bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4853: NRP2b, a unique isoform of NRP2, promotes aggressive lung cancer phenotypes
Authors: Dimou Anastasios , Nasarre Patrick , Nair-Menon Joyce , Cappuzzo Federico , Landi Lorenza , D'Incecco Armida , Uramato Hidetaka , Yoshida Takeshi , Haura Eric , Gooz Monica , Armeson Kent , Gemmill Robert , Drabkin Harry 
Published: July 2017

Abstract
Neuropilins (NRPs) 1 and 2 are highly-related receptors for class 3 semaphorins, and interact with heparin-binding growth factors and their receptors (e.g. HGF-MET, VEGF-VEGFR2 etc.). We previously reported that NRP2 is upregulated by TGFβ and is required for its pro-tumorigenic activity. Here, we show that this upregulation preferentially involves NRP2b, a largely uninvestigated isoform encoding a divergent, yet highly-conserved C-terminus. Importantly, using a panel of lung cancer cell lines and orthotopic metastasis model, NRP2b promoted migration, invasion, metastasis and tumorsphere formation, whereas the prototype receptor, NRP2a had opposite effects. TGFβ-mediated resistance to gefitinib in EGFR mutated tumors also was dependent on NRP2b expression. In addition, NRP2b, but not NRP2a, linked MET activation by HGF to AKT phosphorylation. Mechanistically, in co-immunoprecipitation assays, we found that NRP2a robustly interacted with PTEN, while the interaction with NRP2b was weak. At the clinical level, NRP2b expression was commonly upregulated in patient lung cancer samples and this upregulation was a significant poor-prognostic factor. Collectively, these data indicate that NRP2b plays an important role in lung cancer invasion, metastasis and EGFR inhibitor resistance. Furthermore, isoform-specific interactions between NRP2 and PTEN may be responsible for the observed differences in MET signaling in response to HGF.
Citation Format: Anastasios Dimou, Patrick Nasarre, Joyce Nair-Menon, Federico Cappuzzo, Lorenza Landi, Armida D'Incecco, Hidetaka Uramato, Takeshi Yoshida, Eric Haura, Monica Gooz, Kent Armeson, Robert Gemmill, Harry Drabkin. NRP2b, a unique isoform of NRP2, promotes aggressive lung cancer phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4853. doi:10.1158/1538-7445.AM2017-4853
Abstract 4858: AK4 promotes colorectal cancer progression and metastasis
Authors: Yu Yau Hei , Tong Joanna Hung Man , Pan Yi , Lung Raymond Wai Ming , To Ka Fai , Chan Anthony Wing Hung 
Published: July 2017

Abstract
Metastatic colorectal cancer (CRC) is a fatal disease with a poor prognosis. It is crucial to understanding the underlying pathogenesis to battle this dismal condition. We previously identified that AK4, a gene on chromosome 1p31.3 encoding a member of adenylate kinase family enzymes, was progressively up-regulated from normal colon, primary CRC to metastasis by mRNA gene expression microarray of paired CRC samples. This study was aimed to validate the overexpression of AK4 and explore in-vitro effects in CRC. We firstly examined the mRNA expression level of AK4 in a panel of CRC cell lines. AK4 mRNA expression was higher in CRC cell lines (n=8) than normal colon cell line, and significantly higher in advanced stage cell lines (n=4, Dukes’ C and D) than early stage ones (n=4, Dukes’ A and B) (P=0.03). We further evaluated expression level of AK4 in two different cohorts of clinical samples. The first cohort consisted of 18 paired primary CRCs and its corresponding normal colonic mucosa, and 27 metastatic CRC (including 15 cases with paired primary CRC and normal colonic mucosa). AK4 mRNA level was significantly higher in metastatic CRC than normal colon (P&lt;0.001), and metastatic CRC than primary CRC (P&lt;0.001). Among 15 cases with paired primary and metastatic tumors, 14 (93.3%) demonstrated higher AK4 in metastatic tumors than their primary counterparts(P&lt;0.05). The second cohort composed of 190 consecutive primary CRCs. Upregulation of AK4 protein expression evaluated by immunohistochemistry was found in 68.4% of CRC, and associated with advanced AJCC stage (P&lt;0.001), poorer overall survival (P=0.002) and worse disease-free survival (P&lt;0.001). To evaluate functional properties of AK4 in CRC, we knocked down AK4 on a CRC cell lines with high endogenous AK4 expression (DLD1, HCT116 and SW620) by siRNA. knockdown of AK4 significantly reduced anchorage-dependent colony forming ability (P&lt;0.05) and eliminated migratory (P&lt;0.05) and invasive (P&lt;0.05) abilities. In conclusion, AK4 is a potential oncogene upregulated in metastatic CRC and exhibiting in-vitro oncogenic properties. AK4 may play an important role in tumor progression and metastasis.
Citation Format: Yau Hei Yu, Joanna Hung Man Tong, Yi Pan, Raymond Wai Ming Lung, Ka Fai To, Anthony Wing Hung Chan. AK4 promotes colorectal cancer progression and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4858. doi:10.1158/1538-7445.AM2017-4858
Abstract 4863: Aurora-A kinase: a nuclear driver of metastasis
Authors: Marinak Kristina , Kiseleva Anna , Loskutov Yuriy , Smolkin Matthew , Pugacheva Elena 
Published: July 2017

Abstract
Aurora-A Kinase (AURKA) is a serine/threonine kinase that is critical for mitosis. AURKA is overexpressed in 96% of human cancers, including breast cancer. It has been previously shown that AURKA localizes to the nucleus in breast cancer metastases and especially in metastases of Triple Negative Breast Cancer (TNBC). Our objective is to define the role of nuclear AURKA in breast cancer metastasis in TNBC. Here we report that TNBC cells vary in amount of nuclear AURKA and this potentially correlates with their metastatic capabilities. Based on our preliminary findings we hypothesized that nuclear AURKA promotes cell survival and resistance to apoptosis in the metastatic niche. To test this hypothesis we created TNBC cell lines with CRISPR/Cas9 based deletion of endogenous AURKA. We also constructed exogenous AURKA specifically targeted to the nucleus by addition of a nuclear localization signal (NLS) or cytoplasm via addition of a nuclear exclusion signal (NES), respectively. To allow for in vitro and in vivo rescue experiments with exogenous NES or NLS AURKA in sgAURKA expressing TNBC cells, we introduced several silent mutations to avoid sgAURKA targeting. In our pilot orthotopic xenograft study with MDA-MB-231-luc2-Cas9 (TNBC) cells expressing sgAURKA with WT AURKA, NLS-AURKA or AURKA-NES shows a trend of increased metastatic colonization in the AURKA-NLS group. Overall, our results indicate that the amount of nuclear AURKA is increased in metastatic breast cancer cell lines and metastases of TNBC, but the mechanism of this translocation is currently unknown. Elucidation of this mechanism is critical for development of new therapeutical strategies for control and eradication of metastatic disease.
Citation Format: Kristina Marinak, Anna Kiseleva, Yuriy Loskutov, Matthew Smolkin, Elena Pugacheva. Aurora-A kinase: a nuclear driver of metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4863. doi:10.1158/1538-7445.AM2017-4863
Abstract 4864: Role of AIB1 Δ -4 in malignant progression of breast cancer
Authors: Sharif Ghada M. , Ory Virginie , Wellstein Anton , Riegel Anna 
Published: July 2017

Abstract
The nuclear co activator AIB1 is amplified and/or overexpressed in up to 60 % of breast cancers. We have previously described a splice variant of AIB1 (Δ4) missing exon 4 that results in an N-terminally truncated protein. Full length AIB1 transcriptional function can be repressed by the tumor supressor ANCO1/ANKRD11. However, Δ4 is missing the ANCO1 binding domain and is not transcriptionally suppressed. More metastatic variants of isogenic breast or colon cancer cell lines have significantly increased levels of Δ4 relative to full length protein. Δ4 levels also increase in breast tissue samples as they transition in malignant progression. We conjectured that small increases in Δ4 protein in the cell could have potent effects on malignant progression. To determine the functional significance of Δ4 in malignant progression we developed DCIS (ductal carcinoma in situ) cell lines that only express this isoform and not the full length protein. We engineered these lines by using CRISPR technology targeted at the exon 3/4 splice junction. The resulting lines were significantly more invasive in ECIS endothelial invasion assays. In vivo, intracardiac zebrafish injections of the Δ4-DCIS lines showed higher extravasation from the tail vasculature compared to the parental line. Subcutaneous xenografts in athymic nude mice grew larger tumors, presented more invasive lesions and metastases. Also, Δ4-DCIS spheres growing in matrigel, showed disorganization and enhanced invasion into the matrix. In conclusion these data suggest a model where the increased splicing of AIB1 to the Δ4 variant alters transcription at specific target genes and contributes to the metastatic phenotype.
Citation Format: Ghada M. Sharif, Virginie Ory, Anton Wellstein, Anna Riegel. Role of AIB1 Δ -4 in malignant progression of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4864. doi:10.1158/1538-7445.AM2017-4864
Abstract 487: A comprehensive target enrichment panel for fusion detection
Authors: Saraiya Ashesh , Young Brandon , Meißner Tobias , Jones Brian L. , Huelga Stephanie C. , Amorese Doug A. 
Published: July 2017

Abstract
Growing interest in cancer classification and progression has accelerated the rate of novel gene fusions discovery with increasing recognition of their roles as biomarkers. RNA-Seq is an attractive method for expressed fusion discovery and detection because of its ability to provide unbiased fusion sequencing information. The ability to detect low expressing fusion transcripts, however, require high sequencing depth and represents a significant financial barrier and identification of clinically relevant fusion sequences from a large data set can be a bioinformatics challenge.
To address these challenges we have tested the Ovation® Fusion Panel Target Enrichment System V2, a targeted RNA sequencing method using the Single Primer Enrichment Technology (SPET), with a number of control and clinical samples. Initial studies were performed using a comprehensive target enrichment panel targeting 502 genes with three samples from Horizon DX containing known fusions. Target enriched libraries were constructed with 10 ng and 100 ng inputs and the data was analyzed using the NuFuseD pipeline (available as a point and click BaseSpace application or downloadable linux package) which has been optimized for fusion analysis from this data. Expected fusions were identified at both input levels, even when down sampled to 500K reads, with fewer fusion calls compared to other publically available fusion detection software (Chimerascan and SOAPFuse), suggesting a lower false positive rate. NuFuseD fusion calls are provided with a P-value to help prioritize the identified fusions for subsequent validation. Additionally, NuFuseD detected novel fusions in the control samples demonstrating the advantage of a comprehensive panel compared to more restricted panels. We further validated the target panel using control RNA (UHR and Human Brain) and fresh or FFPE cell lines (NCI-H2228, HCC1937) to further demonstrate our ability to identify known fusions.
Finally, the system was evaluated at an external site using patient FFPE samples. These samples (N=8) were from a set of breast, liver and ovarian cancers, containing a unique fusion in 4 of the samples based on DNA based sequencing. Only 1 of the 4 expected fusions were identified using whole transcriptome data (100 million reads) while 3 of the 4 fusions were detected with this assay (10 million reads) demonstrating its ability to generate targeted RNA sequencing libraries with increased sensitivity of gene fusion detection and reduced sequencing costs compared to standard RNA-Seq methods.
Citation Format: Ashesh Saraiya, Brandon Young, Tobias Meißner, Brian L. Jones, Stephanie C. Huelga, Doug A. Amorese. A comprehensive target enrichment panel for fusion detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 487. doi:10.1158/1538-7445.AM2017-487
Abstract 4873: Shedding light on the unknown of Ewing sarcoma: Single cell study shows a co-expression pattern between TAPA-1 and EWSR1-FLI1
Authors: Khoogar Roxane , Phelps Doris , Houghton Peter 
Published: July 2017

Abstract
Introduction: Ewing Sarcoma (ES) is the second most frequent bone cancer found in children, and has the highest rate of recurrence among all childhood cancers. This suggests the need for a better understanding of heterogeneous cancer populations and rare cells that survive intensive cytotoxic therapy and cause recurrence in patients. It is widely accepted that ‘EWSR1-FLI1’ has a major role in determining ES survival and proliferation, but the mechanism is unknown. Most studies in which expression of ‘EWSR1-FLI1’ is correlated with the level of expression of ‘EWSR1-FLI1’ regulated genes have been conducted on bulk populations that ignore potential heterogeneity of ‘EWSR1-FLI1’ in the cell population. To address this we have used single cell RNA-Seq approaches.
Methods: The WaferGen iCell8 system was used to perform SMART whole transcriptome amplification using EW-8 ES cells.We sequenced single-cell RNA-Seq libraries prepared from over 1260 ES parental cells. We combined computational analysis with stringent quality control filters to profile candidate ES cells.We used EWSR1 expression profile to partition the entire population into two clusters. A population of cells with TAPA-1 expression was distinguished and studied for their co-expression patterns with EWSR1.
Results: Results revealed that ES cells show considerable heterogeneity at the transcriptome level between seemingly identical EW-8 cells.
We identified a subpopulation of EW-8 ES cells with a positive correlation between the expression of EWSR1 and Target of the antiproliferative antibody 1 and tetraspanin-28 (TAPA-1/CD81). Our preliminary data from 200 cells indicate that EWSR1 (0-18 unique transcripts, median 1) and TAPA-1/Cd81 (0-8 unique transcripts, median 0) were correlated (r= 0.32, P&lt;0.10). TAPA-1, a surface membrane protein, most frequently associated with hematopoetic cells, that regulates cell development, activation, growth and motility and has been implicated in proliferation of many cancers.
Conclusions: Taken together, our results suggest that there are two classes of cells with respect to the expression of TAPA-1 in EW-8 cells. We also show the relationship between TAPA-1 with EWSR1-FLI1 expression in a single cell level. This type of classification may lead us to identify a rare population with a poor response rate to cytotoxic treatments. Future studies will determine if EW-8 ES cells having elevated TAPA-1 have differential sensitivity to cytotoxic agents compared with populations with low level expression.
Citation Format: Roxane Khoogar, Doris Phelps, Peter Houghton. Shedding light on the unknown of Ewing sarcoma: Single cell study shows a co-expression pattern between TAPA-1 and EWSR1-FLI1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4873. doi:10.1158/1538-7445.AM2017-4873
Abstract 4874: Application of quantitative analysis of mouse cell contamination and purification of human tumor cells in patient derived orthotopic xenograft mouse models of pediatric brain tumors
Authors: Braun Frank K. , Kogiso Mari , Qi Lin , Zhang Huiyuan , Du Yuchen , Lindsay Holly B. , Zhao Sibo , Injac Sarah G. , Li Xiao-Nan 
Published: July 2017

Abstract
Background: Pediatric brain tumors continue to be among the most difficult to cure and are the leading cause of cancer-related deaths in children. Research investigating pediatric brain cancer is still impaired by the lack of cancer models. We established a large panel of orthotopic xenograft models as well as several paired permanent cell lines using in vivo and in vitro culture techniques. However an inherent risk of xenograft models is the contamination of isolates of human tumors with host (mouse) cells. Therefor strategies to correctly and timely identify the human/mouse ratio are essential. In this study we investigated Prostaglandin Receptor EP2 (PTGER2) as a useful target to identifying mouse cell contamination in PDOX models.
Method: Species specific primers based on Alcoster et al., 2011 were used to detect PTGER2 in genomic DNA extracts of xenograft and cultured cells. Real-time qPCR was carried out using a StepOnePlus™ Real-Time PCR System. Reaction mix contained SYBR Green select master mix, respective primers and 5 ng of total genomic DNA in a total reaction volume of 10 μL. The qPCR conditions were as follows: 50°C-2 min, 95°C-10 min, 40 cycles of (95°C-15 sec, 61°C-1 min). Primer specificity was controlled in addition by analysis of amplified products on a 1.2% agarose gel. FACS was used to isolate human cells according to anti-Human HLA-ABC Ab and mouse-specific Ab cocktail surface staining and subjected to qPCR.
Results: Various models of pediatric brain cancer (PXA, MB, GBM, EPN, ATRT, DIPG, PNET) established in our group were investigated for mouse cell contamination. Cells from xenograft isolates as well as from cultured xenografts were routinely analyzed. Our study confirms PTGER2 as a useful target for accurately estimate mouse cell contamination in brain cancer xenograft models. This further enabled us to improve detection and characterization of HLA-ABC/mouse-cocktail double negative population as seen in FACS.
Conclusion: In conclusion we have successfully implemented an easy qRT-PCR approach to determine the human/mouse cell ration in any mixed cell population. Particular for PDOX models it is paramount to have reliable information on mouse cell contamination.
Citation Format: Frank K. Braun, Mari Kogiso, Lin Qi, Huiyuan Zhang, Yuchen Du, Holly B. Lindsay, Sibo Zhao, Sarah G. Injac, Xiao-Nan Li. Application of quantitative analysis of mouse cell contamination and purification of human tumor cells in patient derived orthotopic xenograft mouse models of pediatric brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4874. doi:10.1158/1538-7445.AM2017-4874
Abstract 4895: CT20p as a therapeutic for lung cancer with elevated chaperoning containing TCP1 (CCT) expression levels
Authors: Carr Ana C. , Khaled Amr S. , Bassiouni Rania , Khaled Annette R. 
Published: July 2017

Abstract
Lung cancer is the leading cause of cancer related fatalities worldwide and although there is a substantial effort in the development of improved, more specific, and less debilitating therapies, very little progress has been made accomplishing this goal. We propose the use of CT20p, a therapeutic peptide developed by our laboratory, as novel therapy for lung cancer. We have previously demonstrated that CT20p has tumor specific cytotoxicity in breast cancer cells and it induces tumor regression in xenograft models of breast cancer. We have also determined Chaperonin containing T-complex (CCT) to be the intracellular target of CT20p and that susceptibility to CT20p correlates with its expression levels, with tumor cells expressing high levels of CCT being the most susceptible. CCT is a large macromolecular complex composed of 8 subunits (CCTα, CCTβ, CCTγ, CCTδ, CCTϵ, CCTζ, CCTη, CCTθ). Immunoblot probing against four relevant CCT subunits (CCTβ, CCTγ, CCTδ, CCTϵ) was used to determine their relative expression level in five small cell lung cancer (SCLC) cell lines when compared to normal lung cells. We determined that the expression levels of the four probed CCT subunits varied amongst the five SCLC cell lines, however, the four CCT subunits were always expressed at higher levels when compared to normal lung cells. Immunohistochemistry staining for CCTβ was used on tissue microarray (TMA) of lung cancer progression. Results were interpreted on a scale of 1 to 4 (with 4 being the strongest staining). We determined that CCTβ levels increase with cancer severity and identified a significant correlation between CCTβ levels and cancer progression in both small cell lung carcinoma (SCLC) and Squamous cell lung carcinoma (SqCLC). Using The Cancer Genome Atlas (TCGA) database, we have found CCT gene alterations in clinical lung cancer cases range from 10% to 43%, however, only CCT4 gene amplification in SqCLC cases correlated with decreased survival. Altogether, these results suggest that CT20p has the potential for being a therapeutic for multiple types of lung cancer due to increased target expression.
Citation Format: Ana C. Carr, Amr S. Khaled, Rania Bassiouni, Annette R. Khaled. CT20p as a therapeutic for lung cancer with elevated chaperoning containing TCP1 (CCT) expression levels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4895. doi:10.1158/1538-7445.AM2017-4895
Abstract 4907: Elucidating the inhibitory role of plant alkaloids in breast cancer metastasis
Authors: Iqbal Waqas , Alkarim Saleh , Sabir Jamal S. , Bora Roop S. , Saini Kulvinder S. 
Published: July 2017

Abstract
Despite extremely high morbidity and mortality of &gt;90% from metastasis, it remains one of the most challenging process for targeted therapeutic interventions. Identification and characterization of chemically active and bioavailable compounds from medicinal plants targeting the cell-signaling pathways of Cancer Stem Cells (CSCs), tumor cells and their microenvironment that abet metastasis is of great clinical significance. Hence, MCF-7; a breast cancer cell line, was treated with fractionated alkaloidal extracts from Rhazya stricta with previously documented anti-cancer activity in lung and pancreatic cancer cell lines. RNA-seq. analysis was performed for samples treated with compounds that actively inhibited cell migration in scratch assay to further substantiate their anti-metastatic role at the cellular and molecular level. Genomic data corroborated the presence of anti-metastatic compounds that actively down-regulated genes involved in promoting metastasis (CDC6), cell migration (KIF23, DLGAP5), invasion and CSCs’ expansion (PTTG1). We also found down-regulation of GAS1 expression, an enhancer of Hedgehog signaling pathway. To our knowledge, this study, first of its kind, sets precedence in exploiting the anti-metastatic potential of these compounds. Further proof of concept studies in mouse models of breast cancer to establish precise mechanism-of-action(s), would certainly open up avenues for the development of new chemical entities (NCEs), targeting metastasis regulating gene(s) with precision.
Citation Format: Waqas Iqbal, Saleh Alkarim, Jamal S. Sabir, Roop S. Bora, Kulvinder S. Saini. Elucidating the inhibitory role of plant alkaloids in breast cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4907. doi:10.1158/1538-7445.AM2017-4907