bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3115: A single institution experience with droplet digital polymerase chain reaction (dd-PCR) liquid biopsy (LB) for therapeutic decision in advanced solid tumors
Authors: Murad Andre Marcio , Casali-da-Rocha José Claudio , Carneiro Juliana Garcia 
Published: September 2020

Abstract
Droplet digital polymerase chain reaction (ddPCR) is a promising method for analyzing minor amounts of cell-free circulating free nucleic acid (DNA and RNA) due to its high sensitivity, low cost, and fast reading, since it dispenses bioinformatics, making it an appropriate alternative to new generation sequencing (NGS) for the detection of biomarkers to guide molecularly targeted cancer therapy. The assay covers main actionable hotspot alterations across many actionable genes: EGFR(mutations), ALK (fusion, mutations), ROS1(fusion), BRAF(mutations), KRAS (mutations), NRAS(mutations), PIK3CA (mutations), ERBB2(CNV- copy number variation), ESR1(mutations), KIT(CNV) and PDGFRA(CNV). Therefore, our genes can be used in panels, both in therapeutically applied genotyping and in detecting molecular responses as well as in secondary resistance to tumors such as NSCLC, breast, cervix. rectal, GIST, melanoma and pancreas. METHODS: dd-PCR was performed using the QX200 system (BIO-RAD®, Hercules). The extraction of DNA and RNA was done using the magnetic beads technique of Thermofisher's MagMAX Kit. All samples were tested in duplicate. 54 metastatic cancer patients were tested so far: NSCLC - 14 (26%), breast - 11 (20%), colorectal - 11 (20%), melanoma - 9(17%), pancreas - 4(7%), ovarian - 3(6%) and salivary glands - 2 (4%). RESULTS: Significant genomic alterations were detected in 19 (35%) patients: 5 (9%) mutations in the KRAS G12V gene (all in colorectal cancer), 5 (9%) ERBB2 amplification (breast cancer), 2 (3.65%) EGFR L858R mutations (NSCLC), 2 (3.5%) EGFR del19 mutations (NSLC), 2 (3.5%) EGFR T790M mutations (NSCLC), 2 (3.5%) BRAF-V600E mutations (colon and melanoma), 1 (1.8%) ALK-EML4 fusion (NSCLC). The MAF (Mutant Allele Fraction) ranged from 0.9% to 24%. In all cases, the results were decisive for the indication or change of a targeted therapy. Median turnaround time was 36 hours and the average cost of the panels was around 500 USD (median of 4 genes per panel). CONCLUSION: Our results suggest that dd-PCR is a highly sensitive method and could be used for a routine laboratory detection of the important genomic variations to determine the targeted therapy in patients with varied advanced solid tumors.
Citation Format: Andre Marcio Murad, José Claudio Casali-da-Rocha, Juliana Garcia Carneiro. A single institution experience with droplet digital polymerase chain reaction (dd-PCR) liquid biopsy (LB) for therapeutic decision in advanced solid tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3115.
Abstract 3125: Disturbance of CALR mutation profile in MPNs by NGS and Real-Time PCR
Authors: Rencuzogullari Cagla , Bozdogan Sevcan Tug , Guvenc Birol , Bisgin Atil 
Published: September 2020

Abstract
Myeloproliferative neoplasms (MPNs) are clonal disorders which are driven by one of three driver mutations that cause activation of JAK/STAT signaling. MPNs have classically been divided into three main conditions; essential thrombocythemia (ET), polycythemia vera (PV) and primary myelofibrosis (PMF). CALR mutations act as a driver mutation early in the pathogenesis of these disorders and the mutations in exon 9 of CALR gene occur in approximately 30% of patients with MPNs. Thus, in this study CALR mutation profiling had been performed by real time PCR then the next generation sequencing (NGS) to identify the differential genetic profile of Turkish population in MPNs. Genomic DNA was isolated from peripheral blood samples. A real time PCR test was used to detect c.1092_1143del variant, c.1154_1155insTTGTC variant and other 34 minor variants (Ipsogen CALR RGQ PCR Kit). Then the minor variants and possible other variants were identified via NGS (GeneReader NGS System). CALR mutations were detected in 34/128 of the patients. Among the 34 patients with CALR mutations, 15 of them had at least one mutation and 19 had at two mutations. 22 of 34 patients who were classified as in minor variants by real time PCR, were then studied via NGS to specify the mutations. The detected sub-variants are shown at Table 1. Interestingly, five mutations that are unique and not included in the real time PCR were identified by sequencing. Identification of the driver mutations are important for disease diagnosis and progress. Though, our study shows the disturbance of the mutations in Turkey together with the redundance of real time PCR and NGS data.
Identified CALR mutations by NGSVariant DetectedTotal Number of Patientsc.1099_1150delCTTAAGG10c.1142_1144delAGG7c.1100_1101delTTinsAC1c.1154_1155insTTGTC6c.1124A&gt;G1c.1103_1136del AGGAGGA1
Citation Format: Cagla Rencuzogullari, Sevcan Tug Bozdogan, Birol Guvenc, Atil Bisgin. Disturbance of CALR mutation profile in MPNs by NGS and Real-Time PCR [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3125.
Abstract 314: Micropatterning supported method for cancer spheroid assays under flow and high throughput CAR-T cell potency assay with single cell resolution
Authors: Horn Elias , Balles Miriam , Fischbeck Angelika J. , Schwarz Jan , Thyssen Dane A. , Drell David W. , Noessner Elfriede , Zantl Roman 
Published: September 2020

Abstract
Tumor spheroids, organoids, and cell culture models demand defined cell-cell and cell-matrix interactions, ideally with specific cell attachment on adhesion sites for multicellular spheroids or single cells. Our bioinert based micropatterning technology allows for the creation of adhesion spots while the surrounding passivated area is biologically inert, not interfering with the assay.We use this micro-patterning of adhesion ligands on highly passivated surfaces to generate homogenously distributed spheroids within a microfluidic channel system which can be perfused. Spheroids can either be directly generated by a simple injection of a large number of cells and a self-sorting process or by the addition of pre-formed spheroids, which will bind to the patterned adhesion sites. Perfusion of the spheroid chip enables the homogenous supply of all spheroids with nutrients and oxygen, and also the application of a defined shear stress, metabolite analysis together with toxicological screenings or even co-culture of multiple spheroid types. Applying a flow increases the overall spheroid growth, but condenses the cell aggregate, as well as influences the drug triggered protein expression response towards a more in vivo-like reaction.We also use this technique to generate arrays of homogenously distributed single cancer cells to evaluate cytotoxic T cell activity on a single cell level. By optical analysis combined with machine-learning based image processing of cell / spheroid arrays we obtained efficient label-free analysis of each cancer cell - T cell interaction over time.
Citation Format: Elias Horn, Miriam Balles, Angelika J. Fischbeck, Jan Schwarz, Dane A. Thyssen, David W. Drell, Elfriede Noessner, Roman Zantl. Micropatterning supported method for cancer spheroid assays under flow and high throughput CAR-T cell potency assay with single cell resolution [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 314.
Abstract 3171: Biomarkers of responses to immunotherapy in advanced hepatocellular carcinoma
Authors: Ting Vox Z. , Chew Valerie , Wong Carmen C. , Yau Thomas C. 
Published: September 2020

Abstract
Biomarkers from the peripheral blood may serve as a useful tool to identify who will likely benefit from immunotherapy in patients with advanced hepatocellular carcinoma; hence, oncologists might be able to monitor treatment responses regularly via blood tests in addition to routine radiological assessment. To investigate immune profiles of patients with advanced HCC after exposure to immunotherapy by analysing circulating T cells from peripheral blood, our study included stage IV HCC patients (n = 14) seen at the Department of Medical Oncology, Queen Mary Hospitals. Nine patients received PD-1/PD-L1 inhibitor immunotherapy at the discretion of their clinicians, and five treatment-naïve patients were included as a control group. A control group of healthy subjects was also included in the study. Samples from patients who received PD-1/PD-L1 inhibitor therapy were collected after the treatment response was confirmed by radiological assessment. T cell profiles and exhaustion markers were compared along with treatment response as determined by radiological assessment.
A total of 14 HCC patients were enrolled in the study: 4 patients showed a partial response to PD-1/PD-L1 inhibitor treatment, 5 patients progressed during PD-1/PD-L1 inhibitor treatment, and 5 patients were not treated with PD-1/PD-L1 inhibitors. Five buffy coat samples from healthy subjects were included as controls. Decreases in the percentage of regulatory T cells (0.8% of T cells in responders, p&lt;0.0001) and in the ratio of effector memory T cells to regulatory T cells (EMT/Treg) were noted in patients who responded to PD-1/PD-L1 inhibitor therapy compared to those who did not, and thus may serve as biomarkers for immunotherapy responses in HCC. Similarly, we observed decreases in Tim-3 (2.09%, p&lt;0.0001) and OX-40 (6.12%, p&lt;0.0001) expression between responders and non-responders, and thus expression levels of these factors could potentially serve as response predictors. An increase in the proportion of CD4 CD8 double-positive (DP) T cells in peripheral blood was observed in immunotherapy responders (16.63%) versus non-responders (4.03%, p&lt;0.05). Biomarkers in circulating T cells allow the investigation of immune profiles after treatment with immunotherapy using non-invasive approach from peripheral blood. Coupled with conventional surveillance strategies, we have identified biomarkers may serve as predictors for HCC patients who will likely benefit from immunotherapy.
Citation Format: Vox Z. Ting, Valerie Chew, Carmen C. Wong, Thomas C. Yau. Biomarkers of responses to immunotherapy in advanced hepatocellular carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3171.
Abstract 3192: Quanticell, a novel histopathology technology for visualization and quantitation of membrane PSMA demonstrated in cell lines and clinical tissue
Authors: Dimant Hemi , Gandhi Ankit , Maker Micheal , Markman Adam , Reinhardt Jeanette , Collins Stefan , Hesterman Jacob , Krueger Joseph , Bloom Kenneth , Bailis Julie , Juan Gloria 
Published: September 2020

Abstract
Prostate specific membrane antigen (PSMA), being both a biomarker and a therapeutic target, is important in prostate cancer (PC) diagnosis and treatment. Imaging and pathology are two of the most widely used approaches for PSMA detection in the diagnosis of PC. However, these techniques lack sensitivity for accurate assessment of low levels of PSMA expression and lack the capabilities to properly characterize heterogeneous PSMA expression. When using anti-PSMA imaging ligands, radiotherapies or immunotherapies, these drawbacks may ultimately prevent proper diagnosis and response prediction and could deny anti-PSMA treatment to qualified patients that have low PSMA expression. Better, more sensitive detection methods are needed for improved PSMA-based diagnosis and prediction of response. Quanticell is a novel histopathology technology utilizing fluorescent nanoparticles that are compatible with standard immunostaining practices. Combined with a dedicated software, Quanticell provides increased sensitivity and quantification and a wide dynamic range for improved detection and characterization of a broad range of target expression. A pilot study was conducted to demonstrate this technology on PSMA-expressing cell lines and clinical samples, and to evaluate its utility for discovery research and clinical studies. An anti-PSMA Quanticell protocol was developed and optimized on several PSMA-expressing cell lines, focusing on the lowest expressing sample. A dual-staining protocol for PSMA and a membrane marker was further developed to allow for detection and analysis of membrane-specific PSMA. Staining of negative and positive controls demonstrate high specificity to PSMA with high signal-to-noise that is not affected with increased primary concentration. When compared to DAB (diaminobenzidine) staining, we observed increased sensitivity in a low PSMA-expressing cell line, VCAP, indicated by increased detection of percent PSMA-positive cells. Additionally, using Quanticell, we demonstrate increased dynamic range in high expressing PSMA clinical samples compared to DAB staining, which is subject to saturation.
Citation Format: Hemi Dimant, Ankit Gandhi, Micheal Maker, Adam Markman, Jeanette Reinhardt, Stefan Collins, Jacob Hesterman, Joseph Krueger, Kenneth Bloom, Julie Bailis, Gloria Juan. Quanticell, a novel histopathology technology for visualization and quantitation of membrane PSMA demonstrated in cell lines and clinical tissue [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3192.
Abstract 3197: Serum CEA change predicts tumor regression and prognosis in locally advanced rectal cancer
Authors: Cai Zerong , Huang Lingyu , Lan Ping , Wu Xiaojian 
Published: September 2020

Abstract
Objective: To investigate the value of carcinoembryonic antigen (CEA) change in predicting pathological tumor regression and outcome for locally advanced rectal cancer (LARC) patients received neoadjuvant therapy.
Material and methods: LARC patients who received neoadjuvant therapy and radical tumor resection were retrospectively collected. The predictive value of baseline CEA, post-treatment CEA and post/pre-treatment CEA ratio for tumor regression grade (TRG), overall survival and diseases free survival were estimated by logistic regression or cox proportional hazard regression.
Results: 700 LARC patients were enrolled in the study with 475 (67.9%) cases of male patients and median age of 56 (20-87). Of the all patients enrolled, multivariate analysis showed post-treatment CEA (OR=1.142, 95% CI: 1.073-1.215, P&lt;0.001) was an independent predictor for TRG.
284 patients with elevated baseline CEA were analyzed. Among them, 168 patients (59.2%) have normalized CEA. Multivariate analysis showed post-treatment CEA (OR=1.068, 95% CI: 1.007-1.133, P=0.027), CEA ratio (OR=3.463, 95% CI: 1.269-9.446, P=0.015) were independent predictors for TRG(Table 1).
Of the all patients enrolled, multivariate analysis showed low preoperative albumin level (HR=0.919, 95% CI: 0.886-0.952, P&lt;0.001), tumor deposit (HR=3.226, 95% CI: 1.470-7.077, P=0.003), nerve infiltration (HR=3.602, 95% CI: 1.736-7.476, P=0.001), high post-treatment CEA (HR=1.029, 95% CI: 1.010-1.049, P=0.003) were independent unfavored predictors for overall survival of LARC patients.
700 patients were divided into 3 groups: A group with normal baseline CEA (n=416,59.4%); B group with normalized CEA (n=168,24.0%); C group with elevated baseline and post-treatment CEA (n=116,16.6%). The overall survival and disease free survival of group B were comparable to that of group A (P=0.588,0.053) and significantly better than that of group C (B vs. C: P=0.010, 0.003; A vs. C: P=0.007, &lt;0.001).
Conclusion: 1. Post-treatment CEA is an independent predictor for TRG of LARC patients and higher post-treatment CEA precdicted poor overall survival.
2. Post/pre-treatment CEA ratio is an independent predictor for TRG of LARC patients with elevated baseline CEA.
Citation Format: Zerong Cai, Lingyu Huang, Ping Lan, Xiaojian Wu. Serum CEA change predicts tumor regression and prognosis in locally advanced rectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3197.
Abstract 321: Novel bone microenvironment model of prostate cancer with chitosan fiber matrix and osteoblast in 3D culture
Authors: Samoto Masahiro , Matsumoto Hiroaki , Hirata Hiroshi , Ozawa Sho , Mori Junichi , Inoue Ryo , Yano Seiji , Yamamoto Yoshiaki , Matsuyama Hideyasu 
Published: September 2020

Abstract
BACKGROUND: The interaction between prostate cancer cells and osteoblast is essential for the development of bone metastasis. Recently, novel androgen receptor signal inhibitors (ARSi) have been approved for metastatic castration naïve (mCNPC), or non-metastatic castration resistant prostate cancer (nmCRPC), both of which should be pivotal to investigate the association between bone microenvironment and tumor. We established a novel 3D in vitro culture method reflecting bone microenvironment and evaluated the drug susceptibility of ARSi including enzalutamide, apalutamide, darolutamide, and abiraterone (Abi) with/without dutasteride (Duta).
METHODS: GFP-transferred C4-2 (CRPC cell line) and RFP-transferred human osteoblast differentiated from human-mesenchymal stem cell was co-cultured in chitosan nanofiber, a mimicry of 3D scaffold of bone microenvironment, coated culture plate (Cosmo bio Co., LTD). The growth of C4-2 cell was quantified using live-cell imaging and analysis system, Cell3 iMager duos (SCREEN). Abi metabolites including delta-4 abiraterone (D4A) and 3-keto-5-alfa abiraterone in C4-2 cells were measured by ESI-TOF-MS method.
RESULTS: We could non-invasively quantify the sustained growth of C4-2 cells at maximum of 30 days. IC50 of each drugs and combination effect of Abi and Duta was evaluated using this model. Combination treatment synergistically inhibited the growth of C2-4 cells compared with each drug alone. D4A, the strongest anti-proliferative metabolite of Abi under the CRPC-specific backdoor pathway, was detected from the treated C4-2 cell. These results were coincided with the effective cases of pharmacokinetics of Abi metabolites in our ongoing phase II clinical trial of combination therapy of Abi with Duta for CRPC (UMIN000027795). Furthermore, combination of abiraterone and dutasteride was most potent cell growth inhibitor than other ARis tested in this model. This model is applying for international patent (C12N 5/09).
CONCLUSIONS: Our bone microenvironment model is unique and useful to evaluate the new drug susceptibility testing in prostate cancer cells. This model may help in disclose unknown mechanisms from micro- to clinical bone metastasis in prostate cancer.
Citation Format: Masahiro Samoto, Hiroaki Matsumoto, Hiroshi Hirata, Sho Ozawa, Junichi Mori, Ryo Inoue, Seiji Yano, Yoshiaki Yamamoto, Hideyasu Matsuyama. Novel bone microenvironment model of prostate cancer with chitosan fiber matrix and osteoblast in 3D culture [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 321.
Abstract 322: A unique ex vivo tumor model: 3D co-cultured system with cancer cells and stromal tissue for drug evaluation
Authors: Takahashi Yuki , Tsukamoto Kei , Shimizu Yuki , Katayama Ryohei , Shinozaki Eiji , Nagayama Satoshi , Matsusaki Michiya , Kitano Shiro , Yamaguchi Kensei , Fujita Naoya 
Published: September 2020

Abstract
Background;Recently, three-dimensional culture model has been reported as better tumor model than 2D culture. The importance of interaction between cancer and stromal cells has been widely recognized in tumor progression and resistance against treatment. So that ex vivo model which recaptures the tumor microenvironment is required to perform drug evaluation mimicking the patient tumor tissue.
Methods; Layered 3D stromal tissues with microvascular network were produced by culturing normal fibroblasts and endothelial cells coated with the extra-cellular matrix (ECM) and natural polysaccharide, namely collagen and heparin. The layered 3D stromal tissues and co-cultured tumor were morphologically evaluated by HE staining, immunohistochemistry and immunofluorescence (IF). Drug sensitivity assay were conducted using popular colorectal cancer cell lines, and patient-derived cell lines (PDCs) established in JFCR under approved IRB. Remaining cancer cells post drug treatment were quantified by IF and imaging analysis. Furthermore, in vivo drug sensitivity was also evaluated.
Results: The CD31 positive luminal structures which shows vascular endothelial tube formation were observed intra multi-layered tissues. The dense microvascular network tended to be formed nearby cancer cells. In comparison with 2D culture model, decreased drug sensitivities were represented in the layered 3D co-cultured model. The evaluated drug sensitivities in 3D model may reflect the response of cancer cells in in vivo.
Conclusion; We developed the layered 3D stromal tissue culture system including blood micro-vessels. Our unique 3D ex vivo model appear to be a valuable tool for drug evaluation, and thus further studies are underway to confirm the usefulness of our model. Testing approved and/or developing compounds with PDCs in the model would potentially enable better prediction their efficacy.
Citation Format: Yuki Takahashi, Kei Tsukamoto, Yuki Shimizu, Ryohei Katayama, Eiji Shinozaki, Satoshi Nagayama, Michiya Matsusaki, Shiro Kitano, Kensei Yamaguchi, Naoya Fujita. A unique ex vivo tumor model: 3D co-cultured system with cancer cells and stromal tissue for drug evaluation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 322.