bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4538: Global and phosphoproteomic analysis of AML cell line response to phosphatase inhibitor treatment
Authors: Piehowski Paul D. , McDermott Jason E. , Hansen Joshua R. , Savage Samantha L. , Tognon Cristina E. , Agarwal Anupriya , Tyner Jeffrey W. , Druker Brian J. , Rodland Karin D. 
Published: August 2019

Abstract
In the United States, approximately 21,000 people are diagnosed with AML each year and over 10,000 AML related deaths are reported. Genomic analysis has revealed at least 11 genetic classes of AML, and more than 20 subsets can be assigned when considering the differentiation states of Leukaemic blasts. This variability has generated significant interest in the development of targeted therapies for AML. However, complex mutational patterns and a lack of pharmacological agents for most mutational events have challenged the development of effective treatments. Recent results from the Beat AML clinical trial revealed that response to drugs is associated with mutational status, including instances where drug sensitivity is specific to combinatorial mutational events.
To better understand the molecular mechanisms underpinning drug response, we performed global and phosphoproteomic analyses on 4 AML cell lines that carry mutations associated with AML: K562 with a BCR-ABL fusion, MOLM14 with a FLT3 mutation, HL60 with a RAS mutation, and CMK with a JAK3 mutation. These cell lines were each treated with a different kinase inhibitor drug for which they have a known sensitivity. Cell samples were collected prior to treatment and time points of 30 min, 3h, and 16 hrs. Frozen cell pellets were prepared for analysis using the workflow for multiplexed, deep-scale, proteome and phosphoproteome analysis developed by the NCI CPTAC program.
The goal of our Proteogenomic Translational Research Center is to develop drug response signatures allowing the use of baseline proteome and phosphoproteome measurements to predict patient drug response, providing a foundation for rational selection of combination therapies. Preliminary analysis of the data show a dynamic temporal response to drug treatment in both the global and phosphoproteome, Figure 1. Current efforts are focused on combining knowledge-driven and data-driven analysis approaches to identify the pathways associated with drug response.
Citation Format: Paul D. Piehowski, Jason E. McDermott, Joshua R. Hansen, Samantha L. Savage, Cristina E. Tognon, Anupriya Agarwal, Jeffrey W. Tyner, Brian J. Druker, Karin D. Rodland. Global and phosphoproteomic analysis of AML cell line response to phosphatase inhibitor treatment [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 4538.
Abstract 4542: The use of saliva proteins as biomarkers to predict the risk of lymph node metastasis in oral cancer
Authors: Rossi Tatiane De , Granato Daniela Campos , Ribeiro Ana Carolina , Rivera César , Heberle Henry , Telles Guilherme Pimentel , Carnielli Carolina Moretto , Brandão Thais Bianca , Santos-Silva Alan Roger , Lopes Márcio Ajudarte , Leme Adriana Franco Paes 
Published: August 2019

Abstract
Background. The most common oral cancer in the world is squamous cell carcinoma (OSCC), accounting for more than 90% of all cases of cancer in the oral cavity. Thus, the research on molecular markers associated with the development and progress of human diseases has been the subject of intense research. The findings that saliva has molecular profiles indicating systemic diseases urge the study of non-invasive diagnosis using saliva as source of potential diagnosis, prognosis and predictive based on proteomics.
Methods. 204 proteotypic peptides were selected previously based on DDA data from our own studies or retrieved from the SRMAtlas. Heavy labeled synthetic peptides were synthetized and SRM method was developed using Skyline v3.6. Saliva samples were collected from patients with lymph node metastasis (n=26) and without lymph node metastasis (n=14). Saliva proteins were digested with trypsin. Samples were randomized in R environment and analyzed in a triple-quadrupole mass spectrometer (Xevo TQ-XS, Waters). A Peptide Retention Time Calibration Mixture was spiked into the samples. Data comparison between groups was performed using Wilcoxon Mann Whitney test in R environment.
Results. In the SRM method, we monitored 68 proteins and 24 of them were found decreased in patients with lymph node metastasis in comparison with patients without lymph node metastasis. The data analysis showed that at least one protein has, by itself, a higher relative risk in the development of lymph node metastasis in patients with OSCC. Two other panel of proteins presented the same relative risk described before.
Conclusions. This study indicates a panel of potential OSCC marker proteins, which can contribute to the prognostic evaluation, the patient's risk profile and the possibility of recurrence, and guide therapeutic intervention strategies.
Note: This abstract was not presented at the meeting.
Citation Format: Tatiane De Rossi, Daniela Campos Granato, Ana Carolina Ribeiro, César Rivera, Henry Heberle, Guilherme Pimentel Telles, Carolina Moretto Carnielli, Thais Bianca Brandão, Alan Roger Santos-Silva, Márcio Ajudarte Lopes, Adriana Franco Paes Leme. The use of saliva proteins as biomarkers to predict the risk of lymph node metastasis in oral 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 4542.
Abstract 4548: The chemokine receptor CCR1 is involved in microglia stimulated glioblastoma invasion
Authors: Coniglio Salvatore J. , Ramasundaram Poornema , Fournier Neshama , Hamilton Danielle S. , Marshall Gregory , Smith Keia , Habib Diana , Merritt James R. 
Published: August 2019

Abstract
Glioblastoma Multiforme (GBM) is the most aggressive form of adult brain tumor with a median survival time of twelve months. GBM is highly resistant to conventional therapy which includes surgical resection of the tumor, radiation treatment and chemotherapy. GBM cells are highly motile and invasive resulting in infiltrative tumors with poorly defined borders. GBM tumors are heavily infiltrated with microglia cells which are known to stimulate GBM cell invasion. Our laboratory has previously demonstrated that microglia strongly stimulates GBM invasion both in-vitro and in orthotopic animal models. This interaction was found to be dependent on CSF-1R which is expressed on all tumor infiltrating macrophages/microglia. Blockade of the CSF-1R using compounds such as pexidartinib (PLX3397) can inhibit microglia/macrophage-stimulated GBM invasion in-vitro and in vivo. A variety of chemokines are upregulated in the GBM tumor microenvironment and facilitate “cross-talk” between microglia and GBM cells eliciting a chemotactic response. We have demonstrated that the chemotactic ligand, CCL3, is similarly upregulated in GBM tumors. We postulated that inhibition of CCL3 associated receptors such as C-C receptor 1 (CCR1) might also inhibit GBM invasion, thus, a CCR1 antagonist could prove efficacious for blockade of microglia-induced glioblastoma invasion in vitro. Many potent CCR1 antagonists have been described in the literature. We chose four of these compounds with two distinct structural cores, all with reported IC50’s of less than 200 nM for inhibition of CCR1 binding versus CCL3. We examined the ability of these antagonists to block microglia-stimulated glioblastoma invasion using an in-vitro coculture invasion assay. Using quantitative PCR arrays, we also show that expression of chemokines and chemokine receptor genes is greatly altered in GBM conditioned media-treated microglia. Understanding the pattern of tumor-associated macrophage/microglia chemokine secretion in GBM may present additional targets for chemotherapeutic intervention and enhance immunotherapy.
Citation Format: Salvatore J. Coniglio, Poornema Ramasundaram, Neshama Fournier, Danielle S. Hamilton, Gregory Marshall, Keia Smith, Diana Habib, James R. Merritt. The chemokine receptor CCR1 is involved in microglia stimulated glioblastoma invasion [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 4548.
Abstract 455: Innovations in large scale liquid biopsy analysis and the Broad/IBM Cancer Resistance Project
Authors: Cibulskis Carrie , Blumenstiel Brendan , DeFelice Matthew , Fleharty Mark , Abreu Justin , Adalsteinsson Viktor , Parida Laxmi , Hamilton Susanna , Getz Gad , Lennon Niall 
Published: August 2019

Abstract
Broad Genomics offers a comprehensive liquid biopsy sequencing platform designed to provide the optimal flexibility for conducting research studies in a broad range of applications including: biomarker discovery, treatment resistance monitoring, and clinical grade ctDNA profiling. By utilizing low cost, low coverage whole genome sequencing in conjunction with dual unique molecular indexed (UMI) libraries we can offer a range of analysis that allow researchers to select the most appropriate samples for whole exome profiling or for deeper coverage, higher sensitivity targeted gene panels. To date we have generated over 3000 liquid biopsy whole genome copy number profiles and purity estimates and are supporting driver projects including the Broad/IBM Cancer Resistance Project and Count Me In. The study design for the Broad/IBM effort takes advantage of the discovery potential of tissue-based sequencing combined with serial liquid biopsy analysis to elucidate resistance events by tracking clonal and subclonal populations in patient samples over time. Sourcing samples for this and other similar efforts is a major undertaking and a combination of methods for maximally broad and deep genomic profiling are required to assay patients throughout the course of care, as tumor fraction in blood fluctuates. Responding to this need, and other applications requiring increased sensitivity we have developed a high throughput, automated workflow to efficiently assay cfDNA samples with lower tumor content. Benchmarking data using healthy donor pooled cfDNA samples indicates our assay is capable of detecting &gt; 90% of variants present at ~1% minor allele fraction with less than 1 false positive variant called per megabase. This established laboratory and analytic process forms the basis of our 2Mb, 400 gene CLIA targeted assay currently undergoing validation. Through this suite of products we hope to enable an expansion of cfDNA sequencing efforts in support of clinical and research applications. Early results from emerging studies utilizing this platform to be presented.
Citation Format: Carrie Cibulskis, Brendan Blumenstiel, Matthew DeFelice, Mark Fleharty, Justin Abreu, Viktor Adalsteinsson, Laxmi Parida, Susanna Hamilton, Gad Getz, Niall Lennon. Innovations in large scale liquid biopsy analysis and the Broad/IBM Cancer Resistance Project [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 455.
Abstract 4554: IL-17-CXCR2 axis promotes breast cancer metastasis and therapy resistance through facilitating recruitment of neutrophils
Authors: Wu Lingyun , Saxena Sugandha , Awaji Mohammad , Sharma Bhawna , Singh Rakesh 
Published: August 2019

Abstract
Breast cancer is one of the most common cancer types that happens to global females. The major challenges for breast cancer include therapy resistance and metastasis. Various factors and cancer-related immune cells are involved in tumor chemotherapy resistance process, including pro-inflammatory cytokine, interleukin (IL) 17, CXCR2 ligands (pro-inflammatory chemokines) and neutrophils. They are the key players for promoting cancer progression, and numerous reports indicated them as a potential therapeutic target for various cancer types including breast cancer. However, the detailed mechanism(s) remains unclear. In the present study, we investigate the role of neutrophils in chemotherapy resistance and metastasis in breast cancer.
In our previous study, we have observed increased levels of CXCR2 ligands in chemotherapy-resistant cells comparing with Cl66 parent cells. In this study, we observed upregulated IL17, IL17 receptor (IL-17R), granulocyte colony stimulating factor (GCSF) by qRT- PCR in resistant cells compared with parent cells. We further evaluated the protein levels of CXCR2 and its ligands, IL17 and its receptor, frequencies of neutrophils and T-helper 17 (Th17) cells in primary and metastatic tumors through using immunohistochemistry method. There were higher levels of IL17R, CXCR2, and CXCR2 ligands in metastatic tumor sites in comparison to the primary tumor sites. Moreover, we observed increased levels of IL17R, CXCR2, CXCR2 ligands together with the higher frequencies of neutrophils and Th17 cells in resistant tumors than Cl66 tumors. At the same time, tumor cells treated with IL-17 increased its proliferation rate and its expression of CXCL1 & CXCL5; and the increase was all in a concentration-dependent manner. In addition, the increase of CXCR2 ligands by IL17 was inhibited when we treated the tumor cells with ERK and NF-KB signaling inhibitors, indicating both pathways are involved in the regulation of IL17-induced CXCR2 ligands secretion.
Together, our data demonstrate an IL17-CXCR2 ligands axis plays protumorigenic inflammation, facilitating therapy resistance and metastasis through recruited neutrophils.
Citation Format: Lingyun Wu, Sugandha Saxena, Mohammad Awaji, Bhawna Sharma, Rakesh Singh. IL-17-CXCR2 axis promotes breast cancer metastasis and therapy resistance through facilitating recruitment of neutrophils [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 4554.
Abstract 4558: Mapping tolerized T cell states to exhaustion phenotypes in NSCLC
Authors: Kozlova Edgar , Eikawa Shingo , Gnjatic Sacha , Losic Bojan 
Published: August 2019

Abstract
The promise of checkpoint blockade treatment has yet to be fully realized in part due to a lack of knowledge of immune exhaustion and its efficient characterization, especially in the context of immunosuppressive tumor microenvironments which effectively tolerize the immune system.
We hypothesized that mapping expression signatures defining regulatory T-cell states to previously studied and characterized exhaustion phenotypes of infiltrating T cells in NSCLC would reveal points of contact between T cell tolerization and exhaustion. Concretely, we profiled the gene expression and directly inferred CDR3/1 clonality between tolerized and immunized states in purified CD4+ T-Cells from 10 patients with ovarian or peritoneal and non-small cell lung cancer. The samples were taken before and during immunization therapy for the antigens MAGE-A3 or NY-ESO-1 over a period of 13 weeks, in the presence and absence of adjuvant to emulate the tolerized and immunized states.
Further, by modeling the regulatory T-cell states as an interaction between the tolerized and immunized with time and type of antigen allowed us to identify significant differentially expressed gene clusters and their correlation to clonality. We then projected these signatures onto single cell RNAseq data from NSCLC-TCGA to compare the identified clusters to previously identified exhaustion phenotypes. We show that antigen vaccination is immunostimulating and induces lymphocyte activation, leading to a proinflammatory environment. During an immunized stated an increase in cytokine activity, including IL2, 4, 9, 10, 13 and 17, whereas tolerized T Cells, we observe an increase in clonality, BIRC6 and IL20 apart from alterations in chromosome organization pathways and cell cycle including senescence.
In conclusion, we detail how the differences between tolerized and immunized states help unravel exhaustion mechanisms, which will ultimately identify molecular markers for exhaustion to assist during treatment and prognosis in clinical settings.
Citation Format: Edgar Kozlova, Shingo Eikawa, Sacha Gnjatic, Bojan Losic. Mapping tolerized T cell states to exhaustion phenotypes in NSCLC [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 4558.
Abstract 4559: Tumor-derived Galectin-1 promotes tumor growth in an orthotopic C57Bl/6 NB mouse model
Authors: Fest Stefan 
Published: August 2019

Abstract
Question
We recently introduced the carbohydrate-binding protein Galectin-1 (Gal-1) as a novel tolerogeneic molecule in neuroblastoma (NB). NB-secreted Gal-1 suppressed the maturation of dendritic cells (DC) and inhibited T cell function. Here, we focused on the question whether tumor-derived Gal-1 is the decisive factor to promote tumor growth in our model for NB.
Methods
C57Bl/6J-derived orthotopic growing NB cells (named NB975A) were used for all culture as well in vivo experiments. Gal-1 knock-down clones (GL) were generated by stable transfection of wt NB975A cells (NBA) with the antisense Gal-1 expression vector (NBA-GL), (kindly provided by Dr. Rabinovich). Blasticidine resistant (5 mikrogram/ml) transfectants were cloned by limited dilution. Protein expression of Gal-1 was determined by Western blot. Orthotopic NB tumors were generated in C57Bl/6J wild type and Gal-1-knock-out (Lgals-/-) female mice by subcapsular tumor cell injection of NBA-GL or wild type NBA (1x106, 0,1 ml PBS) into the left kidney. Primary tumor growth was analyzed by using high frequency ultrasound measurement. Mice were sacrificed 23 days after tumor inoculation and tumor tissue was harvested for further analysis.
Results
NBA-GL showed 50% reduced protein expression of Gal-1 compared to control wild type NBA cells. In vitro viability and proliferation of the tumor cells was not affected by the transfection. Mice inoculated with NBA-GL cells had significantly smaller primary tumors when compared with control animals that received the NBA cells. Gal-1 sufficient tumor cells injected in Gal-1-deficient host mice grew normally.
Conclusion
Tumor-derived Gal-1 and not its expression in host is critical for the promotion of tumor growth.
Citation Format: Stefan Fest. Tumor-derived Galectin-1 promotes tumor growth in an orthotopic C57Bl/6 NB mouse model [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 4559.
Abstract 4560: In situ multiplex analysis of regulatory and effector T cells in multiple tumor types
Authors: Baranova Elena , Tliba Maroua , Motte Manon , Defort Naomi , Finan-Marchi Amanda , Lazzaro Domenico , Estermann Fanny , Coton Jean-Philippe , Burrer Renaud 
Published: August 2019

Abstract
Immune-mediated rejection of cancer is prevented in part by the suppression of T effector (Teff) cells by regulatory T (Treg) cells. Favorable survival in numerous types of cancer has been associated with high Teff to Treg cells ratios as determined by flow cytometry or analysis of immunohistochemistry on serial sections. Multiplex immunofluorescence offers a technical advantage by allowing the detection of co-expression and spatial organization of up to 6 targets within a preserved tissue architecture on a single slide. We have designed a multiplex immunofluorescence protocol to identify human and murine Teff and Treg cells in situ. Human tissue microarrays of tumors in a range of tissues were investigated with a multiplex panel consisting of CD3/CD4/CD8/CD45RO/FoxP3/CD25. After multi-spectral acquisition, the T cell populations could be easily phenotyped and localized in all of the tissue types examined. The multiplex panel was then applied to non small cell lung carcinoma tumor and control tissues. Treg and Teff populations were quantified. The approach presented here demonstrates the power of multiplex immunohistochemistry in the identification and quantification of multiple immune cell populations on a single tissue section and the potential application of this method in both preclinical and clinical studies.
Citation Format: Elena Baranova, Maroua Tliba, Manon Motte, Naomi Defort, Amanda Finan-Marchi, Domenico Lazzaro, Fanny Estermann, Jean-Philippe Coton, Renaud Burrer. In situ multiplex analysis of regulatory and effector T cells in multiple tumor types [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 4560.
Abstract 457: HER2, AR protein expression and chromosomal instability in circulating tumor cells (CTCs) of metastatic breast cancer (MBC) patients (pts)
Authors: Ontiveros Priscilla , Landaverde Connie , Levin Maren K. , Hippely Sarah , Landers Mark , Wang Yipeng , Dittamore Ryan , O'Shaughnessy Joyce A. 
Published: August 2019

Abstract
Background: Upregulation of HER2 and AR protein expression, and increase in chromosomal instability, are mechanisms of acquired resistance to endocrine therapy, and are being investigated as treatment-guiding biomarkers. However, measurement of these biomarkers requires metastatic biopsies, which are costly, invasive, and prone to under-sampling which precludes their utility to guide treatment in late stage metastatic pts. A CTC-based test could expand the clinical utility. Using the Epic Sciences platform, MBC blood samples were characterized for CTC prevalence, HER2 and AR expression on CTCs, and CTC chromosomal instability at time of disease progression.
Material and methods: Blood samples were acquired from 127 total pts with HR+/HER2-, HR-/HER2+ and TNBC metastatic breast cancer pts. 114 samples were analyzed for HER2 and 110 were analyzed for AR using the Epic CTC Platform. Single-cell whole genome sequencing was performed on 157 CTCs from 19 pts to assess large scale transitions (a surrogate of chromosome instability) and gene copy number alterations.
Results: 87/114 (76.3%) of pts had detectable CTCs, with a median of 1.1 CTC/mL. 17/114 (14.9%) had at least one HER2(+) CTC, 21/110 (19.1%) had at least one AR(+) CTC, and 10/110 (9%) had both AR(+) and HER2(+) CTCs detected in technical replicates. HER2 expression on individual CTCs showed distinctive cytoplasmic membrane staining, and AR expression on individual CTCs showed frequent nuclear localization. The majority of HER2+ and AR+ CTCs had high cytokeratin expression. Most pt samples showed heterogeneous expression of these markers at disease progression indicating subclonal sensitivity to targeted therapies. CTCs with larger nuclear area and higher N/C ratio had higher frequency of chromosomal instability. ERBB2, FGFR1 gain, PTEN, CDH1, BRCA1, BRCA2 loss were frequently observed and the prevalence were associated with CTC phenotypes.
Conclusions: CTCs are detected in most MBC pts upon disease progression. CTC based biomarkers assessing HER2, AR and chromosomal instability status could guide therapy selection. The results warrant prospective evaluation of these biomarkers on MBC pts’ CTCs as a resistance marker for targeted therapies.
Citation Format: Priscilla Ontiveros, Connie Landaverde, Maren K. Levin, Sarah Hippely, Mark Landers, Yipeng Wang, Ryan Dittamore, Joyce A. O'Shaughnessy. HER2, AR protein expression and chromosomal instability in circulating tumor cells (CTCs) of metastatic breast cancer (MBC) patients (pts) [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 457.