bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4098: A heavy chain only antibody against CTLA4 with outstanding preclinical efficacy and safety profile
Authors: Liu George , Gan Xin , He Yun , Zhao Jiuqiao , Duan Huayan , Rong Yiping 
Published: August 2019

Abstract
Anti-CTLA-4 antibodies are one of the only three types of immune checkpoint inhibitors (together with anti-PD-1 and anti-PD-L1 antibodies) with proven monotherapy value in cancer therapy. Despite demonstrated efficacy, their broad application in monotherapies and combinational therapies are hampered by the safety profiles. Evidence in animal models suggests that efficacy of anti-CTLA-4 antibodies is at least partially due to depletion of regulatory T cells (Treg) via ADCC function, whereas clinically adverse events are positively correlated with systemic exposure.
Here we embarked to develop the next generation anti-CTLA-4 antibody with better efficacy and safety profile. Fully human Heavy Chain only antibody (HCAb) 4003-2 was generated using the Harbour HCAb transgenic mouse platform. 4003-2 specifically binds to CTLA-4 and blocks its binding to B7.1/B7.2. It was optimized to have enhanced ADCC function that affords superior ability to deplete Treg cells both in vitro and in vivo. 4003-2 showed in murine tumor models significantly more potent anti-tumor activity than other CTLA4 antibodies, at least partly driven by substantially enhanced depletion of intra-tumoral Treg cells. In addition, due to its shorter serum half-life, 4003-2 has less systemic drug exposure in vivo at efficacious doses, suggesting potentially improvement of safety profile in clinical applications.
The augmented efficacy and safety profile of 4003-2 present it as an excellent candidate for the development of next generation anti-CTLA4 therapy.
Citation Format: George Liu, Xin Gan, Yun He, Jiuqiao Zhao, Huayan Duan, Yiping Rong. A heavy chain only antibody against CTLA4 with outstanding preclinical efficacy and safety profile [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 4098.
Abstract 41: A novel high-throughput microfluidic drug screening platform using pancreatic ductal adenocarcinoma derived organoids
Authors: Kramer Bart , Paassen Wijnand van , Haan Luuk de , Lanz Henriette , Joore Jos 
Published: August 2019

Abstract
Pancreatic cancer is one of the deadliest tumors due to the limited treatment options and late diagnosis. Here, we describe a novel high throughput drug screening platform combining a microfluidic based 3D-culture plate, and the recently described pancreatic ductal adenocarcinoma (PDAC) derived organoids. The microfluidic plate is a high throughput microfluidic 3D cell culture platform, supporting physiologically relevant models with a minimal requirement of cell material and enabling a wide range of flow and co-culture options (e.g. with blood vessels). Organoids were derived from human PDAC xenografts and seeded in the microfluidic plate. The low amount of tissue material required (4000 cells per chip) and the high number of replicates on one plate (n=96 on a standard microtiter format plate) renders the microfluidic plate an efficient and cost-effective platform for drug screening and toxicity assays on complex, 3D models. Organoids were exposed to various chemotherapeutic drugs for 72 hours. The viability of the organoids before and after drug treatment is monitored with standard viability assays and subsequently used to generate dose response curves. In conclusion, we showed that the microfluidic plate can be used for high throughput drug screening assays and toxicity screening, and demonstrated its compatibility with human pancreatic PDAC derived organoids.
Citation Format: Bart Kramer, Wijnand van Paassen, Luuk de Haan, Henriette Lanz, Jos Joore. A novel high-throughput microfluidic drug screening platform using pancreatic ductal adenocarcinoma derived organoids [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 41.
Abstract 4109: Functional profiling of 17,000 open reading frames identifies regulators of PDL1 expression in HNSCC
Authors: Mann Jacqueline , Devenport Samantha , Kulkarni Aditi , Hoesli Rebecca , Foltin Susan , Michmerhuizen Nicole , Nesvizhskii Alexey , Brenner Chad 
Published: August 2019

Abstract
The interaction of Programmed Death Ligand 1 (PD-L1) with the PD-1 receptor serves as an immune checkpoint, dampening anti-tumor immunity. While immunotherapies targeting this pathway (Pembrolizumab and Nivolumab), were approved for use in recurrent and metastatic head and neck squamous cell carcinoma (HNSCC) in 2016, overall response rates are low and few biomarkers have been identified to differentiate responders. We expect a more detailed understanding of PD-L1 checkpoint regulation in HNSCC to provide insight toward addressing these deficits. Thus, we developed a high- throughput screening protocol to discover signals modulating PD-L1 expression. We have employed a lentiviral open reading frame (ORF) library for overexpression of over 14,000 different genes in a pooled format. UM-SCC-49 cells transduced with this library were stained for cell surface PD-L1 and sorted by flow cytometry to select cells with enhanced PD-L1 expression. Sequencing of the selected sub-population was performed to determine ORFs enriched over an unsorted pool. To validate a role for individual target genes in modulating PD-L1 expression, monoclonal populations were expanded from the sorted pool and evaluated for PD-L1 expression. We confirmed increased PD-L1 expression in 7 of these cell lines over wild-type and LacZ overexpressing controls via western blotting and flow cytometry. Furthermore, we selected 5 ORFs of interest overrepresented in the sorted pool for further validation using stably expressed V5 tagged constructs. Target gene expression was confirmed by western blot, and enhanced cell surface PD-L1 expression was validated via flow cytometry for 4/5 cell lines. Thus, we provide evidence for successful identification of signals regulating PD-L1 using a novel high-throughput overexpression screen. Future experiments will aim to clarify the mechanism of PD-L1 induction in response to the signals identified here, and may ultimately provide a more thorough understanding of genetic factors modulating immunosuppression and response to immunotherapy in HNSCC patients.
Citation Format: Jacqueline Mann, Samantha Devenport, Aditi Kulkarni, Rebecca Hoesli, Susan Foltin, Nicole Michmerhuizen, Alexey Nesvizhskii, Chad Brenner. Functional profiling of 17,000 open reading frames identifies regulators of PDL1 expression in HNSCC [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 4109.
Abstract 412: Application of a serial liquid biopsy ctDNA assay for monitoring efficacy of anti-angiogenic lung cancer therapy
Authors: Minarik Marek , Svaton Martin , Belsanova Barbora , Semyakina Anastasiya , Baxa Jan , Fiala Ondrej , Pesek Milos , Benesova Lucie 
Published: August 2019

Abstract
INTRODUCTION: Patients in advanced stages of non-small cell lung carcinomas (NSCLC), who and unsuited for targeted biological therapy because of lack of actionable molecular predictors are frequently treated by anti-angiogenic therapy. The effectiveness of such therapy is primarily relying on imaging techniques including CT or hybrid PET/CT evaluating a combination of morphological factors (dimensions and volume) and, more recently, also functional parameters including the metabolic activity, tumor vascularization etc. The ability to track the course of the disease at the same time all of these parameters is prerequisite to enable timely monitoring and therapy change in case of an early detection of resistance. This study was aimed at utility of circulating-tumor DNA (ctDNA) as an tool for monitoring of therapy response. and assessment of phenotypic parameters of the tumor.
PATIENTS AND METHODS: A total of 50 patients with confirmed Stage IV lung adenocarcinomas showing negativity on ALK, BRAF, EGFR, RET, ROS1 and MET predictors were prospectively enrolled into the study. Patients were treated under a standard protocol by a combination of paclitaxes/carboplatin/bevacizumab and followed by dual PET/CT. For each patient cytology tissue sample was subjected to test for a panel of somatic mutations. The found mutations were subsequently detected in ctDNA in plasma extracted from peripheral blood collected prior to therapy start and then in 1-month intervals during the therapy. The occurrence and quantity of ctDNA were correlated with the objective therapy response (RECIST) and to the functional imaging parameters of metabolic activity and vascularization.
RESULTS: ctDNA was initially positive in 29 patients. ctDNA levels closely reflected the response to the therapy with complete or partial remission expressed as reduction or absence of ctDNA, while disease stabilization or progression signaled by persisting or increasing ctDNA levels. There was a borderline correlation between ctDNA and vascularization evaluated by dual PET/CT (p=0.055).
CONCLUSION: In a subset of patients ctDNA can readily serve as a surrogate marker for semi-continuous monitoring of the effect of anti-angiogenic therapy. Work supported by Czech Ministry of Health project AZV 17-30748A.
Citation Format: Marek Minarik, Martin Svaton, Barbora Belsanova, Anastasiya Semyakina, Jan Baxa, Ondrej Fiala, Milos Pesek, Lucie Benesova. Application of a serial liquid biopsy ctDNA assay for monitoring efficacy of anti-angiogenic lung cancer therapy [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 412.
Abstract 4226: TNFRSF14 is a cell surface marker of MITF expression in melanoma
Authors: Dutton-Regester Ken , Hayward Nicholas K. 
Published: August 2019

Abstract
Background: Transcriptional ‘cell states’ (defined as the genes expressed in a cell in any given point in time) can determine response to targeted and immune-based therapies in late-stage melanoma treatment. MITF and AXL are common markers of drug-sensitive and drug-resistant ‘cell states’, respectively; and extensive heterogeneity of both cell populations have been observed in melanoma cell lines and tumors. Understanding the mechanisms controlling these ‘cell-states’ may lead to therapeutic strategies to overcome resistance and improve patient survival.
Problem: To date, certain experiments assessing cell population heterogeneity dynamics in melanoma (such as live cell sorting applications) has been limited by the lack of surface markers defining the MITF ‘cell-state’. Furthermore, existing antibodies against MITF commonly detect multiple expressed isoforms which can limit the accuracy of downstream experimental assays, such as in-cell western blot detection.
Methods and Results: To find a suitable cell surface marker defining the MITF ‘cell state’, we used the PARIS GenePattern module with data from the Cancer Cell Encyclopedia. TNFRSF14, our highest ranked gene, was highly correlated to MITF transcript expression in melanoma cell lines. We confirmed this at the protein level through western blot detection and flow cytometry. Using flow cytometry, we could accurately follow ‘cell-state’ population dynamics of AXL and MITF following shRNA knockdown of MITF and during acquired drug resistance in culture.
Outcomes: We have identified TNFRSF14 as a robust cell surface marker of MITF in melanoma. Our TNFRSF14 and AXL live cell flow protocol will be useful for those exploring ‘cell-state’ population dynamics and heterogeneity in melanoma and could contribute to new mechanistic insights of drug resistance.
Citation Format: Ken Dutton-Regester, Nicholas K. Hayward. TNFRSF14 is a cell surface marker of MITF expression in melanoma [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 4226.
Abstract 425: Development and validation of liquid biopsy assay for copy number loss in cancers
Authors: Zhang Simo , Xie Feng , Chang Amy , Zhao Zhixin , Montesinos Carlos , Wang Xiaohong , Zhou Kemin , Jia Shidong , Yu Jianjun , Du Pan 
Published: August 2019

Abstract
Introduction: Copy number loss (CNL) of tumor suppressor genes, such as PTEN, RB1 and BRCA1/2, are common and key characteristics of many cancers. However, non-invasive detection of CNL has represented a strong demand and practical challenge in the clinic. Here we report a high-sensitive liquid biopsy NGS assay coupled with a proprietary bioinformatics pipeline to profile and detect CNL using cell-free circulating DNA (cfDNA).
Method: We developed PrediSeq, a proprietary liquid biopsy NGS assay to detect CNL, in addition to SNV, indels, rearrangement, and copy number gain. We leveraged unique molecular identifier (UMI) and proprietary bioinformatics algorithm to suppress background noise caused by PCR pre-amplification and sequencing steps. In-house developed bioinformatics pipeline, DeepSea, is used for ultra-sensitive detection of CNL and other genomic alterations. Reference materials, matched tissue and plasma samples were used for assay validation.
Results: PrediSeq CNL assay was validated using serially diluted reference materials with known copy number status. The method was evaluated with the orthogonal whole-genome sequencing using a set of clinical plasma samples with matched tissues. About 82% of CNL calls (ATM, BRCA1, BRCA2, CDKN2A, RB1) in were confirmed between plasma PrediSeq and tissue WGS. In alignment with literature, CNL of ATM, CDKN2A, BRCA1, BRCA2, was observed in plasma samples of a cohort of Her2+, HR+, and triple-negative breast cancer patients. Similarly, we observed the dynamic changes of plasma-based CNL of BRCA2, PTEN, RB1, CDKN2A, ATM genes in patients of metastatic castration-resistant prostate cancer (mCRPC) and metastatic hormone sensitive prostate cancer (mHSPC).
Conclusion: PrediSeq CNL assay has been successfully developed and validated to detect copy number loss in circulation, providing valuable molecular biomarkers to guide patient selection and treatment monitoring in precision oncology and clinical drug development.
Citation Format: Simo Zhang, Feng Xie, Amy Chang, Zhixin Zhao, Carlos Montesinos, Xiaohong Wang, Kemin Zhou, Shidong Jia, Jianjun Yu, Pan Du. Development and validation of liquid biopsy assay for copy number loss in cancers [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 425.
Abstract 4273: Inhibition of autophagy increases HNSCC sensitivity to cancer therapies
Authors: Lee Yong-Syu , Skiba Justin , Kubatzke Jaimee , Nickel Kwangok P. , Kimple Randall 
Published: August 2019

Abstract
Background: Radiation and EGFR-targeted therapies are commonly used in the treatment of head and neck squamous cell carcinoma (HNSCC). These treatments fail to control a significant number of cancers resulting in a 5-year survival rate that remains around 40-50%. We have shown that both cetuximab and radiation induce autophagy, a pro-survival cellular stress response, in head and neck cancer. In this study, we examine the consequence of autophagy inhibition and investigate the molecular mechanism underlying therapy-induced autophagy.
Methods: Autophagy was assessed using a nano-Luc LC3 reporter (Promega), immunofluorescence for LC3, p62, and acridine orange in HNSCC cell lines. RNAi knockdown of EGFR and LAPTM4B were used to test the involved signaling molecules. Radiation was delivered using a RS225 cabinet irradiator at a dose rate of approximately 3 Gy/min with dose validation by TLD using custom phantoms. Cetuximab was delivered via intraperitoneal injection. Vps34 inhibitor SAR405 and ULK1 inhibitor SBI-0206965 were used to determine whether inhibition of autophagy reduces cell survival or represses cancer cell growth in the clonogenic assay. A flank xenograft model using A253 cells was used to test the combination of autophagy inhibitors and current therapies in vivo.
Results: As previously shown, both cetuximab and radiation induced autophagy by two times. Knockdown of EGFR and LAPTM4B decreased autophagy (62.5% and 65%, respectively) when assessed using the nano-Luc reporter assay. Similar results were seen using IF. Using a clonogenic survival assay, the combination of SAR405 and radiation resulted in complete loss of cell survival suggesting a radiosensitizing effect. In vivo, SAR405 treatment improved tumor control when combined with radiation or cetuximab when compared to either treatment alone.
Conclusions: Therapy induced autophagy is dependent upon expression of both EGFR and LAPTM4B. Inhibition of autophagy resulted decreased cell survival in vitro and resulted in decreased in vivo tumor growth. These results suggest that inhibition of autophagy may be a viable approach to sensitize HNSCC to anti-cancer treatments.
Citation Format: Yong-Syu Lee, Justin Skiba, Jaimee Kubatzke, Kwangok P. Nickel, Randall Kimple. Inhibition of autophagy increases HNSCC sensitivity to cancer therapies [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 4273.
Abstract 4275: Gastric cancer stem cells under starvation stress might sustain their stemness via autophagy system
Authors: Togano Shingo 
Published: August 2019

Abstract
Background: Cancer stem cells (CSCs) play an important role for the progression of carcinoma. And, CSCs have a potential of resistance to various stresses such as starvation and chemotherapy. Autophagy is an intracellular degradation system which is induced various kinds of cells under various stress. In cancer cells, autophagy is activated and has involved in cancer survival. However, the significance of autophagy in CSCs has still remained to be unknown, especially in starvation and chemotherapy stress. The aim of this study is to clarify the role of autophagy in CSCs under starvation condition.
Materials and Methods: Two scirrhousgastric cancer cell lines, OCUM-2MD3 and OCUM-12 (parent cells) were used. Side population cells (SP cells) which include many CSCs, was known to the fraction of low dyeability of Hoechst 33342 identified by FACScan. Stemness of SP cells, OCUM-2MD3/SP and OCUM-12/SP, were examined by sphere colony assay and RT-PCR using stemness markers, Nanog, Oct3/4, CD44. Then we examined the effect of autophagy in CSCs under starvation condition, as follows.Parents cells and SP cells were evaluated about autophagy. Parents cells and SP cells were incubated in the presence and absence of glucose for various time. The expression level of autophagy molecule, LC3 was examined by western blotting. The effect of an autophagy inhibitor, Chloroquine, to SP frequency was examined by FACScan.
Results: The expression of Nanogand Oct3/4, were significantly higher in OCUM-2MD3/SP rather than parent cells OCUM-2MD3. Also, these stemness markers were significantly higher in OCUM-12/SP cells rather than parent cells. The number of sphere colony was greater in both SP cells rather than that in parent cells. The expression level of LC3 was high in both SP cells, in comparison to that in parent cells under glucose deficient condition.The autophagy inhibitor,Chloroquine, significantly decreased the SP fraction in both cells.
Conclusion: CSCs might have high autophagy activity under starvation stress and sustain their stemness by autophagy system. The autophagy inhibitor,Chloroquine, might be a promising agent for gastric cancer.
Citation Format: Shingo Togano. Gastric cancer stem cells under starvation stress might sustain their stemness via autophagy system [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 4275.
Abstract 4289: ERK3 negatively regulates IL-6/STAT3 signaling via SOCS3 in cancer cells
Authors: Shakya Astha , Chen Minyi , Markey Michael , Long Weiwen 
Published: August 2019

Abstract
Extracellular signal-regulated kinase 3 (ERK3) is an atypical mitogen activated protein kinase (MAPK) which is dysregulated in several cancers including lung cancer, breast cancer and melanoma. It has a single Ser-Glu-Gly (SEG) phospho-acceptor motif in its activation loop, instead of the Thr-Xaa-Tyr (TXY) motif conserved in the classical MAPKs. Moreover, compared to the conventional MAPKs, much less is known about the targets of ERK3 signaling. Hence, to elucidate the ERK3-regulated genes and pathways, we performed gene microarray analyses of both A549 lung cancer cells and A375 melanoma cells after treatment with either a siRNA specifically targeting ERK3 or a non-targeting control siRNA. Interestingly, IL-6 target genes were found to be highly upregulated upon ERK3 knockdown. Interleukin-6 (IL-6) is a pleiotropic cytokine which signals via the JAK/STAT3 pathway. Phosphorylation of STAT3 at Tyrosine 705 (Y705) by JAK activates STAT3 in response to IL-6 stimulation. IL-6 signaling is negatively regulated by a feedback inhibitor SOCS3 (Suppressor of cytokine signaling 3), which binds to and inhibits JAK kinase activity. Interestingly, we noted that ERK3 interacts with SOCS3 from a published Yeast-two-hybrid screening. We validated the interaction between ERK3 and SOCS3 by co-immunoprecipitation assay. In addition, we found that ERK3 downregulates the phosphorylation of STAT3 at Y705. In line with its negative regulation of oncogenic STAT3 activity, ERK3 inhibits melanoma cell growth, migration/invasion and colony formation in soft agar. Taken together, we have revealed a novel role for ERK3 in suppressing IL-6/STAT3 signaling via SOCS3 in cancer cells.
Citation Format: Astha Shakya, Minyi Chen, Michael Markey, Weiwen Long. ERK3 negatively regulates IL-6/STAT3 signaling via SOCS3 in cancer cells [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 4289.