bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2325: Long term time-course monitoring of NK cell-mediated ADCC using the Celigo Image Cytometer
Authors: Chan Leo L. , Andrade Lucas Ferrari De , Thomas Charles A. , Kuksin Dmitry , Wucherpfennig Kai 
Published: August 2019

Abstract
Antibody-dependent cell-mediated cytotoxicity (ADCC) assay has been widely performed for immuno-oncological research. Traditionally, ADCC assays are conducted by measuring the amount of released Chromium, calcein AM, or Lactate dehydrogenase (LDH) molecules after the target cancer cells are killed by effector/antibody pair. These methods can be inaccurate due to indirect measurement of supernatant at the end point of 4 hour, however, there is a need to characterize the effects of antibody-dependent cytotoxicity for longer than 72 hours. Previously, we have demonstrated an image-based ADCC detection method using the Celigo Image Cytometer, where the target cells are stained with calcein AM and other tracer dyes to monitor cell count or viability. However, the fluorescence of these dyes can significantly diminish within a 48 hour time frame. In this work, we demonstrated the time-course monitoring of NK cell-mediated ADCC of A375 cells in the presence or absence of IL2 and antibodies for 76 hours. First, A375-ZsGreen cells were seeded into a 96-well plate with and without target antibodies. Next, NK cells with and without IL2 were added to the wells at 10:1, 5:1, 2:1, and 1:1 E:T ratios. The co-culture was allowed to incubate for 76 hours and the image cytometer was used to scan and analyze at times 0, 3, 4, 6, 24, 27, 30, 51, 74, and 76 hours. The software was able to count individual cells as well as confluence % at each time point by segmenting highly fluorescent objects in the images. We were able to show time-dependent ADCC killing with decrease in ZsGreen positive cells as the read-out. In addition, the uniformity of cell killing can be observed in the Celigo obtained whole well images. One of the most important findings was that there was regrowth of target cells after the initial 30 hours of cell killing, indicating the activated NK cells without antibodies did not eradicate the cancer cells. Therefore, the ability to perform long term time-course monitoring of ADCC is highly important to better characterize the effects of target antibodies on cell killing function.
Citation Format: Leo L. Chan, Lucas Ferrari De Andrade, Charles A. Thomas, Dmitry Kuksin, Kai Wucherpfennig. Long term time-course monitoring of NK cell-mediated ADCC using the Celigo Image Cytometer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2325.
Abstract 2373: The mechanism study of propranolol in suppressing the genesis and development of gastrointestinal cancer through simultaneously activating autologous CD8+T cells and inhibiting tumor AKT/MAPK pathway
Authors: Liao Ping 
Published: August 2019

Abstract
Background: Propranolol may exert the anti-tumor effect in cutaneous and acral melanoma by suppressing AKT and MAPK pathways. Reduced tumor growth following propranolol results from enhanced CD8+T-cell-mediated antitumor immune response.
Objective: To clarify the efficacy and mechanism of propranolol in suppressing the genesis and development of gastrointestinal cancer through simultaneously activating autologous CD8+T cells and inhibiting tumor AKT/MAPK pathway.
Methods: MTS assay was performed to detect gastrointestinal cancer cells viability, TUNEL staining was used to measure apoptosis in cell lines. IHC was used to detect the expressions of Ki67/p-AKT/p-MEK/p-ERK in tumor tissue. Flow cytometry was performed to explore the immune status of the tumor microenvironment. Clinical study has been performed by Case-control design. Subjects who had not been received neoadjuvant were randomly divided into propranolol or placebo group. Then the primary foci of gastrointestinal cancer subjects were removed by D2 gastrectomy. IHC was used to observe the immune status, tumor proliferation in tumor tissue.
Results: We found propranolol reduced cell viability in CT26WT and MFC (mice derived melanoma cell line). Furthermore, propranolol could shrink the tumor size in CT26WT and MFC xenografts (P&lt;0.0001). The frequency of CD3+CD8+ T cells in spleen was significantly elevated in propranolol-treated mice compared with controls. The IFNg and T-bet was significantly increased in the CD8+ T-cell population of propranolol treated mice tumor tissue. Propranolol reduced cell viability and induced apoptosis in AGS, HGC, SW480 and HCT116 cell line. But We did not observe differences in NCM460 cell line (human intestinal epithelial cells). Western Blot showed propranolol reduced the expression of p-AKT, p-MEK and p-ERK. In this prospective clinical study, the frequency of CD8+ was significantly elevated in tumor microenvironment. The expression of p-AKT, p-MEK and p-ERK was decreased in propranolol-treated subjects compared with controls.
Conclusion: The potential of propranolol to suppress the genesis and development of gastrointestinal cancer through simultaneously activating autologous CD8+T cells and inhibiting tumor AKT/MAPK pathway.
Note: This abstract was not presented at the meeting.
Citation Format: Ping Liao. The mechanism study of propranolol in suppressing the genesis and development of gastrointestinal cancer through simultaneously activating autologous CD8+T cells and inhibiting tumor AKT/MAPK pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2373.
Abstract 2377: Development and characterization of scFvs against TIP1/PDZ protein for cancer targeting
Authors: Singh Abhay , Kapoor Vaishali , Diebolder Philipp , Rhee Aaron , Rogers Buck , Thotala Dinesh , Hallahan Dennis 
Published: August 2019

Abstract
We identified TIP1 as a potential target to treat various cancers. TIP1 is over-expressed in glioblastoma, lung, head and neck and breast cancer. It is also a radiation inducible neo-antigen. TIP1consists of a single PDZ domain that binds the c-terminus of various cellular proteins like β-catenin, Rho, FAS, etc. It plays an important role in cell signaling, cancer development, and progression. TIP-1’s involvement in various survival pathways makes it an attractive target for anticancer therapeutics. Cancer can be targeted by different agents like antibodies (monoclonal, scFv, bi-specific, diabodies), peptides and small molecules. We will be targeting TIP1 using single-chain variable fragment (scFv) antibodies. scFv is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a peptide linker. We generated a phage-displayed scFv library (WASHU 2) from patient samples. For library screening, we cloned and purified the recombinant TIP1 protein. We used the TIP1 protein as bait for biopanning to pulldown the TIP1-binding scFvs from the library. Three rounds of biopanning were performed to enrich the specific TIP1 binding scFvs. Phage ELISA was performed to confirm the binding of the identified clones to the TIP1 protein. Approximately fifty-one clones showing positive binding to TIP1 protein were identified.We have sequenced the identified clones to verify the full length of scFv sequence. Unique clones are being characterized and developed further as targeting agents of various cancers. We found cancer specific binding of our lead scFvs in mouse models of cancer. The lead scFvs will be expressed as scFv-Fc to enhance their biological activity. We will characterize the scFv-Fcs for their binding affinity to TIP1, cancer cell surface binding, in vivo tumor targeting and tissue cross-reactivity. The scFvs having the potential to internalize will be developed as immunotoxins.
Citation Format: Abhay Singh, Vaishali Kapoor, Philipp Diebolder, Aaron Rhee, Buck Rogers, Dinesh Thotala, Dennis Hallahan. Development and characterization of scFvs against TIP1/PDZ protein for cancer targeting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2377.
Abstract 2396: Development of a new generation of dimeric, highly cytotoxic fusion proteins containing active GrB and VEGF targeting tumor neovasculature: Incorporating IgG heavy chain Fc fragments improves cytotoxicity, stability and pharmacokinetics
Authors: Mohamedali Khalid A. , Cheung Lawrence H. , Alvarez-Cienfuegos Ana , Rosenblum Michael G. 
Published: August 2019

Abstract
VEGF121 is a naturally-occurring splice variant that binds to VEGF receptors R-1 and R-2, which are over-expressed on the endothelium of tumor vasculature but not normal vasculature. The serine protease granzyme B (GrB) is capable of inducing intense cellular apoptosis through both caspase-dependent and caspase-independent multiple-cascade mechanisms. We have previously reported the expression of a fusion protein composed of Granzyme B and VEGF121 (GrB/VEGF121) and its subsequent in vitro and in vivo characterization. Here we report on the development and characterization of GrB-Fc-VEGF, which fuses the two domains via an IgG heavy chain Fc-fragment. We hypothesized that this modification, resulting in a relatively high molecular weight (133 kDa vs 80 kDa) would result in improved in vivo circulation and efficacy. VEGF inter-chain dimerization domains were modified such that dimerization occurred only through the Fc domain. GrB-Fc-VEGF121was expressed in HEK-293E cells under serum-free conditions and purified from the media by immobilized metal affinity chromatography (25 mg/L). Western blotting confirmed incorporation of both VEGF121 and GrB moieties into the construct. Comparison of GrB-Fc-VEGF121 with its expected molecular weight suggests significant glycosylation when produced in HEK293E cells. The enzymatic activity of GrB in GrB-Fc-VEGF121 was comparable to that of human GrB. In vitro studies of GrB-Fc-VEGF121 suggests improved cytotoxicity against cell lines expressing high levels of VEGFR-1 or VEGFR-2, unlike GrB/VEGF121, which targeted VEGFR-2+ cells more efficiently. Thus, the GrB-Fc-VEGF121 produced in HEK293E cells is active and has significant potential as a targeted therapeutic. In vitro cytotoxicity against an expanded panel of cells, internalization, and in vivo pharmacokinetics and efficacy against various tumor models are currently ongoing and will be presented. Research conducted, in part, by the Clayton Foundation for Research.
Citation Format: Khalid A. Mohamedali, Lawrence H. Cheung, Ana Alvarez-Cienfuegos, Michael G. Rosenblum. Development of a new generation of dimeric, highly cytotoxic fusion proteins containing active GrB and VEGF targeting tumor neovasculature: Incorporating IgG heavy chain Fc fragments improves cytotoxicity, stability and pharmacokinetics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2396.
Abstract 2421: Factors associated with abnormal cervical cancer screening results among screening compliant women in the United States
Authors: Chido-Amajuoyi Onyema Greg , Shete Sanjay 
Published: August 2019

Abstract
Introduction:
Formal guidelines recommend routine cervical cancer screening using the Papanicolaou (Pap) test and / or screening for high risk Human Papillomavirus (HPV). This study aims to describe the factors associated with abnormal cervical cancer screening outcomes.
Methods:
We analyzed data from 7,716 women, aged 30 to 65 years, who were respondents of the 2015 Cancer Control Supplement (CCS) of the National Health Interview Survey (NHIS). Weighted multinomial logistic regression was used to examine the factors associated with i) abnormal Pap test, ii) positive high-risk HPV test, as well as iii) abnormal Pap and positive high-risk HPV tests.
Results:
Overall, 16.8% [95% CI, 15.6 to 18.0] of women who screened for cervical cancer in the last 3 years, had an abnormal result. Risk of abnormal cervical cancer screening results decreased as age increased. Compared to the younger age group (30-45 years), those aged 56-65 years had lower odds of an abnormal Pap test (aOR: 0.71, 95% CI: 0.55, 0.92), positive high-risk HPV test (aOR: 0.51, 95% CI: 0.27, 0.97) or abnormal Pap and positive high-risk HPV tests (aOR: 0.55, 95% CI: 0.35, 0.88). Similarly, women who were married or living with a partner were less likely to have an abnormal Pap test (aOR: 0.83, 95% CI: 0.69, 1.00), than unmarried women. On the contrary, geographic region, race and cigarette smoking were found increase the odds of an abnormal cervical cancer screening result. Blacks were more likely to have abnormal screening results compared to Whites. Current smokers had increased odds of abnormal Pap test (aOR: 1.33, 95% CI: 1.02, 1.73) and positive high-risk HPV test (aOR: 1.94, 95% CI: 1.13, 3.32), compared to never smokers.
Discussion:
Study findings call for continued surveillance of cancer screening outcomes. More so there is a need for further studies to examine factors promoting an increased likelihood of abnormal cervical cancer screening results in populations identified in this study.
Note: This abstract was not presented at the meeting.
Citation Format: Onyema Greg Chido-Amajuoyi, Sanjay Shete. Factors associated with abnormal cervical cancer screening results among screening compliant women in the United States [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2421.
Abstract 2440: The microRNA-mRNA interactions in ALK-rearranged lung adenocarcinoma
Authors: Subat Sophia , Inamura Kentaro , Ninomiya Hironori , Nagano Hiroko , Okumura Sakae , Ishikawa Yuichi 
Published: August 2019

Abstract
Background: ALK-rearranged lung adenocarcinoma, which is responsive to ALK inhibitors, exhibits distinct clinicopathological and molecular features. In ALK-rearranged lung cancer, miRNA/mRNA expression signatures or individual miRNA-mRNA interactions have been reported. However, no study has performed integrative analysis to identify comprehensive miRNA-mRNA interactive network in this type of tumor. Therefore, we conducted this study to reveal a landscape of miRNA-mRNA interactions present in ALK-rearranged lung adenocarcinoma.
Methods: To identify differentially expressed miRNAs and mRNAs according to ALK-rearranged status, microarray expression profiling was conducted using 77 surgically resected specimens of lung adenocarcinoma with a known ALK status (42 ALK-positive and 35 ALK-negative cases). We made a multistep bioinformatics approach to build an miRNA-mRNA regulatory network observed in ALK-rearranged lung tumors.
Results: Seventy-three miRNAs (comprising 56 downregulated and 17 upregulated miRNAs) were differentially expressed according to ALK-rearranged status. The 56 miRNAs included miR-19a-3p, miR-362-5p, and miR-340-5p, all of which have been reported to be downregulated in ALK-rearranged lung tumors. On the basis of miRNA expression data, we identified 80 distinct biological processes in ALK-positive tumors, which included “proteoglycans in cancer”, “FoxO signaling pathway”, “pathways in cancer”, “mTOR signaling pathway”, and “HIF-1 signaling pathway”. The mRNA expression signature of ALK-rearranged tumors included ALK, ETV1, and CX3CL1, all of which have been
associated with lung tumorigenesis or tumor progression. Integrative analyses of miRNA and mRNA expression data revealed a refined list of putative miRNA-mRNA correlations. Of 136 putative miRNA-mRNA interactions, we identified 101 distinctive interactions with potential involvement in oncogenic machinery in ALK-positive tumors, such as miR-19a-3p/TLR2, miR-362-5p/SLC34A2, miR-1260b/ETV1, and miR-4481/CX3CL1 pairs. Network structural analysis provided a comprehensive view of complex miRNA-mRNA interactions in ALK-rearranged lung adenocarcinoma.
Conclusion: Overall, this observational study provides insight into the unique miRNA-mRNA regulatory network present in ALK-rearranged lung adenocarcinoma. Our findings, if validated, would inform future research examining the interplay of miRNAs and mRNAs in ALK-rearranged tumors.
Citation Format: Sophia Subat, Kentaro Inamura, Hironori Ninomiya, Hiroko Nagano, Sakae Okumura, Yuichi Ishikawa. The microRNA-mRNA interactions in ALK-rearranged lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2440.
Abstract 2463: Prototype open-access biomarker knowledgebase for genetic tests for breast cancer
Authors: Baker Dara , Abrams Natalie Fedorova , Bell Amanda , Colbert Maureen , Dingerdissen Hayley , Holmes Evan , Gupta Samir , Kahsay Robel , Kincaid Heather , Liu David , Mahmood A. S. M. Ashique , Bastian Frédéric B. , Robinson-Rechavi Marc , Schwartz Elena , Vijay-Shanker K. , Crichton Daniel , Mazumder Raja 
Published: August 2019

Abstract
Cancer biomarkers have become integral components of many clinical protocols and research studies. Nonetheless there still is an urgent need for more accurate, less invasive, and cost-effective biomarker tests to advance precision oncology. Despite considerable success in the preclinical setting, most candidate biomarker tests have yet to receive regulatory clearance or approval and gain market acceptance. To better understand the challenges facing modern biomarker research and facilitate access to biomarker-related information, this study aims to delineate the paths to approval of genetic tests for breast cancer. Public databases were searched to identify approved tests and respective biomarkers. A prototype format for unified biomarker information was developed iteratively due to the highly variable presentation of this data. A knowledgebase of FDA-approved genetic biomarkers for breast cancer was built as a pilot implementation of this format. This model is extensible to a larger database of biomarkers to be hosted in OncoMX (https://oncomx.org), which integrates cancer mutation, differential expression, literature mining, and pathway information. Fields in the prototype database were populated based on findings from the FDA website, PubMed, and other open-source databases. The resulting dataset is structured with the corresponding readme following the BioCompute Object (BCO) model. This BCO-compliant approach enables provenance capture and transparency of data processing, both of which are critical to large-scale data integration efforts. The adherence to BCO standards is expected to enhance the usability of the resulting data and to streamline the subsequent integration of multiple biomarker datasets. In the rapidly evolving field of oncologic biomarker research, this open-source biomarker knowledgebase offers clinicians and researchers a streamlined access to genetic tests information including corresponding genes, guides to evidence, clinical trial data, links to archival databases, and context for the behavior of the implicated gene in other disease and normal processes.
Citation Format: Dara Baker, Natalie Fedorova Abrams, Amanda Bell, Maureen Colbert, Hayley Dingerdissen, Evan Holmes, Samir Gupta, Robel Kahsay, Heather Kincaid, David Liu, A. S. M. Ashique Mahmood, Frédéric B. Bastian, Marc Robinson-Rechavi, Elena Schwartz, K. Vijay-Shanker, Daniel Crichton, Raja Mazumder. Prototype open-access biomarker knowledgebase for genetic tests for breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2463.
Abstract 2475: FLT3-Explorer: A bioinformatics pipeline for detecting low signal in FLT3 internal tandem duplications in acute myeloid leukemia
Authors: Laing Christian , Shi Wenge , Pollner Reinhold 
Published: August 2019

Abstract
Introduction. Acute Myeloid Leukemia (AML) is the most common acute Leukemia among adults with a poor overall prognosis. With over 20,000 cases in the US alone, about a third of AML patients pertain to an important oncogenic driver composed of internal tandem duplication (ITD) somatic mutations in exons 14 and 15 of the FMS-like tyrosine kinase 3 (FLT3) gene. Detecting the presence of measurable residual disease in patients with AML who are in morphologic remission has been shown to be a powerful predictor of eventual relapse. Yet, despite its importance, the ability to detect FLT3-ITD mutations is hampered by the limited sensitivity of conventional PCR-based assays in general and in Next Generation Sequencing-based assays, in part due to the difficulty to align ITD-containing reads to the reference genome.
Methods. In order to facilitate the analysis of AML samples, we developed FLT3-Explorer, a comprehensive bioinformatics pipeline composed of open source software, combined with in-house algorithms to accurately detect low levels of FLT3-ITD mutations. The input of the pipeline is unmapped reads in fastq format. The pipeline then searches for either ITD sequences previously observed in our extensive database of historical data, or a de-novo detection procedure is used to determine mutation sequences of variable lengths within the FLT3 gene. To assess the performance of FLT3-Explorer, we considered a cohort of clinical samples from bone marrow and peripheral blood, as well as cell lines. For sample collection, genomic DNA was isolated, and polymerase chain reaction was performed using primers flanking exons 13 and 15 to amplify the FLT3 gene. DNA was then sequenced using NGS Illumina sequencing. Results were validated using fragment size analysis by Capillary Electrophoresis assays. Also, to determine the limits of detection, various dilutions were performed on cell lines. Furthermore, to assess the performance of our pipeline, we performed a comparison with other FLT3-ITD programs publicly available.
Summary. Results from our analysis showed that our method identifies FLT3-ITD mutations of variant allele fraction as low as 0.003%. Also, we found that our pipeline can detect as many FLT3-ITD mutants as other methods, or more, when the mutant signal is considerably low.
Conclusions. FLT3-Explorer constitutes a powerful solution for low FLT3-ITD detection signal of mutant sequences, of diverse lengths, that can be used on FLT3-ITD AML patients to track disease progression and relapse.
Citation Format: Christian Laing, Wenge Shi, Reinhold Pollner. FLT3-Explorer: A bioinformatics pipeline for detecting low signal in FLT3 internal tandem duplications in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2475.