bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 129: RAD17 loss of function is synthetically lethal with the checkpoint kinase inhibitors AZD7762 or MK-1775
Authors: Shen John Paul , Srivas Rohith , Bojorquez-Gomez Ana , Licon Katherine , Sivaganesh Vignesh , Xu Jia L. , Yeerna Huwate , Gross Andrew , Li Jian Feng , Sobol Robert , Ideker Trey 
Published: August 2015

Abstract
Synthetic lethal interactions are a type of genetic interaction in which the simultaneous loss of function of two genes in combination results in cell death. Recently, there has been much interest in the discovery of drugs that are selectively toxic to cancer cells by targeting proteins that form synthetic lethal interactions with tumor specific mutations. He we have identified that RAD17 loss of function is synthetically lethal with AZD7762, an inhibitor of Chk1 and Chk2, and with MK-1775, an inhibitor of Wee1. HeLa or LN428 glioblastoma cells were selectively responsive to AZD7762 or MK-1775 following shRNA-mediated depletion of RAD17. Cells with dual knockdown of CHEK1 and CHEK2 or knockdown of WEE1 were also sensitized to RAD17 knockdown. At baseline, cells with RAD17 knockdown had greater expression of the DNA damage marker H2AX, an effect that was magnified by either chemical inhibition or siRNA-mediated knockdown of CHEK1/2 or WEE1. Accumulation of H2AX was observed primarily in S and G2 phases, RAD17 loss did not have a significant effect on cell cycle progression. The combination of AZD7762 and MK-1775 resulted in synergistic toxicity in RAD17 knockdown but not control cells. Collectively, these results demonstrate that RAD17 loss of function sensitizes cells to inhibition of S and G2/M checkpoint kinases, resulting in greater accumulation of DNA damage and ultimately cell death. We suggest that AZD7762 and MK-1775 may have greater clinical efficacy in tumors with RAD17 mutation or deletion.
Citation Format: John Paul Shen, Rohith Srivas, Ana Bojorquez-Gomez, Katherine Licon, Vignesh Sivaganesh, Jia L. Xu, Huwate Yeerna, Andrew Gross, Jian Feng Li, Robert Sobol, Trey Ideker. RAD17 loss of function is synthetically lethal with the checkpoint kinase inhibitors AZD7762 or MK-1775. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 129. doi:10.1158/1538-7445.AM2015-129
Abstract 1292: Validation study on quantitative analysis method of interrelationships between immune cells and prostate epithelial and cancer cells
Authors: Kramer Gero , Kenner Lukas , Szekeres Thomas , Shariat Shahrokh , Schwarz Sarah 
Published: August 2015

Abstract
Context based image analysis of immunohistochemically stained sections has become a topic after several studies have demonstrated that T-cell infiltration is important for survival and of prognostic value. Software algorithms for CD3 detection, epithelial gland detection and location analysis were validated using CD3 stained prostate biopsies.
Prostate biopsies (n = 96, 38 with and 58 without tumor areas) were stained with anti-CD3-antibody (DAKO) and hematoxylin and were scanned. For validation, epithelial cell (EC) structures were manually annotated in StrataQuest 5.0 (TissueGnostics) using virtual biopsies. Automated enumeration of CD3 positive cells was controlled visually. For image processing, StrataQuests Easy Gland detection algorithm (SQ-GD) was used as provided. Briefly, hematoxylin shade was used for EC nuclei detection. EC structures were segmented using nuclei compactness and area. EC density was used to detect glands. To determine the relationships, distance transform from EC was added as virtual channel. EC proximity for CD3 distribution analysis were grouped into (i) within EC, (ii) 0-20 μm, (iii) 20-40 μm, (iv) 40-60 μm or (v) more from the EC border.
Comparison of automated EC detection by SQ-GD with manually annotated EC showed a significant correlation of both methods (Pearson r = 0.74) although SQ-GD detects significantly more EC. The reason for that was that SQ-GD had to be adjusted so that missing EC areas were below 5%.
CD3+/mm2 In ECCD3+/mm2 in 0 to 20μm EC proximityCD3+/mm2 in 20 to 40μm EC proximityCD3+/mm2 in 40 to 60μm EC proximityCD3+/mm2 in more than 60μm EC proximitymanualautomanualautomanualAutomanualautomanualautoTumor300±230390±213244±131148±126231±131191±138202±134168±151159±128128±184Non tumor416±586430±240270±209147±127243±168180±143240±143171±140172±128124±277Correlation0.8230.7380.7100.8020.815
In conclusion, SQ-GD algorithm detects EC in more than 95% of EC-glands and tumor areas. EC, tumor EC and CD3+ cells detection was highly sensitive to staining artifacts at biopsy borders and to tissue folding, both of which had to be manually excluded. Interestingly, we observed no differences between the biopsies negative for prostate cancer and the positive ones. It is noteworthy that the T-cell numbers gradually decrease in correlation with the distance to the epithelium suggesting a certain immunogenicity of EC.
Note: This abstract was not presented at the meeting.
Citation Format: Gero Kramer, Lukas Kenner, Thomas Szekeres, Shahrokh Shariat, Sarah Schwarz. Validation study on quantitative analysis method of interrelationships between immune cells and prostate epithelial and cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1292. doi:10.1158/1538-7445.AM2015-1292
Abstract 130: PF-06463922, a novel next generation ALK/ROS1 inhibitor, overcomes resistance to 1st and 2nd generation ALK inhibitors in pre-clinical models
Authors: Friboulet Luc , Zou Helen , Kodack David P. , Engstrom Lars D. , Li Qiuhua , West Melissa , Tang Ruth W. , Wang Hui , Tsaparikos Konstantinos , Wang Jinwei , Timofeevski Sergei , Dinh Dac M. , Lam Hieu , Lam Justine L. , Yamazaki Shinji , Hu Wenyue , Patel Bhushankumar , Bezwada Divya , Mahmood Sidra , Lifshits Eugene , Affolter Timothy , Lappin Patrick B. , Gukasyan Hovhannes , Lee Nathan , Deng Shibing , Jain Rakesh K. , Johnson Ted W. , Shaw Alice T. , Fantin Valeria R. , Smeal Tod 
Published: August 2015

Abstract
Overcoming resistance to targeted kinase inhibitors is a major clinical challenge in oncology.
For 1st and 2nd generation ALK inhibitors acquired resistance due to ALK kinase domain mutations and/or pharmacological drug resistance are major causes for disease relapse. Here, we report the preclinical evaluation of PF-06463922, a potent and brain penetrant ALK/ROS1 inhibitor with sub to low nanomolar cell potency against ALK fusions and all known clinically-acquired resistant mutations. PF-06463922 exhibited marked cytoreductive activity in tumor xenografts driven by various ALK mutants. Furthermore, PF-06463922 led to significant regression of EML4-ALK driven lung cancer brain metastasis and prolonged mouse survival. Compared to other clinically available ALK inhibitors, PF-06463922 is unique in its superior potency against a broad spectrum of acquired ALK mutations, including the highly resistant G1202R mutant and its robust antitumor activity in the brain. Furthermore, PF-06463922 demonstrated remarkable selectivity and safety margins in a variety of preclinical studies. These results suggest that PF-06463922 may be highly effective for the treatment of patients with ALK-driven lung cancers, including those who relapsed on clinically available ALK inhibitors due to ALK secondary mutations and/or brain metastases.
Citation Format: Luc Friboulet, Helen Zou, David P. Kodack, Lars D. Engstrom, Qiuhua Li, Melissa West, Ruth W. Tang, Hui Wang, Konstantinos Tsaparikos, Jinwei Wang, Sergei Timofeevski, Dac M. Dinh, Hieu Lam, Justine L. Lam, Shinji Yamazaki, Wenyue Hu, Bhushankumar Patel, Divya Bezwada, Sidra Mahmood, Eugene Lifshits, Timothy Affolter, Patrick B. Lappin, Hovhannes Gukasyan, Nathan Lee, Shibing Deng, Rakesh K. Jain, Ted W. Johnson, Alice T. Shaw, Valeria R. Fantin, Tod Smeal. PF-06463922, a novel next generation ALK/ROS1 inhibitor, overcomes resistance to 1st and 2nd generation ALK inhibitors in pre-clinical models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 130. doi:10.1158/1538-7445.AM2015-130
Abstract 1302: High complexity flow cytometry panels to monitor target expression, T-cell activation and suppresssion by novel immunotherapies in hematomalignancy clinical trials
Authors: Sarikonda Ghanashyam , Ashok Devika , Pahuja Anil , Lameh Jelveh , Tangri Shabnam , Dakappagari Naveen 
Published: August 2015

Abstract
The renaissance of cancer immunotherapies and the positive clinical responses observed with chimeric antigen receptor modified T cells in the hematomalignancy setting has stimulated substantial interest in monitoring immune cell activation and suppression to determine efficacy, prognosis and safety in new agent investigational trials. However, immunophenotyping capacity has been limited and required multi-test tube panels. To address the growing needs of clinical trials, we have developed three fit-for-purpose high complexity (10 or more markers) T-cell phenotyping flow cytometry panels on a qualified LSR FortessaTM platform that enables detection of up to 15 markers in a single test tube. The first panel allows identification of multiple phenotypes along the T-cell differentiation pathway, namely, T-naive (TN), T-stem cell memory (TSCM), T-effector memory (TEM) and T-central memory (TCM) and T-effector memory RA+ (TEMRA). The second panel identifies the most common helper T-cell phenotypes such as Th1, Th2, Treg, and Th17. A third panel determines the functional status of T-cells (e.g., activation vs. suppression) but also enables quantitation of important checkpoint inhibitor expression (e.g., PD-1) on T-cells of interest. These high complexity flow cytometry panels can serve as powerful tools for comprehensive examination of T-cells in a small volume of patient specimen. We believe these new flow cytometry panels will have a substantial impact on the determination of efficacy and safety correlates of immunomodulating agents administered alone or in combination to patients with leukemia.
Citation Format: Ghanashyam Sarikonda, Devika Ashok, Anil Pahuja, Jelveh Lameh, Shabnam Tangri, Naveen Dakappagari. High complexity flow cytometry panels to monitor target expression, T-cell activation and suppresssion by novel immunotherapies in hematomalignancy clinical trials. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1302. doi:10.1158/1538-7445.AM2015-1302
Abstract 1305: In vitro analysis of T cells effector vs regulatory function in patients with metastatic melanoma and its correlation to patient outcome
Authors: Hegde Upendra P. , Jha Sidharth S. , Chakraborty Nitya G. 
Published: August 2015

Abstract
Back ground: Metastatic melanoma is an aggressive tumor of the epidermal melanocytes with high mortality rates in patients. The anti- melanoma immune response has been extensively studied while immune based treatment strategies are showing promising activity in melanoma patients. A number of immune characteristics are evaluated as predictive and prognostic biomarker.
Methods: With approval from Institution's regulatory board, we analyzed T cells from peripheral blood of 12 metastatic melanoma patients for baseline frequency of T cells reacting against melanoma related Mart-1 27-35 epitope. We expanded CD 8+ T lymphocytes by exposing them to the Mart-127-35 epitope pulsed on autologous mononuclear cell derived antigen presenting cells ex vivo. Using magnetic bead separation techniques, we also isolated from the peripheral blood CD4+CD25+ (naturally occurring Treg) and CD4+CD25- cells and analyzed in vitro proliferation of CD4+CD25- T cells in response to anti CD3 antibody and PHA and analyzed the effects of CD4+CD25+ cells on their proliferation. Finally, we induced CD4+ T cells into Th1 or Th2 type responses and analyzed their function in vitro.
Results: There was variable degrees of CD8+effector T lymphocytes responses to the antigens in in vitro cultures from all the patients studied and their cytokine profile noted. The percentage of nTreg activity in the PBL averaged about 5% that demonstrated suppression of the CD4+CD25- T cells proliferation in response to anti CD3 antibody in about 50% of patients, but lacked suppression activity in about 50% of the patients. It was possible to generate Th1 type cells from all the patients but generation of the Th2 type cells was limited to 50%. Favorable immune characteristics were observed in majority of the patients who are responding to the treatment.
Conclusion: Our findings suggest that in vitro functional T cell immune characteristics could be examined in patients diagnosed with metastatic melanoma. Examination of these characteristics in larger number of patients diagnosed with melanoma might provide predictive marker for immune intervention.
Citation Format: Upendra P. Hegde, Sidharth S. Jha, Nitya G. Chakraborty. In vitro analysis of T cells effector vs regulatory function in patients with metastatic melanoma and its correlation to patient outcome. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1305. doi:10.1158/1538-7445.AM2015-1305
Abstract 1309: Fitness of T cells for use in cellular therapy of pediatric malignancies
Authors: Singh Nathan , Hulitt Jessica , Grupp Stephan A. , Barrett David M. 
Published: August 2015

Abstract
Despite promising clinical trial results, many patients are ineligible to receive cellular therapy, either due to an inability to harvest sufficient lymphocytes, or that the harvested cells fail to yield a clinically viable product. The ideal time to harvest these cells remains unclear, and is of significant clinical relevance.
We collected blood from pediatric patients with acute lymphoblastic leukemia (ALL) or non-Hodgkin lymphomas (NHL) at time of diagnosis and after each cycle of chemotherapy. We plated these samples overnight to deplete adherent cells, quantified the CD3+ T cell population by flow cytometry, combined these T cells with CD3/CD28 stimulatory beads at a ratio of 3 beads/cell, and measured expansion over time. These studies (Table 1) revealed that ALL samples harvested earlier in therapeutic course demonstrated enhanced ex vivo expansion. We stratified our samples into standard (SR) and high-risk (HR+VHR) disease and found that SR patients have even more robust early expansion and that this expansion ability is maintained, while high-risk samples lose ex vivo expansion ability after consolidation. Broadening this analysis to lymphoma revealed that only a fraction of NHL diagnosis samples expand ex vivo, and nearly no expansion is observed after initiation of chemotherapy.
We also examined T cell phenotype from our ALL samples, and found a correlation between expansion capability and presence of naïve T cells, and that larger terminal effector pools correlate with poor expansion.
These data represent the most detailed analysis of T cell number, function and phenotype during chemotherapy for pediatric B cell malignancies to date. They suggest that T cell fitness is considerably affected by type of chemotherapy as well as underlying malignancy, and that fitness may correlate with phenotype. These findings have direct clinical relevance, suggesting that T cells should be harvested as early as possible after diagnosis. This practice has the potential to significantly expand the pool of patients eligible for cellular therapy.
Table 1. Percentage of samples with &gt;5-fold ex vivo expansion
ALL (total)ALL (SR)ALL (HR+VHR)NHLDiagnosis80907025*Post induction82768412*Post consolidation668052*0*Post interim maintenance647846*0*Post delayed intensification618534*0*Maintenance37500*0**p&lt;0.01 compared to ALL (SR)
Citation Format: Nathan Singh, Jessica Hulitt, Stephan A. Grupp, David M. Barrett. Fitness of T cells for use in cellular therapy of pediatric malignancies. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1309. doi:10.1158/1538-7445.AM2015-1309
Abstract 1318: A protein microarray signature of autoantibody biomarkers for the detection of HER2+ breast cancers
Authors: Katchman Benjamin A. , Alam Rizwan , Field Matthew S. , Viloria Jennifer , Wallstrom Garrick , LaBaer Joshua , Engstrom Paul , Anderson Karen S. 
Published: August 2015

Abstract
Introduction:
Breast cancer is a heterogeneous disease, clinically defined by expression of the biomarkers ER, PR, and HER2, with 15-30% of breast cancers overexpressing the HER2 protein. Antibodies to tumor antigens that are present in patient sera are potential biomarkers for early detection and prognosis of breast cancer. The purpose of this study is to identify a panel of novel serum biomarkers for the early diagnosis of HER2+ breast cancer.
Methods:
We screened sera from breast cancer patients for autoantibodies using custom nucleic acid programmable protein microarrays (NAPPA). Plasmid cDNAs encoding 10,000 full-length human proteins with c-terminal GST or FLAG tags were printed on arrays with anti-GST or anti-FLAG antibodies, and transcribed and translated in situ using HeLa expression lysate. Serum samples were obtained at diagnosis from patients with stage I-III HER2+ breast cancer classified by IHC and/or FISH testing (HER2+/ER-/PR-, 47%; HER2+/ER+/PR+, 48%; HER2+/ER-/PR+, 5%). Control sera were age-matched and obtained from women undergoing screening mammography or diagnostic mammography for benign breast disease. The microarrays were screened with sera from 29 cases and 29 controls. 850 antigens were selected, displayed in microarray format, and screened with an independent set of sera 27 cases, 29 benign breast disease controls, and 25 healthy controls. Bound IgG was detected by fluorescence.
Results:
From the initial 10,000 proteins, we identified 850 proteins using cutoff values of AUC (0.68), sensitivity (0.29), and pAUC (0.0075) at 94% specificity for further analysis. From these, 50 candidate autoantibody biomarkers for the detection of HER2+ breast cancer were identified based on visual analysis and statistical cutoff values of 15% sensitivity at 98% specificity and K-statistic (≥ 0.9).
Conclusion:
We identified a 50-autoantibody serum signature for the detection of HER2+ breast cancer. Blinded validation studies are ongoing.
Citation Format: Benjamin A. Katchman, Rizwan Alam, Matthew S. Field, Jennifer Viloria, Garrick Wallstrom, Joshua LaBaer, Paul Engstrom, Karen S. Anderson. A protein microarray signature of autoantibody biomarkers for the detection of HER2+ breast cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1318. doi:10.1158/1538-7445.AM2015-1318
Abstract 1325: Evaluation of immuno-oncology related treatment in syngenic and human reconstituted immune systems
Authors: Hillairet de Boisferon Marc , Bichat Francis , Mignard Caroline , Tizon Xavier , France Damien , Mirjolet Jean-François 
Published: August 2015

Abstract
Immunotherapy based on monoclonal antibodies targeting cancer cells is now developed as a valid approach to treat cancer. Modulation of novel immune checkpoints and other targets are highly promising approaches against cancer and many other diseases. They have the potential to activate the immune system and to establish an active defense against pathological conditions. In addition, antibodies, antibody fragments, and other biologics can also have a strong impact on the immune system which needs to be evaluated early on. In order to develop and accurately evaluate these immunology linked approaches, appropriate preclinical models with relevant immunological readouts are needed at different stages of therapy development. Ideally, methods should be available that allow predictive readouts in vivo and ex vivo.
A comprehensive panel of tools was constructed and validated aiming at evaluating the modulation of the immune system by new therapies.
In immunocompetent mice, immune cells were studied for the detection of their cell surface markers, induction of proliferative phenotype, antigen-specific T lymphocyte detection, secretion of soluble mediators using FACS phenotyping, cytometric bead assay (CBA) or Luminex multiplex technologies and ELISPOT. We report on a panel of syngenic tumor models (4T1, B16-F10, CT26, EMT6, AY27, LLC1, MBT-2 and Renca) our capacity to correlate subpopulation of immune infiltrating cells (as T cells, macrophages, NK cells, granulocytic and monocytic cells) and the therapeutic effects of critical antibodies directed against Cytotoxic T lymphocyte antigen-4 (CTLA-4) and programmed death 1 membrane protein (PD-1).
In immunodeficient mice, the reconstitution of the mature human immune system with PBMC or naïve human immune system using hematopoietic stem cells was used to evaluate the modulation of those immune cells by therapies through human cytokine release and onset of graft versus host disease.
All of these tools were used in the context either of rodent syngenic models or humanized mouse models. In addition to their use in immune system modulating anti-cancer therapies, these humanized or syngenic models also have a potential application in many other therapeutic areas such as autoimmune diseases, inflammation, anti-infectives.
Citation Format: Marc Hillairet de Boisferon, Francis Bichat, Caroline Mignard, Xavier Tizon, Damien France, Jean-François Mirjolet. Evaluation of immuno-oncology related treatment in syngenic and human reconstituted immune systems. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1325. doi:10.1158/1538-7445.AM2015-1325