bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-163: A phase I trial investigating apoptosis induction with tumor necrosis factor or radiation alone prior to intratumoral injection of autologous dendritic cells in patients with locally advanced or low volume metastatic pancreatic cancer.
Authors: Zervos Emmanuel E. , Mule James J. , Brigham Denise , Janssen William , Cooper Jennifer , Rosemurgy Alexander S.
Published: August 2014

The purpose of this trial was to determine the safety, feasibility and efficacy of intra-tumoral injection of an autologous dendritic cell (DC) based vaccine following apoptosis induction with a tumor necrosis factor expressing adenovector (TNF) or low dose radiation therapy (XRT).

Methods: Between August 2006 and August 2011, 24 patients with locally advanced (n= 17) or low-volume metastatic (n=7) pancreatic cancer were enrolled to receive either: TNF on day 1 followed by vector activating XRT (2 Gy/d on days 1-3) and then an autologous, KLH pulsed DC vaccine (50M cells, day 4) for 3 weeks; or, XRT (1.9 Gy/d on days1-4) followed by DC vaccine (50M cells, day 5) for 3 weeks. Feasibility endpoints included our ability to produce the vaccine and the subject's ability to complete all phases of the protocol. Serious adverse events (SAE) were recorded to establish safety. Efficacy was established by radiographic and biochemical tumor response, progression free (PFS) and overall survival (OS).

Results: All but 2 patients completed the protocol (92%). One patient died prior to initiation of treatment (not included in survival analysis) and one disenrolled during treatment due to deep venous thrombosis. 50 of 66 (76%) total vaccines produced contained greater than 50M DC. There was no vaccine related toxicity. In the TNF group, there were 19 SAEs including one death. In the XRT group, there were 33 SAEs mostly characterized by pain, nausea, dehydration and vomiting. Two (4%) SAEs led to hospital admission, one for duodenal bleeding and one for bacteremia. Tumor response favored the radiation group as did survival. (table)

Conclusions: DC based vaccines are feasible and safe in patients with advanced pancreatic cancer. Apoptosis induction using TNF, though less complicated, imparted no survival advantage over radiation alone and may have provided some disadvantage.

Efficacy O.S. (mos) P.F.S. (mos) Stable or partial response (%) Stable or decreased Ca19-9(%) TNF (n = 15) 5.8±2.05 4.7±2.17 60 62 XRT (n = 8) 8.7±3.48 6.9±3.79 75 100 Total 6.9±2.92 5.4±2.96 65 76

Citation Format: Emmanuel E. Zervos, James J. Mule, Denise Brigham, William Janssen, Jennifer Cooper, Alexander S. Rosemurgy. A phase I trial investigating apoptosis induction with tumor necrosis factor or radiation alone prior to intratumoral injection of autologous dendritic cells in patients with locally advanced or low volume metastatic pancreatic cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-163. doi:10.1158/1538-7445.AM2013-LB-163
Abstract LB-164: Treatment of advanced stage colorectal cancer with ETBX-011 immunotherapeutic.
Authors: Gabitzsch Elizabeth S. , Morse Michael A. , Lyerly H. Kim , Jones Frank
Published: August 2014

In this Phase 1/2a non-randomized study, 32 patients having advanced stage metastatic colorectal cancer (mCRC) were treated with a novel immunotherapeutic, ETBX-011 (Ad5 [E1-, E2b-]-CEA(6D)). The trial included increasing doses of the agent and was found to be safe and well-tolerated at all doses assessed. There were no dropouts or treatments stopped due to adverse effects. Specific anti-CEA immune responses were observed in the majority of patients after they were treated three times over 6 weeks by subcutaneous injections of ETBX-011. Long-term follow-up in some of the patients reveled that the CEA directed immune responses persisted for up to 6-9 months after treatment and median overall-survival was 11 months. These results demonstrate that in mCRC patients the ETBX-011 immunotherapeutic generated significant CMI responses to the tolerized tumor antigen CEA. mCRC patients treated with ETBX-11 may experience extension of life and we are preparing to initiate a randomized, multicenter Phase 2b trial to further evaluate the clinical benefit.

Citation Format: Elizabeth S. Gabitzsch, Michael A. Morse, H. Kim Lyerly, Frank Jones. Treatment of advanced stage colorectal cancer with ETBX-011 immunotherapeutic. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-164. doi:10.1158/1538-7445.AM2013-LB-164

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.
Abstract LB-190: Time to treatment of Latinas with breast cancer utilizing patient navigation: the Six Cities Study.
Authors: Ramirez Amelie G. , Perez-Stable Eliseo , Talavera Gregory A. , Penedo Frank J. , Carrillo J. Emilio , Fernandez Maria E. , Holden Alan E. C. , Munoz Edgar , Long-Parma Dorothy , de Mejors Sandra San Miguel , Gallion Kipling
Published: August 2014

BACKGROUND: Breast cancer is the leading cause of cancer deaths in Latinas. Time from cancer diagnosis to treatment initiation is critical in optimizing cancer care. Patient navigation is a potentially effective means of promoting timely treatment of breast cancer, yet efficacy is insufficiently documented. Redes en Accion here evaluates a culturally sensitive patient navigation program to reduce time from cancer to diagnosis to treatment and increase proportions of women treated within 30 days of diagnosis.

METHODS: We analyzed 109 Latinas diagnosed with breast cancer from July 2008-January 2011 (42 navigated, 67 controls). Women were navigated by locally trained navigators or non-navigated (data abstracted from charts). Kaplan-Meier, Cox proportional hazards, and logistic regression were used to determine group differences.

RESULTS: Time from cancer diagnosis to 1st treatment was lower in the navigated group (MED 21 days, control 32 days, HR 1.6, p=0.02). 64.3% began treatment within 30 days of cancer diagnosis, compared to 47.8% of non-navigated Latinas (p=0.015) controlling for stage of cancer at diagnosis and numerous characteristics of clinics and participants. Effects were due to navigator activities compared to those who did not need or utilize them, including appointment reminders, transportation arrangements, accompaniment to appointments, and translation services.

CONCLUSIONS: Patient-centered navigation to assist Latina women with breast cancer diagnoses significantly reduces time from diagnosis to treatment, and increases the proportion of women who begin treatment within 30 days of diagnosis. Improvement appears to be associated with specific navigator activities.

Acknowledgement: Redes En Acción: The National Latino Cancer Research Network (NCI U01 CA114657-05) and the Cancer Therapy and Research Center at the University of Texas Health Science at Center San Antonio (Grant # P30CA054174).

Citation Format: Amelie G. Ramirez, Eliseo Perez-Stable, Gregory A. Talavera, Frank J. Penedo, J. Emilio Carrillo, Maria E. Fernandez, Alan E. C. Holden, Edgar Munoz, Dorothy Long-Parma, Sandra San Miguel de Mejors, Kipling Gallion. Time to treatment of Latinas with breast cancer utilizing patient navigation: the Six Cities Study. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-190. doi:10.1158/1538-7445.AM2013-LB-190
Abstract LB-2: Open innovation drug discovery: A study in JQ1.
Authors: Shaw Daniel L. , Lin Charles Y. , Oakley Richard P. , Semenkovich Nicholas P. , Qi Jun , Bradner James E.
Published: August 2014

Collaborative research from our laboratory, in 2010, produced a first-in-class inhibitor of BET bromodomain proteins (JQ1). As an effort to promote a more open-innovation model of drug discovery, we endeavored to provide JQ1 without restriction of cost or delay to the scientific community. Toward this objective, we have optimized and completed a facile scaling synthesis capable of producing 100 g quantities of the active (+)-JQ1 stereoisomer. In the past 30 months, JQ1 has been provided to over 350 laboratories in more than a dozen countries. Through this research, BET bromodomain proteins have emerged as pharmacologically validated targets in multiple model systems of cancer including squamous carcinoma of the lung, head and neck, acute myeloid leukemia, multiple myeloma, Burkitt lymphoma, B-cell acute lymphoblastic leukemia, neuroblastoma and non-small cell lung cancer. More than 800 cancer cell lines and 25 murine models of cancer have been systematically screened with JQ1 for sensitivity to bromodomain inhibition, identifying additional therapeutic opportunities. Open availability of JQ1 has also lead to unexpected innovation outside of cancer research through studies identifying opportunities for BET bromodomain inhibition in such diverse fields as male contraception and HIV therapeutics. Since publication of the chemical structure and synthetic route to JQ1, seven new BET bromodomain inhibitors have appeared in the literature each derivatized from and/or benchmarked to the JQ1 molecule. Importantly, BET bromodomain inhibition has already accomplished clinical translation. To more objectively assess the consequence of open-innovation as a model of drug discovery, we have systematically analyzed metadata collected from published research and our ongoing efforts in compound distribution. Here, we present an interim analysis which relates the effect of open-innovation in drug discovery to the scope, productivity, reproducibility and importantly the pace of scientific research in epigenetic reader proteins. These results identify open-innovation in drug discovery as a catalyst for scientific discovery, bridging a gap between fields of research and the basic and clinical sciences.

Citation Format: Daniel L. Shaw, Charles Y. Lin, Richard P. Oakley, Nicholas P. Semenkovich, Jun Qi, James E. Bradner. Open innovation drug discovery: A study in JQ1. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-2. doi:10.1158/1538-7445.AM2013-LB-2
Abstract LB-20: Serum antioxidant levels and survival time in advanced non-small cell lung cancer patients.
Authors: Wirasorn Kosin , Hongprabhas Pranithi , Pisprasert Veeradej , Klarod Kulthida , Boonsiri Patcharee
Published: August 2014

Background: Oxidative stress is involved with carcinogenesis of lung cancer and promotes tumor growth. Antioxidants play roles in inhibition of oxidative stress; consequently slow progression of tumor growth. This study aimed to show the correlation between median survival in advanced-stage non-small cell lung cancer (NSCLC) patients and antioxidant levels.

Methods: Newly diagnosed advanced-stage NSCLC patient in Khonkaen University Hospital during June 2006 and June 2008 were enrolled. Participants who had history of taking dietary supplements were excluded. Tumor data and nutritional status were evaluated in all patients. Serum from each participant was taken since the date of diagnosis to determine non-enzymatic antioxidants, trace element antioxidants, and peroxidase levels. Each antioxidant level was categorized into quartiles to analyze the correlation with survival time. Both univariate analysis and COX regression model which included nutritional status were used in the analysis.

Results: Thirty patients with mean age of 59.8 (range, 35-82) were enrolled. The majority of patients was male (76%), malnourished (90%), had a history of smoking (80%), and received chemotherapy for treatment of NSCLC (73%). Patients with the highest quartile of zinc had significantly longer survival time than with the lowest quartile (14.7 Vs 5.6 months) in both univariate and multivariate analysis (P = 0.01 and 0.007, respectively); while the significance of manganese was proven in only univariate model. Other antioxidants levels including retinol, α-tocopherol, β-carotene, lycopene, β-cryptoxanthin, selenium, copper, and peroxidase did not demonstrate relationship with survival time.

Conclusion: The low level of some antioxidants, particularly zinc, produced a significantly poor prognosis in advanced-stage non-small cell lung cancer patients.

Citation Format: Kosin Wirasorn, Pranithi Hongprabhas, Veeradej Pisprasert, Kulthida Klarod, Patcharee Boonsiri. Serum antioxidant levels and survival time in advanced non-small cell lung cancer patients. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-20. doi:10.1158/1538-7445.AM2013-LB-20
Abstract LB-207: Dissecting the functional landscape of triple-negative breast cancer.
Authors: Maxfield Kimberly , Prat Aleix , Corcoran Kathleen , Whitehurst Angelique
Published: August 2014

Triple negative breast cancer (TNBC) is the most aggressive form of breast cancer with poor patient prognosis. Patients who respond poorly to the current standard of care cytotoxic chemotherapeutic regimens only have about a 55% five-year survival rate due to the lack of other effective TNBC therapeutics. To uncover new therapeutic entry points for TNBC, we employed a pangenomic loss of function siRNA screening approach. To account for heterogeneity within the patient population, we screened 4 triple negative tumor-derived breast cancer cell lines that represent the spectrum of oncogenic aberrations and molecular subtypes in TNBC. By intersecting the datasets from these 4 cell lines, we revealed core modulators of viability and chemotherapy-induced cellular stress that have not been previously implicated in TNBC biology. For example, our screen uncovered a tractable energy-sensing AMPK family member that supports tumor cell viability in a subset of TNBC tumors. We also discovered tumor cell vulnerabilities unique to the Basal-Like and Claudin-Low TNBC molecular subtypes. In particular, Basal-Like tumor cell division is sensitive to perturbations in specific cytokine signaling. With respect to Claudin-Lows, we found an increased sensitivity to depletion of transcriptional modulators and downstream targets of TGFβ signaling, which suggests that TGFβ signaling may not only be required for a mesenchymal phenotype but also for Claudin-Low tumor cell survival. Our findings suggest that a set of tumor cell vulnerabilities can partition TNBC into functional subgroups and these vulnerabilities could lead to new therapeutics improving overall TNBC patient prognosis.

Citation Format: Kimberly Maxfield, Aleix Prat, Kathleen Corcoran, Angelique Whitehurst. Dissecting the functional landscape of triple-negative breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-207. doi:10.1158/1538-7445.AM2013-LB-207
Abstract LB-215: Concomitant targeting of tumor cells and induction of T cell response synergizes to effectively inhibit trastuzumab-resistant breast cancer.
Authors: Wang Qingfei , Li Shau-Hsuan , Wang Hai , Xiao Yi , Sahin Ozgur , Brady Samuel W. , Li Ping , Jaffee Elizabeth M. , Hortobagyi Gabriel N. , Yu Dihua
Published: August 2014

Introduction: Trastuzumab is an iconic example of rationally designed targeted therapy for HER2-positive breast cancers; however, trastuzumab resistance is a imposing clinical challenge that calls for novel approaches to better benefit patients. The purpose of this study was to find alternative combinatorial targeted therapies to overcome trastuzumab resistance.

Methods: We used two distinct PTEN-loss mediated trastuzumab resistant mammary tumor mouse models. Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and Akt inhibitor triciribine (TCN) were applied alone or in combination with 7.16.4 antibody, the mouse equivalent of the trastuzumab, for the treatment of tumor-bearing mice. Immunoblotting, immunohistochemistry, in vivo cytotoxicity assay and quantitative real time PCR were employed to dissect the in vivo effects of the treatments and molecular changes.

Results: Concomitant targeting of tumor cells with Akt inhibitor TCN plus trastuzumab, and activation of T cells with anti-CTLA-4 antibody in the tumor microenvironment results in a synergistic inhibitory effect on tumor growth and overcomes trastuzumab resistance in both mammary tumor mouse models. In vivo combinatorial treatment with the 7.16.4 HER2/Neu antibody and TCN effectively inhibited tumor growth in both models via inhibiting PI3K/AKT and MAPK signaling accompanied by increased T cell infiltration in the tumor microenvironment. We demonstrated that both CD8+ and CD4+ T cells were essential to the optimal antitumor effect of the combination treatment in an IFN-γ-dependent manner. Importantly, the antitumor activities of HER2/Neu antibody and TCN combination treatment were further improved when we blocked co-inhibitory receptor cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) to enhance the T cell response.

Conclusion: Our data indicate that multi-targeted combinatorial therapies targeting tumor cells and concomitantly enhancing T-cell response in the tumor microenvironment cooperated to exert maximal therapeutic activity. We propose that concomitant targeting tumor cells and tumor microenvironment is a promising clinical strategy for treating trastuzumab-resistant breast cancers and other advanced malignancies.

Citation Format: Qingfei Wang, Shau-Hsuan Li, Hai Wang, Yi Xiao, Ozgur Sahin, Samuel W. Brady, Ping Li, Elizabeth M. Jaffee, Gabriel N. Hortobagyi, Dihua Yu. Concomitant targeting of tumor cells and induction of T cell response synergizes to effectively inhibit trastuzumab-resistant breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-215. doi:10.1158/1538-7445.AM2013-LB-215
Abstract LB-223: A specific Isoform of Gli1 binds the promoter region of c-fos in A2780-CP70 human ovarian cancer cells.
Authors: Amable Lauren , Kudo Kenji , Gavin Elaine , Fain Jason , Reed Eddie
Published: August 2014

The transcription factor Activator Protein 1 (AP1), is an important regulator in cisplatin resistance. AP1 is comprised of the two proteins, c-jun and c-fos. The transcription factor Gli1, a member of the hedgehog signaling pathway, is also an important factor in cisplatin resistance and transcriptionally regulated c-jun. The c-jun interface with Gli1 is mediated by a 130 kDa isoform of Gli1. We have investigated whether Gli1 may regulate c-fos by selectively knocking down Gli1 expression using anti-Gli1 shRNA or by treating cells with a Hedgehog pathway inhibitor, cyclopamine.

A2780-CP70 cells were treated with an IC50 dose of anti-Gli1 shRNA and the changes in RNA and protein levels were analyzed over a 72 hour time course. No changes in the expression of c-jun or c-fos RNA transcripts were observed versus control. Western blot analyses showed Gli1 protein expression was reduced at 24 hours and undetectable at 48 and 72 hours. Sonic hedgehog (Shh) protein levels were dramatically reduced by 24 hours, low but measureable at 48 hours, and undetectable at 72 hours. Indian hedgehog (Ihh) expression increased at 24 hours and remained stable for the remainder of the 72 hour time course.

Treatment of A2780-CP70 cells with an IC50 dose of cyclopamine resulted in a different intracellular response than treatment with Gli1 shRNA. Cyclopamine specifically targets the cell membrane receptor Smoothened. Experiments were performed analyzing RNA and protein expression over a 72 hour time period after treatment with cyclopamine. C-jun and c-fos RNA transcript levels were higher than control 6 hours after treatment and remained high for the duration of the 72 hour experiment. Western blot analyses after cyclopamine treatment showed Gli1 protein expression gradually decreasing during the 72 hours, but were never fully depleted. Expression of Shh increased over 72 hours, while Ihh levels remained stable.

The identical Gli-Binding-Site (GBS) in the c-jun promoter was found in the promoter of c-fos. We investigated whether the Gli1 isoform that binds c-jun, also binds c-fos. Simultaneous Western and Southwestern blots show only one of the known Gli1 isoform binds the promoter of c-fos. Further studies with Chromatin Immunoprecipitation (ChIP) assays confirmed the 130 kDa isoform of Gli1 binds the GBS of the c-fos promoter. We conclude that the 130 kDa Gli1 isoform binds both components of AP1, c-jun and c-fos, and modulates the cellular resistance to cisplatin.

Citation Format: Lauren Amable, Kenji Kudo, Elaine Gavin, Jason Fain, Eddie Reed. A specific Isoform of Gli1 binds the promoter region of c-fos in A2780-CP70 human ovarian cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-223. doi:10.1158/1538-7445.AM2013-LB-223
Abstract LB-228: The identification of recurrent non-coding mutations in melanoma.
Authors: Huang Franklin W. , Hodis Eran , Xu Mary Jue , Kryukov Gregory , Chin Lynda , Garraway Levi A.
Published: August 2014

Cancer genome sequencing efforts have identified many recurrent coding mutations in human cancer genes. To date, non-coding “driver” mutations within regulatory regions have rarely been observed. Here we describe the identification of two somatic mutations within the TERT core promoter that were observed in 71% of melanomas. Each mutation generated a de novo consensus ETS binding motif. Reporter assays showed that these mutations could increase transcriptional activity from the TERT promoter. We observed the same mutations in cancer cell lines from diverse tumor types with preliminary evidence of elevated frequency in bladder and hepatocellular cancer cells. Our findings suggest that somatic mutations in non-coding regulatory regions of the genome may represent important events in carcinogenesis.

Citation Format: Franklin W. Huang, Eran Hodis, Mary Jue Xu, Gregory Kryukov, Lynda Chin, Levi A. Garraway. The identification of recurrent non-coding mutations in melanoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-228. doi:10.1158/1538-7445.AM2013-LB-228
Abstract LB-231: Decoding complex patterns of structural variations in hepatocellular carcinoma.
Authors: Fernandez-Banet Julio , Lee Nikki P. , Chan Kin Tak , Gao Huan , Liu Xiao , Sun Wing Kin , Tan Winnie , Fan Sheung Tat , Poon Ronnie T. , Li Shiyong , Ching Keith , Rejto Paul , Mao Mao , Kan Zhengyan
Published: August 2014

Elucidating the molecular basis of Hepatocellular Carcinoma (HCC) is crucial to developing targeted diagnostics and therapies for this deadly disease. Somatically acquired structural variations (SVs) can lead to oncogenic gene fusions and gene expression deregulation in tumors. Although recent studies have delineated HCC genomic alterations including copy number variations, somatic mutations and HBV integrations, the landscape of SVs remains poorly characterized in HCC. We have predicted 4,314 SVs including large-scale insertions, deletions, inversions and translocations based on the whole-genome sequencing data for 88 primary HCC tumor/non-tumor tissues. We identified chromothripsis in 5 HCC genomes (5.7%) recurrently affecting chromosomal arms 1q and 8q. TP53 and RB1 alterations appear to cause increased levels of genomic arrangement and chromosomal instability. Albumin (ALB) was found to be the most significantly affected by SVs and harbor genomic alterations including deactivating mutations and deletions in 10.2% of cohort. Integrative analysis revealed a causal link between genomic rearrangements and copy number variations, such as focal amplifications of the CCND1/FGF19 loci, and distinctive patterns of copy number variation flanking SV breakpoints. Furthermore, we predicted 260 gene fusions which frequently result in aberrant over-expression of the 3′ genes in tumors.

Citation Format: Julio Fernandez-Banet, Nikki P. Lee, Kin Tak Chan, Huan Gao, Xiao Liu, Wing Kin Sun, Winnie Tan, Sheung Tat Fan, Ronnie T. Poon, Shiyong Li, Keith Ching, Paul Rejto, Mao Mao, Zhengyan Kan. Decoding complex patterns of structural variations in hepatocellular carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-231. doi:10.1158/1538-7445.AM2013-LB-231
Abstract LB-233: Identification of DNA palindromes in the MCF-7 breast cancer cell line.
Authors: Yang Hui , Volfovsky Natalia , Rattray Alison , Chen Xiongfong , Tanaka Hisashi , Jeffrey Strathern
Published: August 2014

DNA palindromes are implicated as a causative agent in cancer formation due to their association with genomic instability and DNA amplification. However, the unique properties of palindromes render them refractory to current methods of analyses including PCR amplification and cloning into bacterial vectors. Consequently, sequencing protocols that are dependent on PCR amplification fail on DNA palindromes. New tools are required for their discovery and characterization. Here we report our analysis of DNA palindromes from MCF-7, a widely used cell line model for estrogen receptor positive breast cancer. We developed a new strategy to identify and clone palindrome junctions by high throughput sequence analysis of DNA isolated by the Genome-wide Analysis of Palindrome Formation technique. We identified 35 palindrome candidates from MCF-7 and have cloned and sequenced 4 of the centers of the palindromes. None of these identified palindromes are present in other published data sets, despite the fact that MCF-7 DNA has been extensively sequenced and breakpoints analyzed, confirming that conventional methods fail on DNA palindromes. Our results provide further support for a correlation between palindromes and gene amplification in cancer, and underscore the importance of developing new tools for identifying and characterizing palindromes.

Citation Format: Hui Yang, Natalia Volfovsky, Alison Rattray, Xiongfong Chen, Hisashi Tanaka, Strathern Jeffrey. Identification of DNA palindromes in the MCF-7 breast cancer cell line. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-233. doi:10.1158/1538-7445.AM2013-LB-233
Abstract LB-239: Mutational and clonal analyses across TCGA cancer types using the MuSiC suite of tools.
Authors: Kandoth Cyriac , McLellan Michael D. , Miller Christopher A. , Lu Charles , Dees Nathan , Ye Kai , Niu Beifang , Wendl Michael C. , Wilson Richard K. , Ding Li
Published: August 2014

Within the field of cancer genomics, advances in next-generation sequencing and variant detection methods have tremendously reduced the costs of generating genomic data for large cohorts of patients in translational cancer research. These large datasets have enabled statistical analyses of somatic events in tumor-normal pairs, with the ultimate goal of understanding the molecular mechanisms underlying various cancer phenotypes. Here, we present results from the suite of tools collectively called MuSiC (Mutational Significance in Cancer), specifically designed towards this goal. Somatic alterations of more than 5000 tumors across 20 cancer types are now publicly available as part of The Cancer Genome Atlas (TCGA). This includes point mutations and small indels from exome sequencing, copy-number variants from SNP arrays, and gene and allele-specific expression from mRNA sequencing. We present results from the suite that integrates these data types to identify significantly altered genes, gene families, protein domains, and pathways. Also presented are the distribution of mutation types, frequencies, and patterns across cancer types, or across histological subtypes of tumors. Further, we identify mutations that can distinguish broader expression and/or methylation subtypes and clinically relevant phenotypes across the combined pan-cancer data set. Finally, we perform clonality analysis across several cancer types by integrating copy number data to identify important mutations that drive the development of new clones.

Citation Format: Cyriac Kandoth, Michael D. McLellan, Christopher A. Miller, Charles Lu, Nathan Dees, Kai Ye, Beifang Niu, Michael C. Wendl, Richard K. Wilson, Li Ding. Mutational and clonal analyses across TCGA cancer types using the MuSiC suite of tools. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-239. doi:10.1158/1538-7445.AM2013-LB-239
Abstract LB-245: MicroRNA-100 targets silencing mediator for retinoid receptors (SMRT), reduces proliferation, and improves survival in glioblastoma.
Authors: Alrfaei Bahauddeen M. , Vemuganti Raghu , Kuo John S.
Published: August 2014

Improved therapeutic approaches are needed for the most common primary adult brain cancer, Glioblastoma (GBM) because of the current dismal median survival of less than two years. We identified and tested the differentially expressed microRNA-100 (MiR-100) as a candidate ‘tumor suppressor’ in GBM. Quantitative PCR validated differential microRNA array results showing high miR-100 expression in normal cells and low expression in multiple GBM lines. MiR-100 overexpression via transfection of 4 GBM lines with miR-100 precursor (U87, U251, patient-derived 22T and 33T) reduced proliferation on MTS assays (average 50% ± 15; p < 0.05). TUNEL assays showed that transient transfection of 15 pmole of miR-100 per 500K GBM tumor cells triggered apoptosis 70% more than scrambled control miR after 24 hrs (p < 0.01). SMRT was identified as a candidate miR100 target in multiple miRNA databases, and validated with miR100-specific inhibition in a luciferase-SMRT 3′UTR reporter assay. In addition, a single dose of pre-mir-100 (60 pmol) injected directly into intracranial GBM xenografts significantly extended survival 30% more than mice injected with control scrambled miRNA (p < 0.01; n=8). GBM lines that stably overexpressed miR-100 two-fold over similar control transfected GBM lines were created for in vivo studies: 10x6 cells were implanted for tumor xenograft histology and survival analysis. Significantly reduced Ki-67 proliferation index was observed compared to control (mir-100 vector: 18±14% Ki-67+; empty vector: 100±11% Ki-67+; p < 0.01). Two-fold over-expression of miR-100 in vivo showed an average of 70% reduction in Ki-67 proliferation index. Furthermore, miR-100 overexpressing cells were associated with significantly smaller xenografts than injection of sibling control GBM cells. These studies establish the ‘tumor suppressor’ activity of miR-100 in GBM, which may lead to further developments as novel GBM therapies.

Citation Format: Bahauddeen M. Alrfaei, Raghu Vemuganti, John S. Kuo. MicroRNA-100 targets silencing mediator for retinoid receptors (SMRT), reduces proliferation, and improves survival in glioblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-245. doi:10.1158/1538-7445.AM2013-LB-245
Abstract LB-258: The human Aurora-A kinase Phe31Ile polymorphism affects cancer susceptibility in a knock-in mouse model.
Authors: Song Ihn Young , Kumar Atul , Delrosario Reyno , Mao Jian-Hua , Balmain Allan
Published: August 2014

Aurora-A kinase is a serine/threonine kinase that is essential for faithful chromosome segregation during mitosis. A single nucleotide polymorphism T91A (amino acid Phe31→Ile) present in the coding region of human Aurora-A is associated with susceptibility to multiple cancer types, yet the precise biochemical mechanisms by which these different polymorphisms function are still not well characterized. To investigate the functional differences between the two alleles of Aurora-A, we have generated a knock-in mouse that carries the human-specific Aurora-A Phe31 allele. Normally, rodents only carry the Ile allele. Homozygous (F/F) and heterozygous (F/I) mice for this knock-in allele were born healthy and fertile with no obvious phenotype. Growth rates of MEFs isolated from F/F, F/I, and I/I embryos showed no significant differences. To investigate the oncogenic properties of each variant in tumor development in the context of different p53 status, we generated a series of Aurora-A knock-in/p53-deficient double mutant mice. All mice were exposed to a single dose of 4Gy whole-body γ-radiation at 5 weeks of age and observed daily until they were moribund, then sacrificed and autopsied. While the I/I genotype conferred increased risk (reduced latency) compared to the F/F genotype in the p53+/- mice (p=0.037), the reverse was observed in the p53-/- mice (p=0.009); 43% of the I/I mice versus 25% of the F/F mice developed lymphomas in the p53+/- background, while 55% of the I/I mice versus 76% of the F/F mice developed lymphomas in the p53-/- background. These results support our hypothesis that the two polymorphisms confer differential susceptibility to lymphoma development in a p53-dependent manner. Interestingly, Aurora-A+/- heterozygous null mice (F/- and I/- on the p53+/- background) showed increased incidence and decreased latency of tumor formation compared to the Aurora-A+/+ mice. These data suggest dual roles for Aurora-A as both an oncogene and a haploinsufficient tumor suppressor in lymphomagenesis. There exist complex regulatory mechanisms between Aurora-A and p53, emphasizing that a balanced level of Aurora-A is critical for cell survival and maintenance of genome integrity. These data highlight the critical role of interactions between common inherited genetic variants in determining tumor susceptibility, a phenomenon that may underlie the “Missing heritability” noted in GWAS in human populations.

Citation Format: Ihn Young Song, Atul Kumar, Reyno Delrosario, Jian-Hua Mao, Allan Balmain. The human Aurora-A kinase Phe31Ile polymorphism affects cancer susceptibility in a knock-in mouse model. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-258. doi:10.1158/1538-7445.AM2013-LB-258
Abstract LB-269: PPARγ maintains ERBB2-positive breast cancer stem cells.
Authors: Wang Xianhui , Sun Yan , Wong Jason , Conklin Douglas
Published: August 2014

Overexpression of the adverse prognostic marker ERBB2 occurs in 30% of breast cancers and is associated with aggressive disease and poor outcomes. Our recent findings have shown that NR1D1 and the peroxisome proliferator-activated receptor (PPAR) γ-binding protein (PBP) act through a common pathway in upregulating several genes in the de novo fatty acid synthesis network, which is highly active in ERBB2-positive breast cancer cells. NR1D1 and PBP are functionally related to PPARγ, a well-established positive regulator of adipogenesis and lipid storage. Here we report that inhibition of the PPARγ pathway reduces the ALDH positive population in ERBB2 positive breast cancer cells. Conversely, fatty acid synthase inhibitor C75 increases the fraction of ALDH-positive cells. In vitro tumorsphere formation assays demonstrate that the PPARg antagonist GW9662 decreases the tumorsphere formation in ERBB2-positive cells, but not other breast cells. We show that the mechanism by which GW9662 treatment causes a reduction in ALDH-positive population cells, is partially due to ROS, as it can be rescued by treatment with NAC. Furthermore, global gene expression analyses show that GW9662 treatment suppresses the expression of several lipogenic genes including ACLY, MIG12, FASN and NR1D1; and the stem cell related genes KLF4 and ALDH in BT474 cells. GW9662 also decreased the level of acetylation in histone 3 and histone 4 in BT474 cells, compared with MCF7 cells. In vivo, GW9662 pre-treatment inhibits the tumor-seeding ability of BT474 cells. Together, these results show that the PPARγ pathway is critical for the cancer stem cell properties of ERBB2 positive breast cancer cells.

Citation Format: Xianhui Wang, Yan Sun, Jason Wong, Douglas Conklin. PPARγ maintains ERBB2-positive breast cancer stem cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-269. doi:10.1158/1538-7445.AM2013-LB-269
Abstract LB-270: Targeting USP1 decreases glioblastoma stem cell survival and tumor growth.
Authors: Oh Young Taek M. , Kim Eunhee , Lee Jeongwu , Nam Do-Hyun
Published: August 2014

Glioblastoma multiforme (GBM) is the most common and lethal primary brain tumor. GBM cells are highly resistant to standard-of-care therapies including radiation and chemotherapy, indicating an urgent need for the development of novel therapeutics. Recent evidence suggests that deubiquitinating enzymes are overexpressed or activated in various cancers, and they contribute to tumor progression and recurrence. Here, we report that the deubiquitinating enzyme ubiquitin-specific peptidase 1 (USP1) is highly expressed in GBMs and the targeting USP1 decreases cell survival and tumor growth. Targeting USP1 by RNA interference or treatment with a chemical USP1 inhibitor attenuated self-renewal and survival of GSCs. As one of the molecular mechanism that link USP1 to pro-tumorigenic roles, we found that the USP1 stabilized the inhibitor of DNA binding protein1 (ID1) and checkpoint kinase 1 (CHEK1), both of which are positive GSC regulators and implicated in radioresistance. Inhibition of USP1 in GBM cells leads to hypersensitivity to ionizing radiation through the decrease in DNA damage repair capacity. Finally, USP1 inhibition in orthotopic GBM xenografts significantly reduced tumor growth and prolonged the survival of tumor bearing mice. Together, our findings suggest that USP1 is a promising therapeutic target for GBMs and provide a rationale for positioning USP1 inhibitor as a GBM radiosensitizer.

Citation Format: Young Taek M. Oh, Eunhee Kim, Jeongwu Lee, Do-Hyun Nam. Targeting USP1 decreases glioblastoma stem cell survival and tumor growth. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-270. doi:10.1158/1538-7445.AM2013-LB-270
Abstract LB-283: Prognostic significance of BRMS1 promoter methylation in operable breast cancer.
Authors: Chimonidou Maria , Kallergi Galatea , Georgoulias Vasilis , Welch Danny , Lianidou Evi
Published: August 2014

Introduction: Breast Cancer Metastasis Suppressor-1 (BRMS1) encodes a predominantly nuclear protein that differentially regulates expression of multiple genes, leading to suppression of metastasis without affecting orthotopic tumor growth. We examined the clinical relevance of BRMS1 promoter methylation in early breast cancer.

Methods: We analyzed 118 formalin-fixed paraffin embedded samples: 5 pairs of breast tumors and adjacent non-cancerous tissues, 14 non-cancerous tissues, 10 benign fibroadenomas, and 84 primary breast tumors. Peripheral blood mononuclear cells were isolated from 39/84 of these patients and were fixed in cytospins. BRMS1 methylation status was investigated in all FFPE and cytospin stained circulating tumor cells using methylation specific PCR. BRMS1 expression was examined using double-immunofluorescence in isolated PBMC cytospins using anti-BRMS1 and pancytokeratin A45-B/B3 antibodies.

Results: BRMS1 promoter methylation was observed in 0/19 noncancerous breast tissues, 0/10 benign fibroadenomas and 31/84(37.8%) breast tumors. During the follow-up period 27/84(32.1%) patients relapsed of which 19/84(22.6%) patients died as a consequence of disease progression. BRMS1 methylation was detected in 15/27(55.6%) patients that relapsed and in 10/19(52.6%) of patients that died. BRMS1 promoter methylation was associated with reduced disease-free interval (P=0.009) while a trend towards a reduced overall survival (OS) was also observed (P=0.071). Expression of BRMS1 on CTC was very heterogeneous: CTC with high BRMS1 expression were found in 7/13(53.8%) CTC positive samples while exclusively CTC with high BRMS1 were found in only 3 patients (23.0%). CTC with low BRMS1 expression were found in 3 patients. CTC negative for BRMS1 were found in 8/13(61.5%) patients. Exclusively CTC with low or negative BRMS1-expression were identified in 6/13(46.1%) patients. 4/13(30.8%) patients had both high and low or negative BRMS1 expression in their CTC.

Conclusions: BRMS1 promoter methylation provides important prognostic information for disease free survival in early breast cancer patients. BRMS1 promoter methylation and protein expression were evaluated in primary tumors and corresponding CTC for the first time. BRMS1 expression in CTC was heterogeneous in individual patient samples. CTC expressing epithelial markers but no BRMS1 seem to define a worse prognosis group of patients. These results need to be further evaluated and validated in a larger cohort of breast cancer patients.

Citation Format: Maria Chimonidou, Galatea Kallergi, Vasilis Georgoulias, Danny Welch, Evi Lianidou. Prognostic significance of BRMS1 promoter methylation in operable breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-283. doi:10.1158/1538-7445.AM2013-LB-283
Abstract LB-304: ATSP-9172, a novel Stapled Peptide inhibitor of HIF-dependent transcriptional activity with in vivo antitumor efficacy in a preclinical model of prostate cancer.
Authors: Sun Kaiming , DeMarco Steven J. , Guerlavais Vincent , Mukherjee Aditi , Irwin Sean , Shi Eric , Cai Hongliang , Darlak Krzysztof , Santiago Solimar , Pero Jessica , Olson Karen A. , Nash Huw M. , Chang Yong
Published: August 2014

Hypoxia-inducible transcription factors (HIF) are key regulators of cellular adaptation to hypoxia in solid tumors, and HIF-1α controls the expression of genes involved in anaerobic metabolism, angiogenesis, cell growth and survival. Hydrocarbon cross-linked alpha helical peptides (Stapled Peptides) are a breakthrough approach to create new class of drugs that modulate intracellular protein-protein interactions. Here, we have mimicked the structure and function of the CITED2 protein, an endogenous negative regulator of the interaction between HIF-1α and p300 proteins, by designing a Stapled Peptide derived from CITED2 to generate the first example of a potent and selective Stapled Peptide inhibitor of HIF-1α-dependent transcription. ATSP-9172 bound to the CH1 domain of p300 and disrupted the HIF-1α C-TAD/CH1 interaction in biochemical assays and inhibited HIF-dependent reporter gene activity in ME-180 cells. Examination of endogenous transcript levels in ME-180 cells revealed that ATSP-9172 down-regulated the transcription of HIF-1α target genes, such as adolase C, angiopoietin-like 4, and carbonic anhydrase 9 in a dose-dependent manner, but did not affect the expression of non-HIF target genes, verifying a specific and on-target mechanism of action. ATSP-9172 exhibited a dramatic improvement in solubility and plasma stability profile relative to the linear peptide, and demonstrated favorable pharmacokinetic properties in mice by providing high systemic exposure, low plasma clearance and long elimination half-life. Finally, intravenous administration of ATSP-9172 on an every other day schedule significantly inhibited tumor growth in a PC-3 human prostate tumor xenograft model (p < 0.05); this inhibition was found to be dose-dependent. Our results demonstrate that a Stapled Peptide mimicking the HIF inhibitory function of the native CITED2 protein provides a novel and specific strategy to suppress HIF-1α-dependent gene expression for cancer therapy.

Citation Format: Kaiming Sun, Steven J. DeMarco, Vincent Guerlavais, Aditi Mukherjee, Sean Irwin, Eric Shi, Hongliang Cai, Krzysztof Darlak, Solimar Santiago, Jessica Pero, Karen A. Olson, Huw M. Nash, Yong Chang. ATSP-9172, a novel Stapled Peptide inhibitor of HIF-dependent transcriptional activity with in vivo antitumor efficacy in a preclinical model of prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-304. doi:10.1158/1538-7445.AM2013-LB-304
Abstract LB-311: Development of mutant-specific small molecule inhibitors of K-Ras.
Authors: Ostrem Jonathan M. , Peters Ulf , Ren Pingda , Liu Yi , Wells James A. , Shokat Kevan M.
Published: August 2014

Activating mutations in K-Ras are among the most common lesions found in human cancer, and such mutations are generally associated with poor prognosis. Despite numerous efforts in academia and industry, small molecule inhibitors that directly target K-Ras remain elusive. Even more highly desired are molecules that selectively target mutant K-Ras while sparing the wild type protein. We have used a fragment-based screen to discover oncogenic mutant-specific inhibitors of K-Ras. Crystallographic studies with multiple inhibitors in complex with K-Ras reveal that the compounds bind in a novel hydrophobic pocket that is not apparent in any published crystal structure of Ras. These inhibitors disrupt the conformations of Switch I and Switch II, domains that are essential for the association and activation of downstream signaling partners. Our medicinal chemistry effort has greatly improved potency, showing that this pocket is particularly amenable to chemical optimization. In vitro biochemical characterization of these inhibitors confirms that they block Ras function. Our discovery of a new druggable pocket in K-Ras, and a set of inhibitors that bind to it in a mutant-specific fashion, provides a promising new avenue for the direct pharmacological inhibition of oncogenic Ras.

Citation Format: Jonathan M. Ostrem, Ulf Peters, Pingda Ren, Yi Liu, James A. Wells, Kevan M. Shokat. Development of mutant-specific small molecule inhibitors of K-Ras. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-311. doi:10.1158/1538-7445.AM2013-LB-311