bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A09: The long noncoding RNA SPRIGHTLY regulates cell proliferation in primary human melanocytes
Authors: Zhao Wei , Mazar Joseph , Lee Bongyong , Sawada Junko , Li Jian-Liang , Shelley John , Govindarajan Subramaniam , Towler Dwight , Mattick John S. , Komatsu Masanobu , Dinger Marcel E. , Perera Ranjan J.
Published: May 2016

The long non-coding RNA (lncRNA) SPRIGHTLY (formerly SPRY4-IT1), which lies within the intronic region of the SPRY4 gene is upregulated in human melanoma cells compared to melanocytes. SPRIGHTLY regulates a number of cancer hallmarks including proliferation, motility, and apoptosis. To better understand its oncogenic role, SPRIGHTLY was stably transfected into human melanocytes, which resulted in increased cellular proliferation, invasion, and development of a multinucleated dendritic-like phenotype. RNA sequencing and mass spectrometric analysis of SPRIGHTLY-expressing cells revealed changes in the expression of genes involved in cell proliferation, apoptosis, chromosome organization, regulation of DNA damage responses, and cell cycle. The proliferation marker Ki67, minichromosome maintenance genes (MCM2-5), and the anti-apoptotic genes X-linked inhibitor of apoptosis (XIAP) and baculoviral IAP repeat-containing 7 (livin) were upregulated in SPRIGHTLY-expressing melanocytes, while the pro-apoptotic tumor suppressor gene DPPIV/CD26 was downregulated. Since downregulation of DPPIV is known to be associated with malignant transformation in melanocytes, SPRIGHTLY-mediated DPPIV downregulation may play an important role in melanoma pathobiology. These findings provide novel insights into how SPRIGHTLY regulates proliferation, and apoptosis in primary human melanocytes.

Citation Format: Wei Zhao, Joseph Mazar, Bongyong Lee, Junko Sawada, Jian-Liang Li, John Shelley, Subramaniam Govindarajan, Dwight Towler, John S. Mattick, Masanobu Komatsu, Marcel E. Dinger, Ranjan J. Perera. The long noncoding RNA SPRIGHTLY regulates cell proliferation in primary human melanocytes. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A09.
Abstract B12: Rapamycin-induced miR-21 promotes the survival of mTORC1 hyperactivated cells in tuberous sclerosis complex models
Authors: Lam Hilaire C. , Filippakis Harilaos , Cottrill Katherine A. , Lope Alicia Llorente , Khabibullin Damir , Priolo Carmen , Ogorek Barbara , Chan Stephen Y. , Pereira Ana , Henske Elizabeth P.
Published: May 2016

Background: Tuberous sclerosis complex (TSC) is a multisystem, hamartomatous disease associated with tumors of the brain, skin and kidney, as well as progressive cystic lung destruction characteristic of lymphangioleiomyomatosis (LAM). TSC is caused by mutations in TSC1 or TSC2, resulting in hyperactive mechanistic Target of Rapamycin (mTOR) 1 signaling. Rapamycin and related rapalogs inhibit mTORC1 activity and stabilize tumors in TSC patients, but tumor progression proceeds at pretreatment rates following cessation of therapy. MicroRNA repress target gene expression and are commonly dysregulated in cancers. In previously published work, we identified a group of rapamycin responsive miRNA, rapa-miRs. Surprisingly the most upregulated rapa-miRs, miR-21 in particular, are known pro-survival oncogenic miRNA (oncomiRs). We hypothesize that inhibiting miR-21 and downstream targets may lead to more complete and durable responses to mTORC1 inhibitors.

Methods: We utilized qRT-PCR to determine the kinetics of miR-21 induction with rapamycin in various cell types and in mouse xenografts. Mimics and inhibitors were used to determine the functional consequences of miR-21 in TSC2-null cells. Expression profiling was used to identify miRNA target genes. Bioinformatics and network analysis approaches were implemented to identify biological relationships between the miR-21 targets.

Results: Our initial screens identified miR-29b, -21, -24, -221, -106a and -199a as candidate rapa-miRs. Rapamycin induced miR-21 greater than 1.5 fold in diverse cell lines and in mouse xenografts. We have identified pro-cell death targets, PPIF, TP53BP2 and PDCD4, which are negatively regulated by miR-21 upon rapamycin treatment. Network analysis using the Consolidated Interactome (CI) revealed that rapa-miRs inhibit multiple key pro-apoptotic targets. These data suggest that rapa-miRs regulate proteins critical for cell fate determination and survival in response to rapamycin treatment.

Conclusions: Rapamycin induces pro-survival oncomiR, miR-21, which may be a valuable target for therapeutic intervention in TSC.

Citation Format: Hilaire C. Lam, Harilaos Filippakis, Katherine A. Cottrill, Alicia Llorente Lope, Damir Khabibullin, Carmen Priolo, Barbara Ogorek, Stephen Y. Chan, Ana Pereira, Elizabeth P. Henske. Rapamycin-induced miR-21 promotes the survival of mTORC1 hyperactivated cells in tuberous sclerosis complex models. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B12.
Abstract B24: Identification of immunosuppressive networks in colon cancer
Authors: Sarver Anne E. , Sarver Aaron L. , Subramanian Subbaya
Published: May 2016

Despite important improvements over the past two decades in preventive screening and targeted therapies, colorectal cancer remains the third major cause of cancer-related deaths in the U.S. The majority (~85%) of colon cancer tumors are non-immunogenic, i.e. they lack a significant number of infiltrating cytotoxic T cells, and are typically unresponsive to the new immune-checkpoint inhibitor based therapies that have dramatically changed the way we treat many cancer patients. These non-immunogenic colon cancer tumors are also characterized by chromosome instability and are microsatellite stable (MSS). Microsatellite instable (MSI) tumors present a greater variety of antigens and are significantly more immunogenic. We analyzed the paired mRNA and microRNA RNA-Seq expression profiles contained in The Cancer Genome Atlas (TCGA), representing MSS colon cancer, MSI colon cancer, and normal colon tissues. These expression profiles reflect the heterogeneity of the tumor samples, with MSI samples showing distinct immune cell signatures. Integrative analysis of mRNA and microRNA expression patterns revealed signaling networks that may represent, in part, the molecular mechanisms by which cancer cells modulate the host response to create an immune privileged microenvironment. These findings could result in a novel therapeutic avenue, targeting a tumor's ability to suppress the immune response, addressing a critical barrier to treatment for non-immunogenic tumors.

Citation Format: Anne E. Sarver, Aaron L. Sarver, Subbaya Subramanian. Identification of immunosuppressive networks in colon cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B24.
Abstract B30: High-throughput, purification-free, multiplexed profiling of circulating miRNA for discovery, validation, and diagnostics
Authors: Stoner Isaac , Tackett Michael , Rafferty Conor , Windemuth Andreas , Atabakhsh Elnaz , Tytell Jessica , Pregibon Daniel
Published: May 2016

To address the needs for circulating miRNA biomarker validation, we developed the Multiplexed Circulating microRNA assay. This assay enables the detection of up to 68 microRNA targets per sample in 96-well format with readout on standard flow cytometers and analysis with an included bioinformatics software package. The Circulating microRNA assay combines particle¬-based multiplexing, using patented Firefly hydrogel particles, with single¬ step RT-PCR signal amplification using universal primers. Thus, the Circulating microRNA assay leverages PCR sensitivity while eliminating the need for separate reverse transcription reactions and mitigating amplification biases introduced by target¬-specific qPCR. Furthermore, the ability to multiplex targets in each well eliminates the need to split valuable samples into multiple reactions. Results from the Circulating microRNA assay are displayed and interpreted using our included Firefly Analysis Workbench, which allows visualization, normalization, and export of experimental data with only a few mouse clicks. To aid discovery and validation of biomarkers, we have generated fixed panels for Oncology, Cardiology, Neurology, Immunology, and Liver Toxicology. These carefully curated panels include hemolysis markers to assess sample quality, as well as critical normalization factors. Here we present the data from several studies investigating circulating and tumor microRNA profiles using the Firefly Circulating microRNA Assay Fixed Panels.

Together, this novel combination of bioinformatics tools and multiplexed, high¬-sensitivity assays enables rapid discovery and validation of microRNA biomarker signatures from fluid specimens.

Citation Format: Isaac Stoner, Michael Tackett, Conor Rafferty, Andreas Windemuth, Elnaz Atabakhsh, Jessica Tytell, Daniel Pregibon. High-throughput, purification-free, multiplexed profiling of circulating miRNA for discovery, validation, and diagnostics. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B30.
Abstract IA08: Functional long noncoding RNAs in lung cancer
Authors: Diederichs Sven
Published: May 2016

The majority of the human genome is transcribed into non-protein-coding RNA. Hence, RNA is also the primary product of the cancer genome. We have defined the ncRNA expression landscape of lung, breast and liver cancer providing a comprehensive expression map of over 17000 long ncRNAs and discovering new lncRNAs associated with cancer whose molecular and cellular functions we are currently elucidating exploiting our custom siRNA library targeting 638 tumor-associated lncRNAs.

The nuclear lncRNA MALAT1 was one of the first lncRNAs associated with cancer: it is associated with metastasis development in lung cancer. However, its high abundance and nuclear localization have hampered its functional analysis. To uncover its functional importance, we developed a MALAT1 knockout model in human lung tumor cells by genomically integrating RNA destabilizing elements site-specifically into the MALAT1 locus. This approach yielded a 1000-fold silencing of MALAT1 providing a unique loss-of-function model.

Proposed mechanisms of MALAT1 action include regulation of splicing or gene expression. In lung cancer, MALAT1 does not alter alternative splicing but regulates gene expression inducing a signature of metastasis-associated genes. Consequently, MALAT1-deficient cells are impaired in migration and form fewer tumor nodules in a mouse xenograft model. Encouraged by this discovery of the essential function of MALAT1 in lung cancer metastasis, we analyzed whether MALAT1 could serve as therapeutic target for an Antisense oligonucleotide (ASO). Notably, MALAT1-ASO treatment prevented metastasis formation after tumor implantation. Thus, targeting MALAT1 with ASOs provided a therapeutic approach to prevent lung cancer metastasis with MALAT1 serving as both, predictive marker and therapeutic target.

In summary, ten years after the discovery of the lncRNA MALAT1 as a biomarker for lung cancer metastasis, our loss-of-function model unraveled the active function of MALAT1 as a regulator of gene expression governing hallmarks of lung cancer metastasis.

Citation Format: Sven Diederichs. Functional long noncoding RNAs in lung cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr IA08.
Abstract IA12: Mechanisms of tumorigenesis due to somatic mutations in DICER1 and DROSHA in childhood kidney cancers
Authors: Chen Kenneth S. , Rakheja Dinesh , Liu Yangjian , Shukla Abhay A. , Mendell Joshua T. , Amatruda James F.
Published: May 2016

Wilms tumor is the most common pediatric kidney cancer and the fourth most common childhood cancer overall. Wilms tumor is treated with a combination of surgery, chemotherapy, and radiation, and, while most children are cured, patients suffer adverse late effects of therapy and survival remains poor in those with advanced-stage disease. Known driver mutations (in WT1, WTX, and β-catenin) account for only one-third of Wilms tumor cases. To better define the genomic landscape of Wilms tumor, we performed whole-exome sequencing of 44 Wilms tumors to identify somatic mutations. Through this approach, we identified recurrent somatic mutations in MYCN, DROSHA, and DICER1, which were mutually exclusive with known Wilms tumor driver mutations in WT1 and β-catenin. DROSHA and DICER1 somatic hotspot mutations occur at or near critical metal-binding residues in RNase III domains and partially or completely disrupt enzyme activity. Examination of miRNA expression in tumors, in vitro processing assays, and genomic editing in human cells demonstrate that DICER1 and DROSHA mutations influence miRNA processing through distinct mechanisms. While DICER1 RNase IIIB mutations preferentially impair processing of miRNAs that derive from the 5′ arm of pre-miRNA hairpins, DROSHA RNase IIIB mutations globally inhibit miRNA biogenesis through a dominant-negative mechanism. Despite their distinct mechanisms of action, DROSHA and DICER1 mutations result in decreased expression of several common tumor-suppressing miRNAs, including multiple members of the let-7 and miR-15/16 families. We also identified a patient carrying a germline DICER1 loss-of-function allele who subsequently developed multiple malignancies with distinct DICER1 RNase IIIB somatic hotspot mutations, suggesting that DICER1 can act as both a tumor-suppressor and an oncogene depending on the nature of the mutation. These results provide new insights into the mechanisms through which mutations in miRNA biogenesis components reprogram miRNA expression in human cancer and suggest that mutations causing impairment of miRNA processing define a distinct subclass of Wilms tumors.

Citation Format: Kenneth S. Chen, Dinesh Rakheja, Yangjian Liu, Abhay A. Shukla, Joshua T. Mendell, James F. Amatruda. Mechanisms of tumorigenesis due to somatic mutations in DICER1 and DROSHA in childhood kidney cancers. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr IA12.
Abstract IA26: Selective activation of gene expression by targeting long noncoding RNA
Authors: Barsoum Jim
Published: May 2016

Long noncoding RNA (lncRNA) can regulate transcription by recruiting epigenetic regulatory complexes to target genes. Polycomb repressive complex 2 (PRC2), an epigenetic transcriptional repressor, is recruited to its target genes via lncRNA. PRC2 represses transcription through the action of the histone methyltransferase EZH2, which methylates histone H3 at lysine 27 (applying the H3K27me3 repressive mark). Using RIP-Seq, we identified the genome-wide pool of RNA sequences that interact with PRC2. We design short single-strand oligonucleotides that hybridize to an individual lncRNA, and sterically block its binding to PRC2, without degrading the lncRNA. These oligonucleotides selectively block PRC2 binding to a specific lncRNA, thereby de-repressing the expression of an associated target mRNA, resulting in increased amounts of the therapeutic protein. This approach was used to increase SMN2 transcription as a potential treatment for Spinal Muscular Atrophy (SMA). Oligonucleotides that target an antisense lncRNA selectively increase SMN2 mRNA and protein levels in SMA patient cells in vitro and in a mouse SMA model that carries the human SMN2 locus. Data support a mechanism of action whereby the oligonucleotides block recruitment of PRC2 to SMN2 chromatin, decrease the H3K27me3 repressive chromatin mark, increase the presence of activating chromatin marks and increase RNA polymerase II association along the SMN2 gene. This therapeutic approach potentially can be used to elevate the expression of many genes whose gene products are limiting in various human diseases.

Citation Format: Jim Barsoum. Selective activation of gene expression by targeting long noncoding RNA. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr IA26.
Abstract A29: Balanced translocations disrupting SMARCB1 are hallmark recurrent genetic alterations in renal medullary carcinomas
Authors: Calderaro Julien , Masliah-Planchon Julien , Richer Wilfrid , Planque Laetitia , Maille Pascale , Taille Alexandre de la , Boussion Helene , Delattre Olivier , Allory Yves , Bourdeaut Franck
Published: May 2016

Renal medullary carcinoma (RMC) is a rare and highly aggressive neoplasm that most often occurs in young patients or children with sickle cell trait or disease (SCD). Although BAF47 staining is constantly negative in these tumors, the genetic mechanism underlying this phenotype remains unknown, since all cases reported so far show SMARCB1 hemizygous deletion only. By investigating a series of five RMC by gene expression profiling, array-CGH, and RNA and whole-exome sequencing, we demonstrated that SMARCB1 inactivation is related to an original mechanism of inter-chromosomal balanced translocations that disrupt SMARCB1 sequence and thus contribute to its inactivation. RMC were also characterised by a simple genome, with a low mutation rate and a lack of recurrent molecular alterations other than SMARCB1 deficiency, emphasizing its potency as single genetic event to drive oncogenesis. Finally, gene expression profiling revealed that RMC share common oncogenic pathways with pediatric malignant rhabdoid tumors, another lethal tumor subtype characterised by SMARCB1 deficiency

Citation Format: Julien Calderaro, Julien Masliah-Planchon, Wilfrid Richer, Laetitia Planque, Pascale Maille, Alexandre de la Taille, Helene Boussion, Olivier Delattre, Yves Allory, Franck Bourdeaut. Balanced translocations disrupting SMARCB1 are hallmark recurrent genetic alterations in renal medullary carcinomas. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A29.
Abstract A42: Precision medicine for pediatric, adolescent, and young adult patients with newly diagnosed or refractory/recurrent cancer: Lessons learned from N=1 studies on rare tumors
Authors: McEachron Troy A. , Zabokrtsky Keri B. , Sassoon Aaron , Manoljvic Zarko , Craig David W. , Carpten John D. , Sender Leonard S.
Published: May 2016

Next-generation sequencing has rapidly emerged as the preferred method for unbiased genomic interrogation and is increasingly being integrated into clinical practice. Utilizing this technology, we have developed a precision medicine clinical research protocol focused on pediatric, adolescent, and young adult (AYA) patients with cancer. Our objectives are two-fold: 1) To arrive at genome informed treatment recommendations for individual patients suffering from aggressive and/or worsening disease in a clinically relevant time-frame; 2) To survey the genomic landscape of patients with newly diagnosed and/or recurrent/refractory disease. To accomplish this, we have employed an interdisciplinary workflow including a customized bioinformatic analysis pipeline, contextual biological interpretation of the data, and case reviews during regularly scheduled molecular tumor board meetings. To date we have sequenced over 50 patients. Here, we present the data from those patients diagnosed with rare malignancies. Factors affecting the successful identification of actionable targets and subsequent intervention are varied. Furthermore, we highlight the realistic opportunities, challenges, and insight gained from an ongoing single institution experience.

Citation Format: Troy A. McEachron, Keri B. Zabokrtsky, Aaron Sassoon, Zarko Manoljvic, David W. Craig, John D. Carpten, Leonard S. Sender. Precision medicine for pediatric, adolescent, and young adult patients with newly diagnosed or refractory/recurrent cancer: Lessons learned from N=1 studies on rare tumors. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A42.
Abstract B19: Inactivation of KLF4 in T cell acute lymphoblastic leukemia promotes the expansion of leukemia cells by activating the Map2k7/Jnk pathway.
Authors: Shen Ye , Suppipat Koramit , Park Chun Shik , Mistretta Toni-Ann , Horton Terzah , Rabin Karen , Lacorazza Daniel
Published: May 2016

Acute lymphoblastic leukemia is the most common hematological malignancy in pediatric patients, and disease relapse is the leading cause of cancer-associated death in children. Despite steadily improved outcomes in patients with newly diagnosed disease, little progress has been made to treat relapse leukemia and to reduce the incidence of relapse by increasing the cure rates of frontline therapy. Targeted therapy is currently not available for T-ALL and the development of novel agents requires a better understanding of how leukemia-initiating cells (LIC) are maintained. In contrast to normal blood cells, we found that the transcription factor KLF4 is significantly downregulated in pediatric T-ALL. Next-generation bisulfite sequencing revealed that the KLF4 promoter is hypermethylated in lymphoblasts from T-ALL patients but not in normal bone marrow cells, T cells, and pediatric B-ALL. Deletion of the Klf4-floxed gene with Vav-iCre transgene and transplantation of Klf4Δ/Δ bone marrow cells transduced with the Notch1-L1601P-ΔP mutant resulted in a significant acceleration of T-ALL due to a 9-fold expansion of LIC and increased G1-S transition in leukemic T cells. A combined analysis of global gene expression and genome-wide binding revealed that KLF4 directly represses the dual specificity mitogen-activated protein kinase 7 (Map2k7) and thus Klf4Δ/Δ T-ALL mice exhibit increased Map2k7 expression. Most remarkably, T-ALL cells from both mouse model and pediatric patients showed elevated levels of total and phosphorylated Map2k7 and subsequent activation of downstream targets JNK, c-Jun, and ATF2. Finally, we tested several JNK inhibitors in T-ALL cell lines, primary patient samples, and pre-clinical xenograft models of T-ALL and confirmed that JNK inhibition blocks ATF2 activation and controls expansion of leukemia cells, validating the Map2k7/Jnk pathway as a selective target for T-ALL therapy. Thus, KLF4 emerges as a novel tumor suppressor in T-ALL and Jnk inhibition as a novel therapeutic approach for adjunctive therapy in T-ALL patients with refractory or relapse disease.

Citation Format: Ye Shen, Koramit Suppipat, Chun Shik Park, Toni-Ann Mistretta, Terzah Horton, Karen Rabin, Daniel Lacorazza. Inactivation of KLF4 in T cell acute lymphoblastic leukemia promotes the expansion of leukemia cells by activating the Map2k7/Jnk pathway.. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B19.
Abstract B23: Selective and rapid killing of mixed lineage leukemia and CALM-AF10 leukemia by SM7, a novel small molecule identified by chemical library screening
Authors: Chudakova Daria , Somers Klaartje , Middlemiss Shiloh , Wen Victoria , Kwek Alan , Liu Bing , Clifton Molly , Pan Sukey , Cruikshank Sarah , Scandlyn Marissa , Failes Tim , Hoang Wendy , Kees Ursula , Chernova Olga , Gudkov Andrei V. , Haber Michelle , Norris Murray , Henderson Michelle
Published: May 2016

Translocations involving the Mixed Lineage Leukemia (MLL) gene define the major proportion of infant leukemia, a disease that is characterised by a dismal prognosis due to treatment toxicity and therapy resistance. There is an urgent need for the development of less toxic, more selective and targeted therapies for this disease. In this study, we performed a cell-based chemical library screen on an infant MLL cell line, PER-485, in order to identify selective inhibitors of MLL leukemia. After screening initial hits for viability against a panel of 25 cell lines including MLL rearranged and wild-type MLL leukemia, solid tumors and control cells, SM7 was identified as a compound that significantly and selectively decreased the viability of MLL-rearranged (four out of seven) and related CALM-AF10 (two out of two) leukemia cell lines, without killing cell lines derived from wild-type MLL leukemia, solid tumours or normal cells. In contrast to currently developed MLL-inhibitors, the effect of SM7 in suppressing the characteristic MLL-driven gene expression signature in MLL-rearranged cells, with downregulation of leukemogenic HoxA9 and Meis1 expression, occurred within an hour after treatment. The transcript levels of cMyc and Bcl2, important survival proteins regulated by HoxA9, were also rapidly decreased in response to SM7. SM7 induced a rapid caspase-dependent apoptosis, with mitochondrial depolarization within twenty four hours of treatment. This is distinct from the action of other previously described MLL small molecule inhibitors. The rapid and selective toxicity of SM7 towards MLL-rearranged and CALM-AF10 leukemia cell lines suggests an important new avenue in the development of targeted therapies for this disease.

Citation Format: Daria Chudakova, Klaartje Somers, Shiloh Middlemiss, Victoria Wen, Alan Kwek, Bing Liu, Molly Clifton, Sukey Pan, Sarah Cruikshank, Marissa Scandlyn, Tim Failes, Wendy Hoang, Ursula Kees, Olga Chernova, Andrei V. Gudkov, Michelle Haber, Murray Norris, Michelle Henderson. Selective and rapid killing of mixed lineage leukemia and CALM-AF10 leukemia by SM7, a novel small molecule identified by chemical library screening. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B23.
Abstract B31: Combined siRNA and small molecule screening identifies Aurora B kinase as an effective target in MYCN-driven neuroblastoma
Authors: Bogen Dominik , Wei Jun S. , Azorsa David O. , Ormanoglu Pinar , Buehler Eugen , Guha Rajarshi , Keller Jonathan M. , Griner Lesley A. Mathews , Ferrer Marc , Song Young K. , Liao Hongling , Mendoza Arnulfo , Gryder Berkley E. , Sindri Sivasish , He Jianbin , Wen Xinyu , Wen Xinyu , Zhang Shile , Shern John F. , Yohe Marielle E. , Taschner-Mandl Sabine , Shohet Jason , Thomas Craig J. , Martin Scott E. , Ambros Peter F. , Khan Javed
Published: May 2016

Despite advances in multimodal treatment, neuroblastoma (NB) is often fatal for children with high-risk disease and many survivors need to cope with long-term side effects from high-dose chemotherapy and radiation. To identify new therapeutic targets, we performed a siRNA screen of the druggable genome combined with a small molecule screen of 465 compounds targeting 39 different mechanisms of actions in four NB cell lines. We identified 58 genes as targets, including AURKB, in at least one cell line. In the drug screen, aurora kinase inhibitors (nine molecules) and in particular the AURKB-selective compound, barasertib, were the most discriminatory with regard to sensitivity for MYCN-amplified cell lines. In an expanded panel of NB cell lines, those with MYCN amplification and wild-type TP53 were the most sensitive to low nanomolar concentrations of barasertib. Inhibition of the AURKB kinase activity resulted in decreased phosphorylation of its known target histone H3, and upregulation of p53 pathway in MYCN-amplified NB cells with wild-type TP53. Both wild-type and p53-mutant MYCN-amplified cell lines arrested in G2/M phase upon AURKB inhibition. Additionally, barasertib induced endoreduplication and apoptosis. Treatment of MYCN-amplified/TP53 wild-type neuroblastoma xenografts resulted in profound growth inhibition and tumor regression. Therefore, aurora B kinase inhibition is highly effective in aggressive neuroblastoma and warrants further investigation in clinical trials.

Citation Format: Dominik Bogen, Jun S. Wei, David O. Azorsa, Pinar Ormanoglu, Eugen Buehler, Rajarshi Guha, Jonathan M. Keller, Lesley A. Mathews Griner, Marc Ferrer, Young K. Song, Hongling Liao, Arnulfo Mendoza, Berkley E. Gryder, Sivasish Sindri, Jianbin He, Xinyu Wen, Xinyu Wen, Shile Zhang, John F. Shern, Marielle E. Yohe, Sabine Taschner-Mandl, Jason Shohet, Craig J. Thomas, Scott E. Martin, Peter F. Ambros, Javed Khan. Combined siRNA and small molecule screening identifies Aurora B kinase as an effective target in MYCN-driven neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B31.
Abstract B40: Autocrine and paracrine IL-6 and IL-8 drive osteosarcoma lung tropism and facilitate metastasis
Authors: Roberts Ryan D. , Gross Amy C. , Bid Hemant K. , Phelps Doris , Wedekind Mary F. , Houghton Peter J.
Published: May 2016

Osteosarcoma originates in bone, but metastasizes predictably to the lungs. Patients who develop lung metastases become much more difficult to treat. Metastatic lung disease responds poorly to traditional chemotherapy. We know very little of the mechanisms that mediate this lung tropism, or predilection for spread to lung tissue. A better understanding of this process could facilitate disruption of pathways which drive the metastatic process, potentially preventing or even treating lung metastasis. We thus sought to identify tumor-lung interactions that facilitate extravasation, survival, and growth of tumor cells specifically within the lung environment.

Drawing on published signatures of osteosarcoma metastasis, we curated a list of 59 candidate genes that might facilitate lung metastasis. By comparing expression in metastatic lung lesions relative to paired primary tumors, we found that metastatic tumors reliably express two cytokines, IL-6 and IL-8, at much higher levels than matched primary bone tumors. In a mouse model of osteosarcoma, we found that tumors expressing high levels of autocrine IL-6 and IL-8 established lung metastases much more readily than tumors which expressed low or no IL-6 or IL-8.

Using immunohistochemistry to identify sources of these cytokines within human metastatic lesions, we found higher levels of IL-6 and IL-8 coming from non-malignant cells within the tumor, especially mononuclear infiltrates and peri-bronchiolar cells. Modelling tumor-lung interactions in vitro using a co-culture system, much higher levels of IL-6 and IL-8 were produced when osteosarcoma cells were cultured with bronchial epithelial cells, smooth muscle cells, or macrophages suggesting that paracrine interactions drive production of these cytokines upon interaction of tumor cells with resident lung cells. In murine models of osteosarcoma metastasis, blocking IL-6 and/or IL-8 production within tumor cells using inducible shRNA-expressing lentiviruses dramatically reduced metastatic efficiency.

Our data suggest that IL-6 and IL-8 play a primary role in the development of osteosarcoma lung metastasis. The readily targetable nature of these pathways makes them attractive candidates for therapies designed to prevent and possibly treat osteosarcoma lung metastasis.

Citation Format: Ryan D. Roberts, Amy C. Gross, Hemant K. Bid, Doris Phelps, Mary F. Wedekind, Peter J. Houghton. Autocrine and paracrine IL-6 and IL-8 drive osteosarcoma lung tropism and facilitate metastasis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B40.
Abstract IA27: Glioma stem cells: What are they?
Authors: Parada Luis F.
Published: May 2016

We have generated mouse models of GBM by driving loss of function of in the NF1, p53 and Pten tumor suppressors in the adult mouse brain. Using genetic cell labeling and lineage tracing approaches, our models support the hypothesis that stem/progenitor cells are the most likely cells to accumulate mutations over time and become the source of GBM. We have succeeded in reporter labeling the putative “Cancer Stem Cell” population and demonstrate their requirement for effectively mediating endogenous tumor recurrence after chemotherapy and in successfully supporting serial transplantation of tumors in intracranial allografts. The availability of enriched Cancer Stem cells should provide a powerful tool for identifying critical molecular properties and novel therapeutic targets.

Citation Format: Luis F. Parada. Glioma stem cells: What are they? [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr IA27.
Abstract ES4-2: Tailoring chemotherapy
Authors: Ring A
Published: May 2016

Numerous advances have been made in the management of advanced breast cancer over the last decade. Many of these have focused on the development of targeted agents, capitalising on our increased understanding of the molecular pathways involved in breast cancer biology. Nonetheless for many patients the backbone of treatment remains cytotoxic chemotherapy, either as a sole therapy (in those with cancer phenotypes where additional targeted therapy is not indicated) or combined with targeted therapy. Whilst most of the chemotherapy agents indicated in the treatment of advanced breast cancer have been available in the clinic for many years there remain controversies and variations in practice around the use of these standard agents.

This presentation will discuss the indications and factors which should be taken into account in making the choice between combinations as compared sequential single agent chemotherapy. The clinical trial evidence will be overviewed with examples from clinical practice. The continuation of chemotherapy beyond maximal response and the advantages and disadvantages of maintenance chemotherapy will then be discussed. This will lead on to a discussion of whether there is a population of patients in whom metronomic low-dose chemotherapy might be indicated. In the final part of the presentation whether choice of chemotherapy should be influenced by tumour phenotype as defined by estrogen receptor status, HER2 status and the patient's germline BRCA mutation status will be discussed.

At the conclusion of this educational session it is anticipated that the attendees will have a good understanding of the evidence underlying these areas, as well as practical knowledge which will help in clinical practice. It is hoped that better understanding of the optimal use of chemotherapy will maximise the benefit of these agents for our patients: gaining longest possible control of disease with best possible quality of life.

Citation Format: Ring A. Tailoring chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr ES4-2.
Abstract ES7-1: Neoadjuvant endocrine therapy
Authors: Ma CX
Published: May 2016

Neoadjuvant endocrine therapy has become a standard approach in clinical practice to improve the chance of breast conservation in postmenopausal women with locally advanced estrogen receptor positive breast cancer based on results from several neoadjuvant endocrine trials. Although data is limited, neoadjuvant endocrine therapy appears to as effective as chemotherapy in converting mastectomy to lumpectomy. In addition, neoadjuvant endocrine therapy allows an early assessement of tumor responsiveness to endocrine therapy so that adjuvant treatments could be tailored accordingly. Persistent cell proliferation on neoadjuvant endocrine therapy predicts a high risk of early relapse, for whom novel treatment strategies are in great need. In contrast, the Preoperative Endocrine Prognostic Index score of 0 (pathologic T2/3 N0 Ki67 <2.7% ER+) in response to neoadjuvant endocrine therapy is being prospectively evaluated in the ongoing Alliance A011106 (ALTERNATE) as a marker of endocrine sensitive disease, for whom chemotherapy could be avoided. Furthermore, neoadjuvant endocrine trials provide a unique research platform for biomarker studies and the testing of novel therapeutic hypothesis.

Citation Format: Ma CX. Neoadjuvant endocrine therapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr ES7-1.
Abstract P1-06-05: The impact of ethnicity on normal breast biology
Authors: Nakshatri H , Anjanappa M , Bhat-Nakshatri P
Published: May 2016

The incidence of/mortality from the most aggressive triple negative breast cancer (TNBC) is higher in African American- (AA) than Caucasian (CA)-women. In contrast, breast cancer in Hispanic-women is generally less aggressive. There is an ongoing debate as to whether AA-women have an increased incidence of TNBCs that have poor outcome or there are unique biological factors in AA-women that promote aggressive biology. Through unique approaches, we provide evidence for distinct biology in the normal breasts of CA-women, AA-women, and Hispanic-women. Using resources from the Komen Normal Tissue Bank and a primary cell culturing system that enabled propagation of normal epithelial cells of different lineages including mature-luminal, luminal-progenitor, and stem cells from different ethnic groups, we have identified a subpopulation of CD44high/CD24- cells that are unique to AA-women (p=0.0001). This AA-women-specific subpopulation expressed higher levels of Collagen 3A1, Collagen 5A2, CTNNB1 (β-Catenin of Wnt), FOXC2, and ZEB1 compared to common CD44+/CD24+ subpopulation in every breast. Gene expression pattern in the AA-specific CD44high/CD24- population showed marked similarity to gene expression pattern in the recently described PROCR+ multi-potent mammary stem cells. Indeed, the breast epithelial cells of AA-women were enriched for PROCR-positive stem cells compared to CA-women or Hispanic-women (p=0.015). In contrast to cells from CA- and AA-women, cells isolated from the healthy breast of Hispanic-women displayed mostly differentiated features as they were enriched for CD49f-/EpCAM+ and CD271-/EpCAM+ mature cells. Cells from CA-women, AA-women and Hispanic-women are currently being immortalized to determine the cell types that are preferentially immortalized in each of these ethnic groups. These results suggest ethnicity-dependent differences in Wnt, extracellular matrix, and epithelial to mesenchymal transition (EMT) signaling in normal breast epithelial cells and differences in the proportion of cells that are susceptible to immortalization/transformation.

This work is supported by Susan G. Komen for the Cure to HN (SAC110025).

Citation Format: Nakshatri H, Anjanappa M, Bhat-Nakshatri P. The impact of ethnicity on normal breast biology. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-06-05.
Abstract P1-09-10: Mammographic density: Its inherent epidemiology in 12000 women from 22 diverse countries
Authors: McCormack VA
Published: May 2016

The International Pooling Project on Mammographic Density Consortium

Background: Over the past 25 years, the epidemiologic knowledge for mammographic density (MD), as a strong marker of breast cancer risk, has expanded greatly, aided by the availability of mammograms in countries with wide-scale mammography-based breast cancer screening programs. The known epidemiology of this breast-tissue specific marker is thus that of women in high incidence countries, and not of that in countries with lifestyles that are characterized by very different life-long hormonal influences, especially during the reproductive years. The International Pooling Project on Mammography Density (IPPMD) aimed to examine the epidemiology of MD internationally, to benefit from breast cancer risk and breast cancer risk factor heterogeneity.

Methods: From diverse breast cancer risk populations, IPPMD sought to include samples of 200 premenopausal and 200 postmenopausal general population women for which risk factor data and mammograms, not taken for symptomatic reasons, were available. To date we have included 11447 women from 22 countries, consisting of 40 ethnicity and location-specific population groups. 5 to 6 countries were included in each of Europe, Africa and the Middle East, Asia and the Americas. Populations not previously studied in terms of MD include South Africa, Kenya, Turkey, Egypt and Brazil.

Digitized/digital films for every woman were anonymised, transferred to the study and read using Cumulus 6 by 3 readers, to obtain standardized quantitative and comparable MD estimates across the entire sample. Readers were blind to all woman and study/country identifiers. Normal errors regression models were used to analyse square root percent density and absolute dense area, after standardizing reader-specific values to a single reader's distribution.

Results: All risk factor data and MD readings have recently been pooled. Initial findings are as follows. Mean percent MD and absolute dense area varied over 2-fold between the 40 population groups, after adjusting for age and BMI. There is striking consistency in several epidemiologic features of MD across all population groups, including the rate of decline of density at both pre and post-menopausal ages and the decline associated with the menopausal transition. We are exploring to what extent these and other factors such as menarche, parity, age at first birth and breastfeeding, account for between population-group differences in MD.

Conclusions: This international perspective provides a valuable insight to the epidemiology of MD worldwide.

Citation Format: McCormack VA. Mammographic density: Its inherent epidemiology in 12000 women from 22 diverse countries. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-09-10.
Abstract P1-14-21: Predictive factors of pathologic complete response of HER2-positive breast cancer after preoperative chemotherapy with trastuzumab: Development of a specific predictor
Authors: Jankowski C , Guiu S , Cortet M , Hudry D , Arnould L , Charon-Barra C , Desmoulins I , Rouzier R , Fumoleau P , Coudert B , Reyal F , Coutant C
Published: May 2016

Purpose: The aim of this study was to assess the M.D Anderson Cancer Center / Gustave Roussy Institute (MDACC/IGR) nomogram in predicting pathologic complete response (pCR) to preoperative chemotherapy in a cohort of HER2 tumors treated with preoperative chemotherapy with trastuzumab. Then, we combine clinical and pathological variable associated with pCR into a new nomogram specific of HER2 tumors treated by preoperative chemotherapy with trastuzumab.

Methods: Data from 270 patients treated with preoperative chemotherapy with trastuzumab at Curie Institute and at Georges Francois Leclerc Cancer Center were used to assess MDACC/IGR nomogram and then to develop a nomogram for pCR based on multivariate logistic regression. Model performance was quantified with respect to calibration and discrimination.

Results: The IGR/MDACC was not accurate to predicting pCR in HER2 tumors treated by preoperative chemotherapy with trastuzumab with poor discrimination (AUC=0,54, IC [0,51-0,58]) and poor calibration (p=0,01). After uni and multivariate analysis, the new pCR nomogram was based on T stage (TNM), hormonal receptor status, and ki67(%). The model had a good discrimination 0,74 (IC95% : [0,70-0,79]) and a good calibration (p=0,93).

Conclusion: To our knowledge, this is the first nomogram to predict pCR in HER2 tumors treated by preoperative chemotherapy with trastuzumab. To ensure exportability, the model need to be evaluate with a external validation set.

Citation Format: Jankowski C, Guiu S, Cortet M, Hudry D, Arnould L, Charon-Barra C, Desmoulins I, Rouzier R, Fumoleau P, Coudert B, Reyal F, Coutant C. Predictive factors of pathologic complete response of HER2-positive breast cancer after preoperative chemotherapy with trastuzumab: Development of a specific predictor. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-14-21.
Abstract P1-16-08: Inhibition of β-catenin pathway to overcome endocrine resistance in breast cancer
Authors: Won HS , Lee KE , Lee KM , Nam EM , Mun Y-C , Seong C-M , Lee SN
Published: May 2016

Background: It is well known that Wnt/β-catenin signaling pathway is involved in hormone receptor negative breast cancer, especially triple-negative breast cancer. In the case of hormone resistant breast cancer cells, they rarely showed hormone receptor expression. So we aimed to investigate whether the β-catenin pathway becomes activated in endocrine-resistant breast cancer cells and inhibition of β-catenin pathway can overcome endocrine resistance.

Methods: We have established an MCF-7-derived tamoxifen-resistant cell line (TamR) by long-term culture of MCF-7 cells with gradually increasing 4-hydroxytamoxifen concentration till 3μM. The levels of protein expression and mRNA transcripts were determined using western blot analysis and real-time quantitative PCR. The transcriptional activity of β-catenin was measured using luciferase activity assay. We used ICG-001 as inhibitor of β-catenin transcription activity.

Results: The expression of estrogen receptor was significantly decreased in TamR cells. On the other hand, the expressions of HER2 and EGFR were increased in TamR cells than in control cells. The active (uncomplexed form) β-catenin level was increased in TamR cells, and also showed a significantly increased β-catenin transcriptional activity. The ICG-001, small-molecular inhibitor of Wnt/β-catenin pathway, treatment significantly reduced β-catenin transcriptional activity in TamR cells. The ICG-001 reduced cell viability fo TamR cells which showed resistance to tamoxifen by 65.3%, and also inhibited target gene cyclin D1 expression. The combination of ICG-001 and mTOR inhibitor, rapamycin reduced cell viability of TamR cells by 81.7% and there was an additive effect of two drugs as a combination index of 1.022.

Conclusions: The β-catenin pathway is activated in endocrine-resistant breast cancer cells and inhibition of that pathway would be a new therapeutic strategy which overcomes endocrine resistance in breast cancer.

Citation Format: Won HS, Lee KE, Lee KM, Nam EM, Mun Y-C, Seong C-M, Lee SN. Inhibition of β-catenin pathway to overcome endocrine resistance in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-16-08.