variants, K-Ras 4A and K-Ras 4B, each of which can contribute to cancer. Nevertheless, differences do exist between these proteins, and ways in which these can be exploited will be discussed. One approach takes advantage of unique properties of K-Ras 4B, the other targets an amino acid that is shared between K-Ras isoforms, but is not present in H-Ras or N-Ras, or other members of the Ras family. K-Ras processing can be prevented by compounds that block the CAAX box cysteine. We have identified compounds that interact covalently with this cysteine and block prenylation by farnesyl transferase or geranylgeranyl transferase. These compounds reduce expression of K-Ras in cells and have specificity for K-Ras relative to H-Ras and N-Ras and represent another approach to targeting K-Ras specifically. We have also used new biophysical methods to target K-Ras, including second harmonic generation. This method detects small allosteric changes in proteins, and thus allows identification of small molecules that bind to K-Ras at novel allosteric sites. Drug resistance is likely to be a problem with Ras inhibitors, as it is for all types of cancer therapies. We have identified an approach to killing drug resistant cells that appears effective against a wide range of resistance mechanisms. This was achieved by targeting persister cells that survive targeted agents, but have unique properties that make them vulnerable to attack. The implications of this new strategy will be discussed.

Citation Format: Frank McCormick. New ways of targeting Ras [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr IA17.
Abstract IA27: A novel cancer-testis antigen protein microarray for autoimmune profiling in cancers: Diagnosis, stratification, and treatment monitoring
Authors: Blackburn Jonathan
Published: December 2017

The cancer-testis antigens are a group of unrelated proteins aberrantly expressed in various cancers in adult somatic tissues. This aberrant expression can trigger spontaneous immune responses, a phenomenon exploited for the development of disease markers and therapeutic vaccines. However, expression levels often vary amongst patients presenting the same cancer type, and these antigens are therefore unlikely to be individually viable as diagnostic or prognostic markers. Nevertheless, patterns of antigen expression may provide correlates of specific cancer types and disease progression. This paper will describe the development and application of a novel, readily customizable cancer-testis antigen microarray platform, together with robust bioinformatics tools, which enable quantification of anti-cancer-testis antigen autoantibody profiles in patient sera. By exploiting the high affinity between autoantibodies and tumor antigens, our highly multiplexed protein microarray platform gives linearity of response over 4 orders of magnitude and an autoantibody quantitation limit in the pg/mL range.

By using oriented attachment of folded, recombinant antigens and a polyethylene glycol microarray surface coating, our platform gives minimal non-specific antibody binding. Unlike other proteomics methods, which typically use lower affinity interactions between monoclonal antibodies and tumor antigens for detection, the high sensitivity and specificity realized using our autoantibody-based approach may facilitate the development of better cancer biomarkers, as well as potentially enabling pre-symptomatic diagnosis. We will illustrate the usage of our platform by monitoring the time-dependent response of melanoma patient cohorts to an experimental therapeutic NY-ESO-1-based cancer vaccine, to combination BRAF and MEK inhibitor treatment, and to anti-CTLA4/anti-PD1 vaccination.

Citation Format: Jonathan Blackburn. A novel cancer-testis antigen protein microarray for autoimmune profiling in cancers: Diagnosis, stratification, and treatment monitoring [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr IA27.
Abstract IA38: Viral cancers: The forgotten culprits in the African cancer problem
Authors: Moore Patrick S.
Published: December 2017

Infection is responsible for approximately one-fifth of cancer cases worldwide. Causes and rates of cancer vary dramatically throughout the world. While infection is often overlooked as a cancer cause in the United States and Europe, it is often the main driving force for cancer in other parts of the world. The first human cancer virus discovered, Epstein-Barr virus (EBV), was isolated from a Ugandan Burkitt lymphoma in 1964. Infectious cancers including hepatocellular carcinoma, cervical carcinoma, Kaposi's sarcoma and gastric carcinoma represent the majority of cancer cases among men and women in some world regions, particularly in Africa. This lecture will focus on how new cancer viruses can be discovered, using Kaposi sarcoma herpesvirus and Merkel cell polyomavirus found in our lab as examples. The common characteristics--as well as the diverse nature--of viral cancers will be described. The extraordinary public health success of vaccines in preventing cancers of particular importance in Africa will be highlighted, and missed opportunities for low-cost, effective prevention and treatment of infectious cancers will be discussed. As with discovery of EBV, it is quite possible that the next cancer agent will be discovered in cancers unique to African countries but will have important implications to public health throughout the world.

Citation Format: Patrick S. Moore. Viral cancers: The forgotten culprits in the African cancer problem [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr IA38.
Abstract IA6: Lgr5 stem cell-based organoids in human disease
Authors: Clevers Hans
Published: December 2017

The intestinal epithelium is the most rapidly self-renewing tissue in adult mammals. We originally defined Lgr5 as a Wnt target gene, transcribed in colon cancer cells. Two knock-in alleles revealed exclusive expression of Lgr5 in cycling, columnar cells at the crypt base. Using lineage tracing experiments in adult mice, we found that these Lgr5+ve crypt base columnar cells (CBC) generated all epithelial lineages throughout life, implying that they represent the stem cell of the small intestine and colon. Lgr5 was subsequently found to represent an exquisitely specific and almost ‘generic’ marker for stem cells, including in hair follicles, kidney, liver, mammary gland, inner ear tongue and stomach epithelium.

Single sorted Lgr5+ve stem cells can initiate ever-expanding crypt-villus organoids, or so called ‘mini-guts’ in 3D culture. The technology is based on the observation that Lgr5 is the receptor for a potent stem cell growth factor, R-spondin. Similar 3D cultures systems have been developed for the Lgr5+ve stem cells of human stomach, liver, pancreas, prostate and kidney. Using CRISPR/Cas9 technology, genes can be efficiently modified in organoids of various origins.

Citation Format: Hans Clevers. Lgr5 stem cell-based organoids in human disease [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr IA6.
Abstract A20: Depletion of replication factor MCM7 is synthetically lethal to oncogenic KRAS expression
Authors: Gastl Bastian , Klotz-Noack Kathleen , Klinger Bertram , Zuber Johannes , Blüthgen Nils , Schäfer Reinhold , Sers Christine
Published: December 2017

Colorectal cancer (CRC) is a substantial cause of death in the western world. With KRAS being one of the most frequently altered oncogenes in CRC, it is an obvious target for cancer therapy. But despite enormous efforts over the past three decades to target mutated RAS, not a single drug has made it to the clinic.

In order to find vulnerabilities of KRAS mutant cells, we performed a shRNA-based screen. We used CaCo2 cells (wild type for KRAS/BRAF/PIK3CA) with doxycycline (DOX) inducible expression of the oncogenic KRASG12V as a model system. The custom-designed shRNA library comprised 121 selected genes encoding signaling proteins and transcription factors, which we have previously identified to be strongly up- or downregulated after treatment with MEK inhibitors.

We found that CaCo2 cells expressing KRASG12V are highly sensitive to the depletion of the DNA replication licensing factor Minichromosome Maintenance Complex Component 7 (MCM7), whereas wild-type CaCo2 cells are resistant to MCM7 depletion. The screening result was verified with 3 independent shRNAs under anchorage dependent and independent conditions. Similar results were obtained with NRASG12D and in DLD1 (KRASwt/KRASG13D) and DLD1 (KRASwt/-) cells.

The proposed molecular mechanism is RAS-induced genotoxic stress that cannot be resolved after MCM7 reduction. MCM7-containing complexes prime DNA for replication by binding to replication origins. However, only a few of the licensed origins are later used for DNA replication, while most origins stay dormant. The dormant origins are essential for resolving stalled replication forks after replicative stress. Unresolved stalled forks lead to DNA damage, which drives the cell into apoptosis. Further experiments will show the extent of DNA damage upon RAS induction and knock down of MCM7.

Since DNA replication licensing is only required in actively dividing cells and cells with physiological RAS signaling seem to be resistant to partial depletion of MCM7, it might be an ideal target for treating RAS mutated cancers.

Citation Format: Bastian Gastl, Kathleen Klotz-Noack, Bertram Klinger, Johannes Zuber, Nils Blüthgen, Reinhold Schäfer, Christine Sers. Depletion of replication factor MCM7 is synthetically lethal to oncogenic KRAS expression [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A20.
Abstract A30: Identifying microenvironment-dependent vulnerabilities in multiple myeloma using CRISPRi
Authors: Ramkumar Poornima , Tawney Jaime , Acosta-Alvear Diego , Kampmann Martin
Published: December 2017

Acquired drug resistance is a major clinical problem in a variety of cancer types and our understanding of the underlying mechanisms is insufficient. We lack a complete understanding of the interplay of factors between the tumor and its microenvironment controlling drug sensitivity. Several published studies and our preliminary results show that bone marrow microenvironment reduce the sensitivity of multiple myeloma cells to clinically approved proteasome inhibitor, carfilzomib, making it an ideal model system.

Here we employ innovative CRISPR-interference (CRISPRi) based functional genomics platform to identify cell-intrinsic and microenvironment-dependent vulnerabilities in multiple myeloma. This platform utilizes a catalytically dead Cas9 (dCas9) fused to a transcriptional repressor domain to target and silence specific genes using single guide-RNAs (sgRNA). We have engineered the myeloma cells to express components of the CRISPRi system enabling us to perform genome-wide screens to identify factors that modulate sensitivity to carfilzomib. To identify microenvironment-dependent factors that alter carfilzomib sensitivity, we established a co-culture system where the CRISPRi expressing myeloma cells are grown in the presence of bone marrow stromal cells and subject to treatment with carfilzomib. We performed a pilot-screen using a library of sgRNAs targeted towards genes involved in the human proteostasis network and known cancer drug targets. The library expressing CRISPRi-myeloma cells were grown as mono- and co-culture in the presence or absence of carfilzomib. Through this screen we were able to identify several factors knockdown of which had differential effects in mono- and co-culture conditions on the growth of the cells and/or their drug response. Currently we are validating the identified factors using various biochemical assays and available pharmacological tools. This study will pave the way to better understand the crosstalk between the tumor and its microenvironment and enable rational design of combination therapies to overcome drug resistance.

Citation Format: Poornima Ramkumar, Jaime Tawney, Diego Acosta-Alvear, Martin Kampmann. Identifying microenvironment-dependent vulnerabilities in multiple myeloma using CRISPRi [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A30.
Abstract B14: Precision functional genomics for glioblastoma: Identifying molecular therapeutic targets using CRISPR-Cas9 and RNAi technologies in patient isolates
Authors: Hoellerbauer Pia , Feldman Heather , Arora Sonali , Carter Lucas , Girard Emily J. , Corrin Philip , Olson James M. , Holland Eric C. , Paddison Patrick J.
Published: December 2017

Glioblastoma (GBM) is the most aggressive and common form of adult brain cancer and is among the deadliest cancers, with a median survival of 15 months using standard-of-care therapies. Thus, improved treatments for GBM are desperately needed. To identify new GBM molecular therapeutic targets, our group has performed multiple functional genetic screens in patient-derived GBM stem-like cells (GSCs) and non-transformed human neural stem and progenitor cells (NPCs), which represent non-neoplastic controls. These screens, which have used both RNAi and CRISPR-Cas9 platforms, have led to the identification of several key molecular vulnerabilities in GSCs, including GBM-specific defects in: 3' splice site recognition, kinetochore function, and loss of redundancy between the kinase activities of PKMYT1 and WEE1. At this meeting we will present an overview of these studies, as well as our current efforts to: comprehensively retest all GBM-specific vulnerabilities scoring in these screens; address whether vulnerabilities arise from specific genetic alterations in patient samples (e.g. NF1 loss or PTEN loss); determine whether inhibition of specific molecular targets blocks tumor growth and/or maintenance; and demonstrate the mode of GBM-specific death for particular targets (e.g., cell cycle arrest, apoptosis, etc). In addition, we will highlight both strengths and limitations of applications of CRISPR-Cas9 technologies in patient samples. Collectively, our work illustrates the power of combining functional genetic technologies with the use of patient isolates to identify novel, patient-specific therapeutic strategies for GBM.

Citation Format: Pia Hoellerbauer, Heather Feldman, Sonali Arora, Lucas Carter, Emily J. Girard, Philip Corrin, James M. Olson, Eric C. Holland, Patrick J. Paddison. Precision functional genomics for glioblastoma: Identifying molecular therapeutic targets using CRISPR-Cas9 and RNAi technologies in patient isolates [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B14.
Abstract B32: Restoration of beta cell mass as a synthetic lethal strategy to overcome oncogenic Kras-driven pancreatic ductal adenocarcinoma
Authors: Nguyen Thienly , Parajuli Parash , Ahmad Asrar , Singh Purba , Eragameddy Sailaja , Ramakrishnan Gopalakrishnan , Levy Laurence , Ferrigno Oliver , Mo Yin-Yuan , Pochampally Radhika , Razzaque Mohammed S , Prunier Celine , Atfi Azeddine
Published: December 2017

Pancreatic ductal adenocarcinoma (PDAC) is a disease that remains incurable due to diagnosis at advanced stages, which renders any therapeutic intervention impracticable. The vast majority of PDAC patients develop new-onset diabetes, which often culminates in dysfunction of vital organs, leading to severe morbidity and high mortality. How PDAC development leads to diabetes is still unfolding. More than 90% of PDAC cases have an oncogenic mutation that affects the proto-oncogene Kras, mostly G12D. Using several mouse models of KrasG12D-driven PDAC, which faithfully recapitulate the human disease, we observed a massive depletion of beta cell mass, occurring even at early stages of pancreatic intraepithelial neoplasia (PanIN). This phenomenon was selective for beta cells, as PanIN or PDAC formation did not affect any other type of islet cells, including alpha and delta cells, which produce Glucagon and Somatostatin, respectively. Intriguingly, both alpha and delta cells retained their localization at the periphery of islets that are devoid of beta cells, giving rise to PanIN-like structures. Such pattern was observed when KrasG12D expression was combined with genetic inactivation of other tumor suppressor genes frequently inactivated in human PDAC, including TP53 and p16Ink4a. Lastly, we also detected depletion of beta cells and presence of remnant islets resembling PanIN in human PDAC, attesting to the clinical relevance of our findings, and further rise the attractive question of whether restoration of beta cell mass could be utilized to curb PDAC driven by oncogenic Kras.

Citation Format: Thienly Nguyen, Parash Parajuli, Asrar Ahmad, Purba Singh, Sailaja Eragameddy, Gopalakrishnan Ramakrishnan, Laurence Levy, Oliver Ferrigno, Yin-Yuan Mo, Radhika Pochampally, Mohammed S Razzaque, Celine Prunier, Azeddine Atfi. Restoration of beta cell mass as a synthetic lethal strategy to overcome oncogenic Kras-driven pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B32.
Abstract B36: A 1,5-diheteroarylpenta-1,4-dien-3-one inhibits TNBC cell growth by blocking AKT/mTOR/P70S6K pathway
Authors: Atefi Mohammad , Patanapongpibul Manee , Ma Lynn , Chen Qiao-Hong , Wang Guangdi , Wu Yong , Vadgama Jay
Published: December 2017

One in 8 women will develop breast cancer during the course of her life. Recent developments in the field of drug development have provided a significant increase in progression free survival and decrease in mortality of this disease. However, one of the main problems in breast cancer remains the development of resistance to current treatments and relapse of the disease. Moreover, there is no known target for the treatment of the triple negative breast cancers (TNBC) subset, which is more aggressive than the other types of the disease. Therefore, it is imperative to develop new drugs that can block the activity of pro-survival signaling within the cancer cells and inhibit their growth, particularly in the TNBC subset. In an attempt to identify such drugs, we screened a panel of 13 compounds, containing the general structure of 1,5-diheteroarylpenta-1,4-dien-3-one (compounds 34 to 46), for their effectiveness in inhibiting the growth of both TNBC and ER+ breast cancers. The IC50s for these compounds were in the range of 63 to 8346 nM against various breast cancer cell lines. Interestingly, the most potent compound (# 34), (1E,4E)-1,5-bis(1-pentan-2-yl)-1H-imidazol-2-yl)penta-1,4-dien-3-one, showed its highest growth inhibitory activity in the TNBC cell line, MDA-MB-231, while also being effective in inhibiting the growth of ER+ cell lines to a lesser extent. Further investigations were then focused on this TNBC cell line. The mechanism of action of compound 34 was investigated by using a Human Phospho-Kinase Array, which revealed a significant decrease in p-P70S6K and p-mTOR. Additional assays confirmed the same results and also showed significant reductions in total mTOR and Total AKT as well as significant decreases in p-P70S6K and p-mTOR. Moreover, compound 34 treatment induced higher levels of p-c-JUN and p-P38, which may be indications of cell stress upon treatment. Overall our data indicate that compound 34 induces profound decreases in the activity of pro-survival pathways such as AKT/mTOR, which significantly inhibited growth of the TNBC cell line.

Citation Format: Mohammad Atefi, Manee Patanapongpibul, Lynn Ma, Qiao-Hong Chen, Guangdi Wang, Yong Wu, Jay Vadgama. A 1,5-diheteroarylpenta-1,4-dien-3-one inhibits TNBC cell growth by blocking AKT/mTOR/P70S6K pathway [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B36.
Abstract IA10: Finding vulnerabilities of drug resistant cancers
Authors: Bernards René
Published: December 2017

Intrinsic and acquired drug resistance represent major obstacles to effective cures for cancer. Understanding these mechanisms is instrumental for the design of strategies to counter these resistance mechanisms.

In my presentation, I will focus on an example of intrinsic drug resistance and one of acquired drug resistance. As an example of intrinsic drug resistance, I will discuss the lack of response to MEK inhibitors seen in KRAS mutant tumors of various. The consistently poor response of KRAS mutant tumors to inhibition of its downstream kinases is unexpected, as it defies the concept of oncogene addiction. Nevertheless, a subset of tumors responds well to MEK inhibition, but it remains unclear which biomarkers can be used to identify MEK inhibitor sensitive cancer cells. I will demonstrate that inactivating mutations in both MAP3K1 and MAP2K4 will confer strong sensitivity to MEK inhibition in cancers of any tissue origin. Given that most major cancers have a mutation rate in these two genes of around 10%, the use of these mutations may help select patient subgroups that benefit from MEK inhibitor therapy.

As an example of acquired drug resistance, I will discuss resistance of BRAF(V600E) mutant melanomas to drugs that target the BRAF and/or MEK kinases. This acquired resistance is almost always caused by reactivation of signaling through this pathway in the presence of drug. Drug withdrawal in such patients leads to a further hyper-activation of MAPK pathway, leading to a cellular state that has hallmarks of oncogene-induced senescence. I will show that drugs can be identified that maintain high levels of MAPK pathway signaling in BRAF inhibitor resistant melanomas upon cessation of BRAF inhibitor treatment. These drugs are only active in melanoma cells that have acquired resistance to BRAF inhibitors and not in parental melanoma cells, because they require MAPK hyper-activation that is induced by the gained resistance to BRAF inhibitors to be effective. In general, second line treatment of tumors that have acquired resistance to first line therapy is less effective. The unique aspect of the second line therapy identified here is that it exploits a vulnerability that is only gained upon acquisition of resistance to BRAFi therapy. The proposed therapy also takes advantage of the fact that acquisition of resistance to BRAFi follows a predictable path in the clinic making their responses to second line also more predictable.

Citation Format: René Bernards. Finding vulnerabilities of drug resistant cancers [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr IA10.
Abstract IA15: Genetic screens to study cancer
Authors: Sabatini David M.
Published: December 2017

We will describe our efforts to use the CRISPR/Cas9 system to systematically identify the genetic liabilities of cancer cells and the synthetic lethal relationships of common oncogenes.

Citation Format: David M. Sabatini. Genetic screens to study cancer [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr IA15.
Abstract IA17: Synthetic-lethal strategies for MYC-driven cancers
Authors: Goga Andrei
Published: December 2017

MYC is an essential, pleiotropic transcription factor whose amplification or deregulated expression is one of the most commonly occurring events in cancer. Despite the importance of MYC as a therapeutic target, no available drugs directly inhibit MYC transcriptional activity. Our group has undertaken several orthogonal approaches to identify MYC-pathway directed synthetic-lethal interactions. Using cell-based and transgenic animal models we have identified new potential therapeutic targets. These include metabolic, cell cycle and novel kinase vulnerabilities of MYC-driven cancers that will be discussed.

Citation Format: Andrei Goga. Synthetic-lethal strategies for MYC-driven cancers [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr IA17.
Abstract PR16: A druggable transcriptional vulnerability in NRF2-dependent lung cancer
Authors: Bar-Peled Liron , Kemper Esther , Cravatt Benjamin
Published: December 2017

The b-ZIP transcription factor NRF2 is a master regulator of the cellular antioxidant response and frequently activated in Non-Small Cell Lung Cancers (NSCLCs). While direct pharmacological inhibition of NRF2 has proven challenging, its aberrant activation rewires metabolic and signaling networks in cancer cells that may create special vulnerabilities for therapeutic intervention. Here, we use chemical proteomics to map ligandable proteins in NRF2-activated NSCLC cells, leading to the discovery of metabolic and transcriptional pathways that are strictly regulated by NRF2. Principal among these was the orphan nuclear receptor NR0B1, which we show nucleates a multimeric protein complex required for the transcriptional output and anchorage-independent growth of NRF2-driven cancers. We further identify small-molecules that target a conserved cysteine within NR0B1's protein interaction domain and show that these chemical probes disrupt NR0B1 complexes and NRF2-dependent cancer cell growth. Our findings thus designate NR0B1 as a druggable, transcriptional co-dependency target for NRF2-activated lung cancers.

Citation Format: Liron Bar-Peled, Esther Kemper, Benjamin Cravatt. A druggable transcriptional vulnerability in NRF2-dependent lung cancer [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR16.