bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2399: System analysis of adapted and quiescent/dormancy(QD) models of drug resistance in melanoma cell lines
Authors: Liu Feng , Panchal Parvita Paresh , Wang Zi , Farhat Ahmed , Garcia Angela , Fagundes Tcharles , Filipp Fabian , Meyskens Frank L. 
Published: July 2016

Abstract
The biological basis for inherent and acquired drug resistance in melanoma is a prominent issue, highlighted by the recent discovery of various pathways leading to acquired resistance to the mutant BRAF inhibitor Vemurafenib (Plx4032). In order to dissect patterns of drug resistance, we treated 3 melanoma cell lines (A375, 1205Lu and SK-Mel28) under 2 diverse conditions: (1) Increasing drug concentrations over time(4 months)- Melanoma cells treated with increasing concentrations of Plx4032 (initial and increasing concentrations of 0.1, 0.5, 1 and 5 μM PLx4032) exhibited an adaptation response. After an initial pause in proliferation, these cells proliferated in the continuing presence of the drug. Cells able to grow in the presence of 10 or 20 μM of Plx4032 were cultured as pools. RNA-Seq profiling and system biology analysis comparing the gene expression in the parental SK-Mel28 cells and adapted A2-1 revealed three major altered pathways: the PDGF-MAPK-DUSP-HIF2α, TGF-β-SMAD9-FGF1 and EDNRB-GNAI2-PLCB4-PKA-MITF pathway. Our qRT-PCR and western blot experiments have confirmed an up-regulation of PDGF which by-passed the BRAF gene and activated ERK1/2 kinases. These changes were accompanied by increase of NRAS accumulation in the adapted cells. (2) Using high initial drug concentrations of PLx4032 (&gt;10 μM), &gt; 99.9 of cells were killed, but some single cells (Q/D) survived for at least 4 weeks in the continuous presence of drug. After the drug was removed cellular proliferation reoccured 2-3 weeks later (designated post-dormant cells 1, PD1 cells). These cells did not show increased IC50s to Plx4032 after 72 hour of retreatment. However, when treated with high dose of drug again, the PD1 cells produced more dormant cells (PD2 cells), suggesting inheritance of the DQ trait. RNA-Seq profiling studies of the DQ cells are underway. The drug-induced dormancy/quiescence and adaptive response represent 2 different pathways of how cells survive treatment and develop resistance and provide a beginning to understanding the biological basis of the well established clinical phenomenon of long term clinical dormancy of melanoma and potentially other cancers.
Citation Format: Feng Liu, Parvita Paresh Panchal, Zi Wang, Ahmed Farhat, Angela Garcia, Tcharles Fagundes, Fabian Filipp, Frank L. Meyskens. System analysis of adapted and quiescent/dormancy(QD) models of drug resistance in melanoma cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2399.
Abstract 2403: Molecular mechanisms orchestrating intratumoral heterogeneity in Kras-driven carcinomas
Authors: Azimi Roxana 
Published: July 2016

Abstract
The considerable variability within tissue microenvironments as well as the multiclonality of cancers leads to intratumoral heterogeneity. This increases the probablility of cellular states that promote resistance to therapy and eventually lead to reconstitution of the tumor by treatment-resistant cancer cells, which in some cases have properties of normal tissue stem cells. Wnt signals are important in the maintenance of stem cells in various epithelial tissues, including in lung development and regeneration. We hypothesized that Wnt signals contribute to tumor heterogeneity in genetically engineered KrasG12D; Tp53Δ/Δ (“KP”) mouse lung adenocarcinomas (LUAD). We observed that a subpopulation of LUAD cells exhibited high Wnt reporter activity and had increased tumor forming ability, which could be suppressed by silencing of Wnt signaling pathway components or by small molecule Wnt inhibitors in vitro and in vivo. KP LUAD cells show hierarchical features with two distinct populations, one with increased Wnt reporter activity and another forming a niche that provides the Wnt signal. Lineage-tracing experiments in the autochthonous KP tumors demonstrated that Wnt responder cells have increased tumor propagation ability in vivo. Strikingly, selective ablation of the Wnt responder cells resulted in tumor stasis. CRISPR-based targeting or small molecules targeting Wnt signaling reduced tumor growth and prolonged survival in the autochthonous KP mouse lung cancer model. Interestingly, we found that a similar Wnt-driven mechanism operates to establish an intratumoral hierarchy also in other Kras-driven carcinomas. These results indicate that maintenance of heterogeneity within tumors may be advantageous for the tumor cell population collectively, which may be utilized as a therapeutic target to homogenize cancer cell phenotypes within tumors.
Citation Format: Roxana Azimi. Molecular mechanisms orchestrating intratumoral heterogeneity in Kras-driven carcinomas. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2403.
Abstract 2418: Microenvironment-on-chip: Development of a microfluidics-based tumor ecosystem
Authors: Torga Gonzalo , Lin Ke-Chih , Austin Robert H. , Pienta Kenneth J. 
Published: July 2016

Abstract
Despite its limited clinical predictive capacity, conventional cell culture remains the most frequently used preclinical model in biomedical research. For many years, microfluidics-based organ-on-chips have been proposed to overcome conventional cell culture limitations but given their inability to provide reliable and reproducible data, their usage remains anecdotal.
Immune, stromal and cancer cells constitute a complex adaptive system in each tumor microenvironment. To study the causes and consequences of tumor heterogeneity in these complex adaptive systems, we have developed a platform to model and investigate tumor microenvironments at primary and metastatic sites in which multiple nuclear-labelled cell types can be grown in a multi-welled, communicating habitat with controlled gradients for temperature, pH, nutrients, and oxygen tension. In conjunction with labelled-nuclei, genetically-engineered cell lines with fluorescence-based biosensors can be generated to detect specific genetic expression changes in response to cell to cell interactions as well as varying environmental conditions over time.
One of the major caveats for microfluidics prototypes is reproducibility. The proposed design is easily adaptable to most of the commercially available incubation microscopy systems, allowing the experiments to be replicated by independent groups in an effort to provide reliable and reproducible data.
The ability to establish dynamic gradients within individual habitats longitudinally over time and space provides the capacity to study the effect of chemokines and drugs on the tumor ecosystem in order to discover key interactions between host cells and cancer cells and to develop improved therapeutic strategies.
In contrast to previous organ-on-chip models, our technology is not limited to a mere observational platform for automated cell counting and tracking but also provides flexibility for downstream capacities such as immunofluorescence, in situ hybridization or single-cell sequencing, as well as retrieval of single cells or specific subpopulations based on the fluorescent reporters and labelled nuclei.
The presented engineered microenvironment allows continued in vitro quantitative studies of the interactions of multiple cell types as well as varying environmental conditions. Here we propose a cancer-on-chip platform that is able to recapitulate key components and interactions to mimic different tumor microenvironments in a comprehensive manner, yet simple enough to provide reliable and reproducible data.
Citation Format: Gonzalo Torga, Ke-Chih Lin, Robert H. Austin, Kenneth J. Pienta. Microenvironment-on-chip: Development of a microfluidics-based tumor ecosystem. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2418.
Abstract 2419: Anastomotic recurrences are clonally related to primary tumors in sporadic colorectal carcinoma
Authors: Vakiani Efsevia , Shah Ronak H. , Iacobuzio-Donahue Christine , Solit David B. , Weiser Martin R. 
Published: July 2016

Abstract
Background:
Anastomotic recurrences occur in 2-10% of colorectal carcinoma (CRC) cases after surgical resection of the primary tumor. To date there are no molecular data investigating their genetic profile and multiple theories exist as to their pathogenesis including re-growth of tumor cells present within local lymphatics after initial surgery, seeding of anastomosis by metastatic tumor cells and a second primary tumor. The aim of our study was to compare the genomic profile of anastomotic recurrences to that of matched primary tumors and, where available, to that of distant metastases.
Design:
Thirty-six tumors from 14 patients were genotyped using a hybridization capture-based next-generation sequencing assay for targeted deep sequencing of all exons and selected introns of 341 key cancer genes. All patients had resection of their primary tumor with clear margins and recurred either at the anastomotic line or in the peri-anastomotic area 1.1 to 7.0 years following resection of their primary tumor. In 3 patients 2 consecutive anastomotic recurrences were sequenced, while in 6 patients a distant metastasis that occurred 1.2 to 3 years prior to the anastomotic recurrence was also analyzed. All tumors were microsatellite stable except in one patient with genetically confirmed Lynch syndrome.
Results:
A total of 254 somatic mutations were detected including 140 mutations in the microsatellite stable cases. The most commonly mutated genes (mutated in &gt; 3 patients) were APC, KRAS, TP53, PIK3CA, ATM and PIK3R1. In 13/14 patients the anastomotic recurrence(s) and primary tumor shared between 50-100% of mutations, including mutations in key driver genes such as APC, KRAS and TP53, consistent with these tumors being clonally related. In the patient with the Lynch syndrome the 2 tumors showed distinct somatic mutations suggestive of independent primaries. We identified eleven genetic events present in a distant metastasis and not in a primary tumor and none of these events was detected in the anastomotic recurrence arguing against re-seeding of the anastomotic site by a metastatic clone. All five patients with isolated anastomotic recurrence were free of disease 0.9 to 6.1 years following resection of their recurrent CRC.
Conclusions:
Anastomotic recurrences appear to be clonally related to the primary tumor in sporadic CRC cases. Our data also provide molecular data in support of the treatment of anastomotic recurrences as localized disease.
Citation Format: Efsevia Vakiani, Ronak H. Shah, Christine Iacobuzio-Donahue, David B. Solit, Martin R. Weiser. Anastomotic recurrences are clonally related to primary tumors in sporadic colorectal carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2419.
Abstract 2423: Deep phenotyping of dissociated solid tumor cells from breast cancer specimens
Authors: Middlebrook Aaron J. , Llontop Peter , Hanley Mary Beth , Porter Warren , Hahn Friedrich , Snowden Eileen , Blaesius Rainer , Ghanekar Smita 
Published: July 2016

Abstract
Exploring tumor heterogeneity with the goal of improving outcome has led to the need to glean as much information as possible at an individual cell level from these valuable specimens. Traditional approaches to solid tumor analyses fail to reveal the diverse range of cellular compartments beyond tumor cells that comprise the tumor microenvironment. A comprehensive approach to tumor interrogation requires efficient tissue dissociation to facilitate analysis at the single-cell level. Compared to current methods, single-cell analysis of tumor derived cell suspensions by flow cytometry has the potential to provide a more thorough understanding of the many subpopulations within the tumor microenvironment and the cell-to-cell interactions that govern this space.
Here, we demonstrate an efficient workflow that enables comprehensive cell analysis of solid tumors from breast cancers. After dissociating human breast cancer biopsies from primary tumors into cell suspension, we analyzed the immune compartment and the cancer/stromal cell compartment by multicolor flow cytometry, using 26 markers. A comprehensive analysis of this data set reveals the heterogeneity within the tumor microenvironment on a phenotypic level, which might have potentially significant correlations to the clinical status and molecular phenotype of the cancer. These results encourage the expansion of the use of flow cytometry as a means of solid tumor biopsy analysis, highlighting the potential clinical value of this approach in disease management.
Citation Format: Aaron J. Middlebrook, Peter Llontop, Mary Beth Hanley, Warren Porter, Friedrich Hahn, Eileen Snowden, Rainer Blaesius, Smita Ghanekar. Deep phenotyping of dissociated solid tumor cells from breast cancer specimens. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2423.
Abstract 2426: Detection of somatic mutations associated with pulmonary metastasis of osteosarcoma by whole exome sequencing
Authors: Iwata Shintaro , Tatsumi Yasutoshi , Yonemoto Tsukasa , Kamoda Hiroto , Ishii Takeshi , Nagase Hiroki , Ohira Miki 
Published: July 2016

Abstract
Objective: Pulmonary metastasis is a main cause of death for the patients with osteosarcoma (OS), although no specific genetic alteration associated with pulmonary metastasis has been reported. The objective of this study was to identify candidate somatic genetic alteration contributed to pulmonary metastasis in pediatric OS.
Methods: Five sample sets including the tissues taken from primary tumor (P), resected pulmonary metastatic tumor (M), and normal tissue (N) of the same pediatric OS patients were analyzed by whole exome sequencing with Ion Torrent Proton sequencer. 40ng of genomic DNAs extracted from each tissue were used for multiplex PCR amplification with Ion Ampliseq Exome Kit. Data analysis including alignment to the hg19 human reference genome and variant calling was done using the Torrent Suite Software. Obtained genomic data was validated by visualizing in Integrative Genomics Viewer or capillary sequencing. Candidate somatic genetic alterations were annotated by wANNOVAR database. Pathway analysis was performed using GeneMANIA.
Results: Mean read depths on the P, M, and N were 219, 212, and 109, respectively. We identified 1364 and 1311 candidate non-synonymous somatic single nucleotide variants (SNVs) among the P and M, respectively. After the validation and filtering, we detected 135 non-synonymous SNVs within the exon region in M. Among these, 32 SNVs were overlapped with those in P. Only 2 recurrent SNVs were identified within the whole SNVs. C:G&gt;T:A transition mutations were frequently observed in both P and M, and the frequency were higher in M comparing to P. Pathway analysis showed a significant enrichment of the candidate SNVs in genes involved in extracellular matrix regulation (FDR;2.37E-03).
Conclusion: We have identified 137 SNVs associated with pulmonary metastasis from pediatric OS. Extracellular matrix-relating signature might contribute to the genesis of pulmonary metastasis.
Citation Format: Shintaro Iwata, Yasutoshi Tatsumi, Tsukasa Yonemoto, Hiroto Kamoda, Takeshi Ishii, Hiroki Nagase, Miki Ohira. Detection of somatic mutations associated with pulmonary metastasis of osteosarcoma by whole exome sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2426.
Abstract 2435: Amplification of CDK4 and MDM2 is associated with atypical clinical features in high risk neuroblastoma patients
Authors: Fransson Susanne M. , Kryh Hanna , Javanmardi Niloufar , Ambros Inge M. , Berbegall Ana P. , Ora Ingrid , Noguera Rosa , Asmundsson Jurate , Sandstedt Bengt , Ambros Peter F. , Kogner Per , Martinsson Tommy 
Published: July 2016

Abstract
MYCN-amplification and 11q-deletion are important, although incomplete, markers of high-risk neuroblastoma. Thus, characterization of additional genomic alterations that can be used as prognostic and/or predictive markers is of clinical importance in order to provide best treatment possible.
By using SNP-microarrays we identified a small group of neuroblastomas with high grade amplification of one or multiple loci on 12q, commonly involving the potential oncogenic target genes CKD4 (12q13-14) and/or MDM2 (12q15). The CDK4 and MDM2 regions were co-amplified in 13/16 samples, two tumors had CDK4-amplification in absence of MDM2-amplification while one tumor had MDM2-amplification without CDK4-amplification. Exome sequencing was performed on seven tumors and whole genome sequencing (WGS) was performed on tumor and constitutional DNA from one patient with 12q-amplification. No novel protein altering SNVs were detected within the amplified regions except a rare INHBE mutation in one patient. The tumor examined with WGS show high degree of structural rearrangements including chromothriptic features on chromosome 12 leading to high grade amplification of CDK4 and MDM2. This sample displayed 21 somatic protein changing alterations although not in any gene with known function in chromatin stability or DNA repair.
Interestingly, the majority of the 12q-amplified neuroblastomas were of abdominal origin, some with renal location with initial suspicion of Wilms’ tumor. Atypical metastatic pattern were also seen in this patient group showing low degree of bone marrow involvement favoring other metastatic sites such as lung.
The consistent co-amplification of two separate chromosome 12 regions in this subset of neuroblastoma suggests that there are one or more genes with importance in tumor development/progression. Our study indicates that CDK4 appears as main target in this 12q-amplified neuroblastoma subgroup although other genes such as MDM2 and FRS2 also could provide proliferative advantages. The 12q-amplified neuroblastomas exhibit distinct clinical features and may benefit from targeted therapy using a small molecule CDK4/CDK6 inhibitor such as LEE011 (Novartis).
Citation Format: Susanne M. Fransson, Hanna Kryh, Niloufar Javanmardi, Inge M. Ambros, Ana P. Berbegall, Ingrid Ora, Rosa Noguera, Jurate Asmundsson, Bengt Sandstedt, Peter F. Ambros, Per Kogner, Tommy Martinsson. Amplification of CDK4 and MDM2 is associated with atypical clinical features in high risk neuroblastoma patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2435.
Abstract 2451: Cancer stem cell survival postradiation in medulloblastomas requires YAP, YB1, and IGF2
Authors: Dey Abhinav , Maier Caroline , Malhotra Anshu , Kenney Anna 
Published: July 2016

Abstract
Sonic hedgehog (Shh)-mediated medulloblastoma growth requires IGF2 (Insulin-like Growth Factor 2) and we recently showed that Yes Associated Protein (YAP1) induces IGF2 expression by Y-box protein 1(YB1) in Shh-stimulated cerebellar granule neural precursors (CGNPs), proposed cells-of-origin for the Shh molecular subclass of medulloblastoma, and mouse Shh-medulloblastoma cells. We found elevated levels of YAP1, YB1 and IGF2 in tumor cells occupying the peri-vascular niche, a microenvironmental niche proposed to house so-called tumor re-populating cells that survive radiation and contribute to medulloblastoma recurrence, which is fatal. We have developed an ex vivo approach using organotypic brain tumor slice cultures to better understand how YAP1, YB1, and IGF2 regulate peri-vascular niche cell survival post-radiation. We observed that the perivascular niche cell population expressing stem cell markers increases markedly following exposure to radiation. Additionally, on targeting any component of the YAP1-YB1-IGF2 axis we observed increased level of cell death within the niche and compromised cancer stem cell niche expansion post-radiation. These findings strongly indicate that therapeutic approaches intended to impair the function of this pathway could be used to reduce the use of cranio-spinal radiation of medulloblastoma patients, which causes life-long side effects that drastically impair quality of life.
Citation Format: Abhinav Dey, Caroline Maier, Anshu Malhotra, Anna Kenney. Cancer stem cell survival postradiation in medulloblastomas requires YAP, YB1, and IGF2. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2451.
Abstract 2456: Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain
Authors: He Shuning , Mansour Marc R. , Zimmerman Mark W. , Ki Dong Hyuk , Layden Hillary M. , Akahane Koshi , de Groh Eric D. , Perez-Atayde Antonio R. , Zhu Shizhen , Epstein Jonathan A. , Look A Thomas 
Published: July 2016

Abstract
Earlier reports indicated that the role of Nf1 tumor suppressor gene in limiting sympathoadrenal cell growth during embryologic development is independent of its ability to down-modulate RAS-MAPK signaling. This finding raised the question of whether neuroblastoma pathogenesis was also accelerated by loss of a similar non-canonical function of NF1. To elucidate how loss of the NF1 tumor suppressor gene contributes to the development of high-risk neuroblastoma, we relied on a transgenic zebrafish model that overexpresses MYCN and harbors loss-of-function nf1 mutations. We show here that loss of nf1 leads to aberrant activation of RAS signaling in MYCN-induced neuroblastoma, promoting both increased tumor cell survival and rapid tumor cell proliferation. We demonstrate further that the GTPase-activating protein (GAP) activity of the (GAP)-related domain (GRD) is sufficient to suppress accelerated initiation of neuroblastoma in nf1-deficient zebrafish, even though this transgene is unable to restrict abnormal sympathoadrenal cell growth during embryologic development. Hence NF1 exhibits different activities in vivo in the normal development and tumorigenesis of the peripheral sympathetic nervous system. Our findings establish nf1-deficient zebrafish that overexpress MYCN as an ideal animal model system for investigating new strategies to improve treatment of very high risk neuroblastomas with aberrant RAS-MAPK activation. We are currently performing high-throughput in vivo drug analysis using these zebrafish with primary tumors.
Citation Format: Shuning He, Marc R. Mansour, Mark W. Zimmerman, Dong Hyuk Ki, Hillary M. Layden, Koshi Akahane, Eric D. de Groh, Antonio R. Perez-Atayde, Shizhen Zhu, Jonathan A. Epstein, A Thomas Look. Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2456.