bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B22: Potential combinatorial strategies to overcome drug resistance in BRAF-mutant melanoma
Authors: Dompe Nicholas A. , Lin Eva , Peng Jing , Chan Grace , Chan Grace , Chan Grace , Tien Janet , Merchant Mark , Bourgon Richard , Settleman Jeffrey , Wilson Timothy , Neve Richard M. 
Published: May 2015

Abstract
RAF and MEK inhibitors are used to target malignant melanomas harbouring BRAF V600E mutations, but resistance to these therapies remains a significant challenge. Here we conducted a screen of 450 secreted peptides to identify possible cell-autonomous or microenvironment-driven mechanisms of resistance to RAF and MEK inhibitors in ten melanoma cell lines. We identified multiple receptor tyrosine kinase (RTK)-mediated resistance mechanisms and show that drug-resistance in vitro was driven by mechanisms predicted by the screen and that co-targeting FGFR and BRAF prevents tumour regrowth in vivo. We also found that cells can become resistant to rational combinations of targeted inhibitors in a serial manner, again predicted by the screen. In many cases resistance is mediated by reactivation of MAPK-signalling, however, there is also evidence for non-MAPK-dependent mechanisms of resistance once these are exhausted. These data reveal multiple, defined mechanisms of resistance as well as highlight potential challenges of overcoming therapeutic resistance in a highly adaptive tumour type.
Citation Format: Nicholas A. Dompe, Eva Lin, Jing Peng, Grace Chan, Grace Chan, Grace Chan, Janet Tien, Mark Merchant, Richard Bourgon, Jeffrey Settleman, Timothy Wilson, Richard M. Neve. Potential combinatorial strategies to overcome drug resistance in BRAF-mutant melanoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B22.
Abstract IA16: Acquired resistance to targeted therapeutics in hematologic malignancies
Authors: Shah Neil P. 
Published: May 2015

Abstract
Targeted treatment approaches of hematologic malignancies provided many of the first inroads into the successful treatment of human malignancy with the emerging class of targeted therapeutics. Initial responsiveness to targeted therapy provides compelling evidence for the importance of specific targets for the maintenance of disease. Understanding mechanisms of acquired resistance further informs how malignant cells can circumvent target inhibition in patients, and in some instances, these insights have facilitated the successful development of next generation targeted therapeutics, best exemplified by BCR-ABL tyrosine kinase inhibitors for the treatment of chronic myeloid leukemia (CML). As detailed genomic analyses are becoming more readily available, opportunities for developing and incorporating targeted therapeutics are expected to increase. It is becoming clear, however, that tumor heterogeneity in advanced hematologic malignancies can be substantial, and resistant subclones can compromise duration of response to targeted therapy. Several examples of acquired resistance to targeted therapeutics in human hematopoietic malignancies will be presented, as well as the implications of these molecular mechanisms toward future successful management of these diseases.
Citation Format: Neil P. Shah. Acquired resistance to targeted therapeutics in hematologic malignancies. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr IA16.
Abstract IA22: Investigating breast cancer evolution and diversity with single-cell sequencing
Authors: Navin Nicholas E. 
Published: May 2015

Abstract
Sequencing breast tumor cohorts has identified many prevalent mutations, but provides limited insight into the genomic diversity within tumors. Here, we developed a whole-genome and exome single-cell sequencing approach called Nuc-Seq that can achieve 83-97% coverage breadth with low error rates. We applied this method to sequence single normal and tumor cells from an estrogen-receptor positive breast cancer and a triple-negative ductal carcinoma, and performed copy number profiling in parallel. Our data shows that aneuploid rearrangements occurred early in tumor evolution and remained highly stable as the tumor masses expanded. In contrast, point mutations evolved gradually, generating extensive clonal diversity. Many of the diverse mutations were shown to occur at low frequencies (0.03 -10%) in the tumor mass by targeted single-molecule sequencing. Using mathematical modeling we found that the triple-negative tumor cells had an increased mutation rate (13.3X) while the ER+ tumor cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.
Citation Format: Nicholas E. Navin. Investigating breast cancer evolution and diversity with single-cell sequencing. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr IA22.
Abstract PR06: A co-clinical assessment of patterns of BRAF inhibitor resistance
Authors: Kwong Lawrence N. , Boland Genevieve , Frederick Dennie T. , Helms Timothy , Miller John P. , Jiang Shan , Cooper Zachary A. , Protopopov Alexei , Mills Gordon B. , Flaherty Keith , Wargo Jennifer A. , Chin Lynda 
Published: May 2015

Abstract
The acquired resistance of melanomas to BRAF inhibitors is now well-described, indicating many mechanisms including point mutations, amplifications, and alternative splicing. Here, we present a combined assessment of patient samples at both the RNA and protein levels. In parallel, we conducted a co-clinical mouse trial using a novel BRAF-driven model. We demonstrate that the response and resistance of the mouse melanomas closely parallels that of the human patient samples on both phenotypic and molecular levels, demonstrating multiple mechanisms of resistance that mirror the patient findings. On the basis of the combined data, we suggest that BRAF inhibitor-resistant melanomas can readily be categorized using economical and rapid protein array technology. This suggests that analyzing protein patterns offers a means of categorizing tumor resistance mechanisms even in the absence of identified driving genetic or epigenetic lesion(s). In summary, our results demonstrate the utility of a co-clinical assessment system and offer a cost-efficient means of categorizing patterns of BRAF inhibitor resistance in human patient samples within a clinically-meaningful timeframe.
Citation Format: Lawrence N. Kwong, Genevieve Boland, Dennie T. Frederick, Timothy Helms, John P. Miller, Shan Jiang, Zachary A. Cooper, Alexei Protopopov, Gordon B. Mills, Keith Flaherty, Jennifer A. Wargo, Lynda Chin. A co-clinical assessment of patterns of BRAF inhibitor resistance. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr PR06.
A Rapid Embryonic Stem Cell–Based Mouse Model for B-cell Lymphomas Driven by Epstein–Barr Virus Protein LMP1
Authors: Ba Zhaoqing , Meng Fei-Long , Gostissa Monica , Huang Pei-Yi , Ke Qiang , Wang Zhe , Dao Mai N. , Fujiwara Yuko , Rajewsky Klaus , Zhang Baochun , Alt Frederick W. 
Published: May 2015

Abstract
The Epstein–Barr virus (EBV) latent membrane protein 1 (LMP1) contributes to oncogenic human B-cell transformation. Mouse B cells conditionally expressing LMP1 are not predisposed to B-cell malignancies, as LMP1-expressing B cells are eliminated by T cells. However, mice with conditional B-cell LMP1 expression and genetic elimination of α/β and γ/δ T cells (“CLT” mice) die early in association with B-cell lymphoproliferation and lymphomagenesis. Generation of CLT mice involves in-breeding multiple independently segregating alleles. Thus, although introduction of additional activating or knockout mutations into the CLT model is desirable for further B-cell expansion and immunosurveillance studies, doing such experiments by germline breeding is time-consuming, expensive, and sometimes unfeasible. To generate a more tractable model, we generated clonal CLT embryonic stem (ES) cells from CLT embryos and injected them into RAG2-deficient blastocysts to generate chimeric mice, which, like germline CLT mice, harbor splenic CLT B cells and lack T cells. CLT chimeric mice generated by this RAG2-deficient blastocyst complementation (“RDBC”) approach die rapidly in association with B-cell lymphoproliferation and lymphoma. Because CLT lymphomas routinely express the activation-induced cytidine deaminase (AID) antibody diversifier, we tested potential AID roles by eliminating the AID gene in CLT ES cells and testing them via RDBC. We found that CLT and AID-deficient CLT ES chimeras had indistinguishable phenotypes, showing that AID is not essential for LMP1-induced lymphomagenesis. Beyond expanding accessibility and utility of CLT mice as a cancer immunotherapy model, our studies provide a new approach for facilitating generation of genetically complex mouse cancer models. Cancer Immunol Res; 3(6); 641–9. ©2015 AACR.
Targeting cancer with cys-diabody conjugated polymerized liposomal nanoparticles (PLNs)
Authors: Girgis Mark D. , McCabe Katelyn , Federman Noah , Wu Anna M. , Denny Christopher , Denny Christopher , Tomlinson James S. 
Published: May 2015

Abstract
Background: Polymerized liposomal nanoparticles (PLNs) are a promising new technology for delivery of chemotherapeutic drugs to cancer cells. They are easy to prepare, biocompatible, and can carry a wide variety of therapeutics. Additionally, PLNs have the potential to be conjugated to a tumor targeting agent in hopes of delivering a cytotoxic payload directly to the cancer cells, thus minimizing systemic toxicity. Cys-diabodies are the smallest tumor antibody fragment (55 Kd) that retain the bivalency of an intact antibody. The goal of this study was to determine our ability to conjugate various engineered cys-diabody fragments to PLNs and to evaluate the ability to specifically target tumor cells based on the specificity of the diabody-tumor antigen interaction.
Methods: Cys-diabody constructs against tumor antigens (ALCAM, HER2/neu, Ca19.9) were engineered, expressed in NSO myeloma cells and purified using HPLC. A cysteine residue was inserted at the C-terminus to provide the free sulhydryl group necessary for the conjugation reaction. Using malemide chemistry, cys-diabodies were conjugated to PLNs. Immunofluorescence and flow cytometry were performed to evaluate targeting of conjugated PLNs to human pancreatic and breast cancer cell lines. Unconjugated PLNs and tumor antigen negative cell lines were used as controls.
Results: Anti-HER2/neu, ALCAM, and CA19.9 cys-diabodies were characterized by flow cytometry showing specific binding to MCF7 (HER2/neu positive), HPAF (ALCAM positive), and BxPC3 (CA19.9 positive) cell lines, respectively. No binding was observed to antigen-negative cell lines nor with the unconjugated PLNs. Conjugation of cys-diabodies to PLNs was indicated by immunofluorescence showing specific binding of PLN-cys-diabody conjugates to breast and pancreatic cancer cells in vitro (Figure 1). These data were also confirmed by flow cytometry.
Conclusions: We have demonstrated the ability to conjugate our PLN with engineered anti-tumor cys-diabodies. Furthermore, we have demonstrated that after conjugation, the PLNs demonstrate specific tumor-cell targeting based on the specificity of the diabody-tumor antigen affinity. These studies represent an important first step in the development of targeted PLNs with the ultimate goal of delivering high doses of a chemotherapeutic directly to the cancer cells.
Comparison of PTEN protein loss and PI3K gene mutation status in breast cancer
Authors: Gelb Arnold B. , Deng Lynn , Freeman Vicki A. , Astrow Stephanie H. 
Published: May 2015

Abstract
Background: The phosphatidylinositol 3-kinase (PI3K) family of enzymes plays key roles in the transduction of cell signals, and several inhibitors of this pathway are currently in clinical development for the treatment of breast and other cancers. PI3K signaling is activated by growth factor receptors and regulated and terminated by multiple factors including dephosphorylation of the 3′ phosphate of PIP3 by the phosphatase PTEN. Reduced PTEN expression in breast cancer confers susceptibility to inhibitors of the PI3 kinase/Akt pathway. In a subset of breast cancer cases, PTEN protein has been found to be expressed at lower levels (e.g., as compared with normal breast epithelium), however, human breast cancer cells rarely have PTEN mutations. On the other hand PI3K gene mutations have been found in a majority of breast tumors.
Methods: To examine the relationship between PTEN protein loss and PI3K gene mutation, PTEN immunoreactivity was assessed semi-quantitatively using histoscores in freshly-cut sections of paraffin blocks from 26 anonymized breast cancer specimens. Sections from the same tumor blocks were used for PI3K mutation detection. One H&E-stained section was used to mark the area of tumor and 2-4 additional unstained sections were macrodissected to enrich for tumor cells, which then underwent DNA extraction. The DNA was analyzed with a commercial PI3K mutation test kit (DxS PI3K Mutation Test Kit, Manchester, UK) that detects 4 somatic mutations in exons 9 and 20 of PIK3CA in three discrete mutation groups or “buckets.”
Results: Of the 26 breast cancer specimens examined, 7 (27%) had absence of PTEN protein expression (histoscore=0) and an additional 4 (15%) had a reduction in PTEN expression (histoscore&gt;0 to &lt;50), with positive internal controls. PI3K mutations were detected in 8 (31%) of the 26 breast cancer specimens examined. Of the mutations detected, there were 4 (15%) mutations of H1047R (3140 A&gt;G), 1 (4%) of E542K (1624 G&gt;A), and 3 (12%) of E545D (1635 G&gt;T) or E545K (1633 G&gt;A).
Conclusions: There was a statistically significant correlation between PTEN loss (histoscore&lt;50) and the detection of PI3K mutations (Fisher's exact test, 2-tail P=0.003). The percentage of cases with overall PTEN loss in this specimen set was similar to previous reports of PTEN loss in breast tumors. In contrast, another report did not find concomitant PTEN loss and PI3K mutations. However, the investigators evaluated fewer samples, studied HER2 amplified breast cancer specifically, and used a different method (sequencing) to detect mutations. A three-way study that includes HER2 amplification or overexpression may be necessary to explain the discrepancy.
A second-generation microRNA-based assay for diagnosing tumor tissue origin
Authors: Aharonov Ranit , Chajut Ayelet , Spector Yael , Rosenwald Shai , Edmonston Tina B. , Barshack Iris , Feinmesser Meora , Huszar Monica , Mueller Wolf , Fogt Franz , Faerman Alexander , Meiri Eti 
Published: May 2015

Abstract
Background: Cancer of unknown primary (CUP) constitutes 3%~5% of all newly diagnosed cancer cases. It presents a major diagnostic challenge due to the therapeutic implications of the tissue origin of the cancer. Accurate tumor of origin (ToO) assignment could help guide use of specific therapy which may impact survival. MicroRNAs are a family of noncoding, regulatory RNA genes that are involved in development, differentiation and cell cycle and were shown to be involved in oncogenesis. MicroRNAs are highly tissue specific and therefore ideal candidates for CUP diagnosis. We have previously presented a biologically-motivated classification assay to identify the tissue of origin using a set of 48 microRNAs measured on a qRT-PCR platform. This assay can differentiate 25 different tumor types from 17 origins. We present here the development and validation of a second generation assay that can identify 43 different tumor types using a custom array platform. The assay is based on the normalized expression of less than 70 microRNAs. We will present performance data including inter-laboratory concordance from the validation of the assay.
Methods: Over 1200 primary and metastatic tumor FFPE samples were used for the training and development of the next generation assay. High-quality RNA, including the well-preserved microRNA fraction, was extracted from the FFPE blocks using proprietary protocols previously described. Expression levels of all known and additional Rosetta's proprietary microRNAs were profiled using a custom array platform. MicroRNAs containing information about the ToO were identified and two classifiers were developed to utilize the information of the microRNA expression patterns for the diagnosis of ToO. The assay reports a ToO based on these two classifications, where in most cases the assay result is a single ToO reported.
Results: The developed assay is able to accurately identify more than 40 tumor types based on the expression of only several dozens microRNAs. The results of a comprehensive validation study using hundreds of independent tumor and metastases FFPE samples will be presented, including inter-laboratory concordance data.
Conclusions: Previous studies have highlighted the tissue-specificity of microRNA expression, and have demonstrated their potential use for classification of human malignancies. An assay utilizing microRNA expression in a biopsy for identifying the tissue of origin was developed. Here we present the development and the performance of a second generation assay, designed to identify over 40 tumor types. This assay will provide an important new tool for diagnosing tumor tissue origin.
A streamlined, aptamer-based multiplex proteomic assay for diagnostic applications
Authors: Bock Chris , Katilius Evaldas , Keeney Tracy , Kraemer Stephan , Saccomano Nick , Sanders Glenn , Vaught Jonathan , Zichi Dom 
Published: May 2015

Abstract
To enable the application of protein signatures identified in our highly multiplexed biomarker discovery platform to real-world diagnostics, we developed a streamlined, plate-based assay that employs the same principles as the larger SOMAScan assay. The plate-based assay is sensitive (sub-picomolar), robust, rapid, automatable, and can multiplex upwards of 60 analytes. We have used this platform to seamlessly translate sets of biomarkers identified in our SOMAScan assay to a practical non-small cell lung cancer diagnostic.
Gene expression signatures associated with protracted stromal responses to therapeutically relevant cytotoxic stimuli predict breast cancer chemoresponsiveness
Authors: Lee Michael T.-L. , Su Jimmy J.-M. , Li Chi-Rong , Chu Patrick Y.-W. , Liu Ming-Sheng , Chiang Jung-Hsien , Tsai Kelvin K.-C. , Tan Kok-Tong 
Published: May 2015

Abstract
Systemic chemotherapy inflicts cytotoxic injuries on tumor cells and cells in the stromal compartment and their complex interplay may critically affect therapeutic response and outcome. Evidence has shown that gene expression profiles associated with reactive tumor stroma link to prognosis and treatment outcome in breast cancer; however, the specific stromal alterations underlying these associations await further exploration. We here show that breast carcinoma-associated fibroblasts (CAFs) responded to therapeutically relevant magnitudes of cytotoxic stimuli (TRCS) by engaging in a series of cytostatic and pro-death cell programs in a time-dependent manner. By interrogating clinical samples we found a considerable number of CAFs with similar characteristics in the stroma of breast cancer following neoadjuvant chemotherapy (NACT). Profiling the TRCS-induced transcriptomal changes of breast CAFs demonstrated that the genes involved in the protracted (day 3-7) instead of the early (day 1-3) responses were significantly associated with the responsiveness of breast cancer to NACT. To further substantiate this finding we prioritized gene markers and identified a 30-gene chemotherapy-associated stroma signature (CASS) that can predict pathological complete remission (pCR) of breast cancer following NACT with remarkable accuracy (overall accuracy 80%, P &lt; 0.01). The CASS outperformed and complemented standard clinicopathological variables and existing gene expression signatures for the prediction of pCR in several independent data sets. Thus, by exploiting the distinct pathological role of the stromal cytotoxic responses we identified strong and robust predictive markers for the intrinsic chemosensitivity of breast cancer (Supported by NHRI CA-099-PP-19 and Department of Health of Taiwan H99-TD-C-111-004 to KKT).
Navitoclax enhances the activity of taxanes in non-small cell lung carcinoma (NSCLC) models
Authors: Tan Nguyen , Malek Mehnaz , Zha Jiping , Kassees Robert , Berry Leanne , Fairbrother Wayne J. , Sampath Deepak , Belmont Lisa 
Published: May 2015

Abstract
Navitoclax (formerly ABT-263) is a small molecule that potently antagonizes the activity of Bcl-2, Bcl-xL, and Bcl-w. To determine the potential of this molecule in combination with taxane-based chemotherapy, we evaluated a panel of 33 human NSCLC cell lines with a dose matrix of paclitaxel and navitoclax. All cell lines exhibited a greater than additive response to the combination, suggesting a synergistic interaction. These results were extended to mouse xenograft tumor models, in which the combination was more efficacious than either single agent docetaxel or navitoclax. Live cell time-lapse microscopy was used to demonstrate that the addition of navitoclax to paclitaxel decreases the time from mitotic entry to cell death and changes cell fate from mitotic slippage to death during mitotic arrest. The relative levels of Bcl-xL and Mcl-1 correlate with the extent of synergy as measured by a Bliss independence model, suggesting that cancers with high levels of Bcl-xL will be relatively resistant to taxane-based therapy, but could benefit from addition of navitoclax to taxane treatment. Finally, a significant percentage of NSCLC patient samples exhibit high Bcl-xL levels, indicating the potential for broad utility of this combination in lung cancer.
Prostatic acid phosphatase expression in human tissues
Authors: Graddis Thomas J. , McMahan Catherine J. , Tamman Jennifer , Page Keith J. , Trager James B. 
Published: May 2015

Abstract
Introduction: Active cellular immunotherapy seeks to induce tumor-specific immunity in the patient and is consequently dependent on a suitable target tumor antigen. Sipuleucel-T is an autologous cellular immunotherapy that targets prostatic acid phosphatase (PAP), and has demonstrated evidence of survival prolongation in men with asymptomatic or minimally symptomatic metastatic castrate resistant prostate cancer in randomized clinical trials. PAP has been tested as a target antigen due to its high, and relatively specific, expression in the prostate. PAP expression in other human tissues was examined to help anticipate potential safety concerns associated with the development of immunity in this target.
Methods: We used a variety of approaches to analyze PAP expression, including immunohistochemistry, in situ hybridization, and quantitative polymerase chain reaction. These laboratory-based techniques were complemented with an in silico analysis of reported PAP expression in human cDNA libraries.
Results: Our studies confirmed that, while PAP expression is not restricted to prostate tissues, its expression in other human tissues is approx. 1 to 2 orders of magnitude less than that observed in the prostate.
Conclusion: The relative specificity of PAP expression in prostate tissues supports its use in immunotherapies targeting prostate carcinoma. A greater knowledge of the expression of immunotherapy targets through a range of human cancers will better define appropriate clinical settings for their use; detailed assessment of their normal tissue distribution will aid the design of future clinical protocols for monitoring the safety of these potential therapeutic regimens.