bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4651: Multiple platform evaluation of KRAS codon 12/13 reference material
Authors: Garlick Russell , Konigshofer Yves , Tomson Farol L. , Yuzuki Dale , Anekella Bharathi 
Published: July 2017

Abstract
An assay’s ability to detect the presence of a KRAS driver mutation is critical when attempting to determine whether a tumor may respond to anti-EGFR therapy. Currently, there are two FDA approved companion diagnostics that can be used to assess whether there are mutations in KRAS codons 12 and 13, and both include their own internal controls. However, there is a need for external reference materials that allow laboratories to validate such assays - especially, at levels near their limits of detection (LODs). We describe the design of the Seraseq™ FFPE Tumor KRAS Reference Material. This reference material is composed of 7 different 5-micron FFPE curls that contain the 7 different KRAS mutations detected by the companion diagnostics: G12A, G12C, G12D, G12R, G12S, G12V and G13D. Each curl contains a mixture of KRAS wildtype GM24385 cells and a KRAS mutant cell line in sufficient quantity for most assays. KRAS mutant frequencies of about 5% were targeted and subsequently verified by digital PCR. A 5% mutant frequency was selected because it is near the LOD for the existing companion diagnostics, and is close to the minimum reported frequency of many next generation sequencing (NGS)-based assays that test for somatic variants. The reference material was evaluated using different methods, which include digital PCR, the Roche cobas® KRAS Mutation Test, the QIAGEN therascreen® KRAS RGQ PCR Kit and several NGS-based assays. Testing revealed general compatibility with these assays in that sufficient DNA could be extracted, and concordance of the results with the expected calls was high. For example, apparent DNA yields by Nanodrop with the cobas assay exceeded the required amount by more than 3-fold and all 7 curls led to a “mutation detected” result in duplicate testing. Interestingly, not all variants were detected with the therascreen assay, which may be due to some variants being present at slightly below the claimed LODs, however DNA yields were sufficient and the correct variants were identified. Finally, variant frequencies obtained by NGS were consistent with those observed by digital PCR. We conclude that the Seraseq FFPE Tumor KRAS Reference Material may be useful as part of KRAS codon 12/13 assay validation.
Citation Format: Russell Garlick, Yves Konigshofer, Farol L. Tomson, Dale Yuzuki, Bharathi Anekella. Multiple platform evaluation of KRAS codon 12/13 reference material [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 4651. doi:10.1158/1538-7445.AM2017-4651
Abstract 4652: Profiling of immunity biomarkers in whole blood
Authors: Chenchik Alex , Komarov Andrei , Makhanov Michael , Frangou Costa 
Published: July 2017

Abstract
Cancer immunotherapies are rapidly changing traditional treatment paradigms and expanding the therapeutic landscape for cancer patients. However, despite the current success of these therapies, significant number of patients do not respond to immunotherapy and responders often experience significant toxicities. Therefore, there is a growing need to identify predictive and prognostic biomarkers that enhance our understanding of dynamic immunity mechanisms involved in cancer development. The genome-wide expression profiling of whole blood is an attractive method for the discovery of biomarkers due to its non-invasiveness, possibility for retrospective simple clinical site processing, and rich biological content. To this end, we have developed GeneNet, a genome-wide targeted RNA expression assay that profiles 19,000 genes based on multiplex RT-PCR followed by NGS in whole blood samples stabilized in PAXgene. The GeneNet 19K assay provides comprehensive and unbiased profiling of immune cell activation and canonical immune pathway genes for both innate adaptive and humoral immune responses. In this study, we present the performance of the assay for immunophenotyping of immune cells in blood samples from TNBC patients and assess the immune responses to complex immunomodulatory stimuli in ex vivo model system. Preliminary studies demonstrate the assay’s unparalleled specificity and sensitivity resulting in better detection of low abundance mRNA transcripts as well as an improved cost-effectiveness for high-throughput clinical applications.
Citation Format: Alex Chenchik, Andrei Komarov, Michael Makhanov, Costa Frangou. Profiling of immunity biomarkers in whole blood [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 4652. doi:10.1158/1538-7445.AM2017-4652
Abstract 4653: Genomics of regulatory crosstalk between PPAR gamma & 14-3-3 genes in breast cancer cells
Authors: Khalil Ashraf A. , Kabapy Nihal F. , Sharabi Fouad N. 
Published: July 2017

Abstract
PPARγ, a ligand-stimulated transcription factor with differentiation promoting activity is overexpressed in a variety of cancers. Perturbation of PPAR-γ signaling is now believed to be a strategy for treatment of several cancers, including breast cancer. A set of genes regulated by PPAR-γ ligands is expected to mediate the antiproliferative and prodifferentiation effects in cancer cells. Because 14-3-3 family of proteins shows a debatable activity and varying expression levels in different tumors, in the studies presented here we explored the transcriptional regulatory role of Pioglitazone on the seven 14-3-3 isoforms presenting in MCF-7 breast cancer cells. This study demonstrated that the potent PPAR-γ agonist, Pioglitazone exerted a regulatory role on expression of 14-3-3 genes where it upregulated 14-3-3 gamma, epsilon, zeta and tau by 3.8, 5.2, 2.7 and 739 folds, respectively. However, it had a negative regulatory effect on 14-3-3 beta, sigma and Eta by 16.94, 4.58 and 2.12 folds, respectively compared with control cells. These results correlated with growth arrest and a great increase in BRCA1 gene expression by 1076 folds. In summary, these findings are the first time showing that PPAR-γ regulates 14-3-3 genes and raises question whether PPAR-γ ligands mediate their anticancer effects via regulation of 14-3-3 proteins.
Selected References: 1. Bridges, D. and G.B. Moorhead. 2005. 14-3-3 proteins: a number of functions for a numbered protein. Sci. STKE 2005(296):re10. 2. Chearwae, W. and J. Bright. 2008. PPARγ agonists inhibit growth and expansion of CD133+; brain tumour stem cells. Brit. J. Cancer 99(12): 2044-2053
Citation Format: Ashraf A. Khalil, Nihal F. Kabapy, Fouad N. Sharabi. Genomics of regulatory crosstalk between PPAR gamma & 14-3-3 genes in breast cancer cells [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 4653. doi:10.1158/1538-7445.AM2017-4653
Abstract 4654: The primary study of the correlation between mRNA expression and protein phosphorylation of epidermal growth factor receptor EGFR in colorectal and breast cancer cell lines
Authors: Wang Hongwei , Ma Catherine , Zhou Yuan 
Published: July 2017

Abstract
The EGFR family is a group of receptor tyrosine kinases that mediates cell proliferation, migration, and differentiation. Activation of EGFR signaling is triggered by ligand-binding induced receptor dimerization. The dimerization activates the intracellular kinase domains of the receptor, resulting in autophosphorylation of C-terminal tail and the initiation of downstream signaling. EGFR overexpression is correlated with more aggressive clinical indications in multiple types of cancer, including colon, breast, lung, and head and neck carcinoma. Clinical studies show that EGFR-directed therapeutic approaches improved better outcomes of metastatic lung, colorectal, and head and neck cancers. Predictive biomarkers are being developed to deliver personalized therapies. Therefore, it is important to determine the protein as well as molecular biomarker expression for selecting targeted therapies. Here we present a panel cancer cell lines to examine EGFR expressions at a molecular biomarker level (mRNA) as well as a protein level of phosphorylated EGFR(pS1060). Colon cancer cell lines HT29, HCT116, SW620, as well as the breast cancer cell line SKBR3, were cultured and processed onto formalin-fixed paraffin-embedded (FFPE) CellMax pellets. Expression levels of EGFR mRNA in the FFPE slides were examined with RNAScope technology to visualize single RNA molecules per cell by using probes specifically against EGFR. Expression of phosphorylated EGFR was examined by the phosphospecific EGFR (pS1070) antibodies by using immunohistochemistry (IHC). EGFR mRNA expression was detected in HT29 and HCT 116 cells showing strong punctuated signals in the cytoplasm. However, no EGFR mRNA signals were detected in SW620 cells. Breast cancer cell line SKBR3 showed abundant EGFR mRNA expression. Phosphorylated EGFR were found in the cell HT29, HCT 116 and SKBR3 cells with membrane staining pattern. No phosphorylated EGFR was observed in SW620 cells using Immunochemistry staining. Together, our results demonstrated that the EGFR mRNA expression is correlated to the phosphorylation of EGFR in these cancer cell lines. We concluded that the EGFR mRNA probes, phosphorylated EGFR antibodies, and/or the cell lines can be served as the control-references for clinical biomarker screening.
Citation Format: Hongwei Wang, Catherine Ma, Yuan Zhou. The primary study of the correlation between mRNA expression and protein phosphorylation of epidermal growth factor receptor EGFR in colorectal and breast cancer cell lines [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 4654. doi:10.1158/1538-7445.AM2017-4654
Abstract 4655: Elevated level of serum miR-99a is correlated with serous epithelial ovarian cancer and can be a potential biomarker
Authors: Yoshimura Akihiko , Sawada Kenjiro , Nakamura Koji , Kinose Yasuto , Nakatsuka Erika , Mabuchi Seiji , Kimura Tadashi 
Published: July 2017

Abstract
Objective: There is a critical need for improved diagnostic markers to detect ovarian high grade serous cancer (HGSC). microRNAs (miRNAs) stably exist in circulating blood, reflecting tissue or organ conditions and present in circulating microvesicles such as exosomes. We aimed to identify which miRNAs are highly produced from HGSCs and analyze whether serum miRNA can discriminate patients with HGSC from healthy controls.
Methods: Secreted exosomes from ovarian cancer cell lines were collected and exosomal miRNAs extracted. miRNA microarray was performed and several elevated miRNAs specific to ovarian cancer cells were picked up. Among these, we focused on miR-99a. Sera were collected from 15 patients with HGSC (stage III and IV) and 10 healthy controls. Expression level of miR-99a was determined by miRNA RT-qPCR.
Results: miRNA microarray revealed several miRNAs were highly expressed in exosomes in patients with HGSC. In patients, serum miR-99a levels were significantly increased (4.8 fold) compared with those of healthy controls. ROC analysis showed that at the cut-off of 1.4, the sensitivity and specificity were 73 % and 80 % respectively for detecting HGSC (AUC = 0.85).
Conclusion: Exosomal miRNAs can be detected in sera of patients with HGSC and have the potential to predict ovarian cancer.
Citation Format: Akihiko Yoshimura, Kenjiro Sawada, Koji Nakamura, Yasuto Kinose, Erika Nakatsuka, Seiji Mabuchi, Tadashi Kimura. Elevated level of serum miR-99a is correlated with serous epithelial ovarian cancer and can be a potential biomarker [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 4655. doi:10.1158/1538-7445.AM2017-4655
Abstract 4656: Assessment of BCL-2, BCL-xL and MCL-1 in bone marrow biopsy samples using VENTANA BenchMark XT automated slide stainer
Authors: Streator Ashley , Villanueva Eneida C. , Holmes Burton F. , Zhang Liping 
Published: July 2017

Abstract
Immunophenotyping is essential for diagnosis and classification of most hematopoietic malignancies, and often followed by ancillary studies to understand the predictive and prognostic value of biomarkers. Immunohistochemistry (IHC) provides in-situ coupling of antigen expression with morphology of precursor B- from precursor T-lymphoblastic leukemia/lymphoma. The number of different IHC antibodies that can be applied to bone marrow (BM) biopsies is increasing concurrently with development of flow cytometry and molecular diagnostic methods.
IHC detects scattered tumor cells in Hodgkin’s Lymphoma, Multiple Myeloma (MM) and Acute Myelogenous Leukemia (AML), where key biomarkers may not be detectable by current flow cytometry methods. The goal of this study was to detect BCL-2, Bcl-xL and MCL-1 that are able to predict pre-clinical sensitivity to the drug Venetoclax. We examined the expression of these biomarkers in MM bone samples decalcified using commercially available reagents to determine whether decalcification methods impact BCL-2 family IHC Staining.
Results: MM bone samples (n=59) decalcified in Decal STAT® for 20 min, stained for BCL-2 (124) and Bcl-xL (54H6). MM bone samples (n=7) decalcified in Decal STAT® for 60 min stained for BCL-2 and Bcl-xL. Finally, eleven MM bone samples decalcified in Richard Allan Decal Solution® stained for BCL-2 and Bcl-xL. MCL-1 stained poorly with commercially available decalcification solutions. For MCL-1 to be used, additional staining optimization is required. Conclusion: BCL-2 and BCL-xL proteins can be detected in MM bone samples decalcified with commercially available solutions. With these preliminary results, future studies will pursue the potential for sensitivity to "Venetoclax (ABT-199/GDC-0199)".
Citation Format: Ashley Streator, Eneida C. Villanueva, Burton F. Holmes, Liping Zhang. Assessment of BCL-2, BCL-xL and MCL-1 in bone marrow biopsy samples using VENTANA BenchMark XT automated slide stainer [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 4656. doi:10.1158/1538-7445.AM2017-4656
Abstract 467: Analysis of human hypoxia related miRNAs in MDM2 transfected prostate cancer cells
Authors: Alobid Saad Ebrahim , Venkatesan Thiagarajan , Alaseem Ali , Alhazzani Khalid , Rathinavelu Appu 
Published: July 2017

Abstract
Recent studies have shown the crucial role of miRNAs in regulating cancer initiation, progression and metastatic process via influencing gene expression patterns. However, the distinct mechanism by which miRNA regulates tumorigenesis remains as an area requiring detailed research investigations. In our earlier studies, we have demonstrated a positive correlation between MDM2 expression and hypoxia inducible factor -1alpha (HIF-1α) levels in both normoxic and hypoxic conditions using prostate cancer cell lines. Subsequently, we postulated that the upregulation of HIF-1α is most likely regulated by MDM2 in cancers cells that are positive for this gene expression. Hence, to confirm our hypothesis, we utilized miScript miRNA PCR Array analysis (Qiagen, USA) and compared the gene expression profile of the hypoxia signaling pathway in LNCaP (prostate cancer cells) and LNCaP-MST
(MDM2 transfected prostate cancer cells) under normoxic conditions. This study was expected to outline how MDM2 impacts the differential expression of miRNAs and leading to enhancement of tumor angiogenesis via increase in HIF-1α or other genes of the hypoxia signaling pathway. Our preliminary data indicate that hsamiR99a5p, hsamiR125b5p, hsamiR1385p, hsamiR199b5p and hsalet7c5p are significantly upregulated in LNCaP-MST cells compared to LNCaP. In addition, some of the miRNAs such as hsalet7d5p, hsalet7e5p, hsalet7f5p, hsalet7g5p and hsalet7i5p are significantly downregulated in the same cells. Among the upregulated miRNAs, hsamiR125b5p emerged as an important gene that is known to downregulate the protein levels of hypoxia inducible factor 1alpha inhibitor (HIF1AN or FIH), which can normally inhibit the transcriptional activity of HIF-1α in both normoxic and hypoxic conditions. Therefore, overexpression of hsamiR125b5p seems to be associated with the increase in HIF-1α level. From the aforementioned findings, it is confirmed that the MDM2 overexpression is impacting miRNA levels such as hsamiR125b5p that are involved in hypoxia related signaling pathway. Thus, our results offer a convincing evidence that MDM2 can promote angiogenesis and increase metastatic potential of cancers through altering the miRNA expression levels. (The financial support from the Royal Dames of Cancer Research Inc., Ft. Lauderdale, Florida is gratefully acknowledged).
Citation Format: Saad Ebrahim Alobid, Thiagarajan Venkatesan, Ali Alaseem, Khalid Alhazzani, Appu Rathinavelu. Analysis of human hypoxia related miRNAs in MDM2 transfected prostate cancer cells [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 467. doi:10.1158/1538-7445.AM2017-467
Abstract 4682: Genomic profiles in gene expression and methylation help define the molecular characteristics of hairy cell leukemia subtypes
Authors: Edelman Daniel C. , Stevenson Holly S. , Wang Yonghong , Arons Evgeny , Waterfall Joshua J. , Petersen David , Zhou Hong , Meltzer Paul S. , Kreitman Robert J. 
Published: July 2017

Abstract
Hairy cell leukemia (HCL) until recently was characterized as a single blood and bone marrow malignancy, even though clinically at least two pathologies seemed to be at work. This study sought to confirm the clinical observations using genomic evidence. HCL is a chronic mature B-cell malignancy with distinctive immunophenotype, typically expressing CD20, CD22, CD25, CD11c, CD103, CD123, annexin A1 (ANXA1), and tartrate-resistant acid phosphatase (TRAP). Purine analog therapy is highly effective, with most patients achieving durable remissions. HCL- variant (HCLv) was first identified by Cawley et al. (1980) and recently recognized by the World Health Organization as a separate cancer. HCLv lacks CD25, ANXA1, TRAP, and BRAF V600E expression, and patients respond poorly to purine analogs. In order to find detailed biological information involving these two diseases, we studied the genome-wide gene expression and methylation profiles of 75 HCL patient samples; 67 were tested by both methods. Our study results indicate that HCL and HCLv show very distinct gene expression and methylation patterns. Many genes that are differentially expressed are involved in immunological and inflammatory response pathways. Several cancer associated genes such as ANXA1 and FLT3 are down-regulated in HCLv compared to HCL. Correlation patterns between methylation and gene expression for many genes such as ANXA1 suggest that methylation plays an import role in gene expression regulation for these malignancies. This study has begun the process of identifying better biomarkers for disease discrimination between HCL and HCLv and providing potential new targets for strongly needed therapies for HCLv.
Citation Format: Daniel C. Edelman, Holly S. Stevenson, Yonghong Wang, Evgeny Arons, Joshua J. Waterfall, David Petersen, Hong Zhou, Paul S. Meltzer, Robert J. Kreitman. Genomic profiles in gene expression and methylation help define the molecular characteristics of hairy cell leukemia subtypes [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 4682. doi:10.1158/1538-7445.AM2017-4682
Abstract 4685: Immune checkpoint protein VISTA is a critical regulator of the IL-23/IL-17 inflammatory axis
Authors: Li Na , Xu Wenwen , Yuan Ying , Ayithan Natarajan , Imai Yasutomo , Wu Xuesong , Miller Halli , Olson Michael , Hwang Samuel T. , Malarkannan Subramaniam , Wang Li 
Published: July 2017

Abstract
V-domain Immunoglobulin Suppressor of T cell Activation (VISTA) is an inhibitory immune-checkpoint molecule that suppresses CD4+ and CD8+ T cell activation when expressed on antigen-presenting cells. Vsir-/- mice developed loss of peripheral tolerance and multi-organ chronic inflammatory phenotypes. Vsir-/- CD4+ and CD8+ T cells were hyper-responsive towards self- and foreign antigens. Whether or not VISTA regulates innate immunity has not been demonstrated. Our current study shows that VISTA-blocking monoclonal antibody (mAb) enhanced anti-tumor T cell response, and synergized with a peptide vaccine and TLR7 agonist imiquimod as adjuvant to suppress tumor growth in the B16 melanoma model. Surprisingly, the therapeutic effect of this combination therapy was abolished in the IL17R knockout hosts, indicating that the IL-17-mediated inflammation is regulated by VISTA and is required for anti-tumor immunity in the context of VISTA blockade. To better define the regulatory role of VISTA in inflammation, we employed a murine model of psoriasis induced by topical treatment of IMQ. Our data show that VISTA deficiency exacerbated the psoriasiform inflammation. Enhanced TLR7 signaling in Vsir-/- dendritic cells (DCs) led to the hyper-activation of Erk1/2 signaling and augmented the production of IL-23. IL-23, in turn, promoted the expression of IL-17A in both TCRgd+ T cells and CD4+ Th17 cells. Furthermore, VISTA regulates the peripheral homeostasis of CD27- gd T cells, and their activation upon TCR-mediated or cytokine-mediated stimulation. IL-17A-producing CD27- gd T cells were expanded in the Vsir-/- mice and amplified the inflammatory cascade. Together, these results indicate that VISTA is a critical regulator of the IL-23/IL-17-mediated inflammatory axis. Ongoing studies will define how IL-17 regulates tumor-reactive immunity in the context of VISTA blockade and TLR vaccine adjuvant.
Citation Format: Na Li, Wenwen Xu, Ying Yuan, Natarajan Ayithan, Yasutomo Imai, Xuesong Wu, Halli Miller, Michael Olson, Samuel T. Hwang, Subramaniam Malarkannan, Li Wang. Immune checkpoint protein VISTA is a critical regulator of the IL-23/IL-17 inflammatory axis [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 4685. doi:10.1158/1538-7445.AM2017-4685