bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4540: Development of well characterized breast, lung, and brain cancer copy number variation reference materials
Authors: Lowe Dana Ruminski , Dickens Jessica , Huang Catherine , Konigshofer Yves , Anekella Bharathi 
Published: August 2018

Abstract
Introduction: Copy number variation (CNV), including gene amplification and deletion, can be a key driver of oncogenesis. Pathogenic CNVs are often associated with unfavorable prognosis and drug resistance, therefore detection of these types of genetic changes will be important for personalized treatment. Many tumor profiling workflows can detect CNVs in addition to somatic mutations, but well-characterized reference materials for CNVs are not widely available, which makes it difficult to assess accuracy and sensitivity. CNV content of cell lines can be variable and may change with passages, the genomic background may not be diploid, and germline and somatic variants may not be well characterized. Remnant patient samples often lack characterization and the volumes needed for such characterization and larger validation studies. Therefore, we developed and evaluated Seraseq CNV reference materials to serve as accuracy, precision, and limit-of-detection (LOD) controls for tumor profiling assay development and validation. By providing a consistent source of purified DNA with stable CNV content, these reference materials allow for repeatable assessment of clinical diagnostic assays targeting CNVs. Methods: Seraseq CNV reference materials were prepared by mixing genomic DNA with additional copies of target genes from the well-characterized cell line GM24385. Copies of ERBB2, FGFR3, and MYC were combined with genomic DNA to simulate CNVs found in breast cancer, while sequences for EGFR, MET, and MYCN were used to mimic lung and brain cancer CNVs. Three levels of amplification were targeted: +3, +6, and +12 additional copies. The copy number of each gene was precisely quantified using digital PCR and confirmed on several NGS-based assays internally and externally. Results & Conclusions: Testing revealed CNVs of each target gene were close to the expected copy number. Good correlation was observed between digital PCR data and NGS data generated internally with the Archer VariantPlex Solid Tumor assay. In addition, internal and external NGS data showed correlation and broad assay compatibility. While CNVs observed clinically can be upwards of 50 additional copies and more easily detectable, LOD controls such as those described here are imperative in evaluating assay performance. Collectively, the data demonstrate the utility of biosynthetic Seraseq CNV reference materials, which serve as superior alternatives to DNA from cell lines or patient-derived material.
Citation Format: Dana Ruminski Lowe, Jessica Dickens, Catherine Huang, Yves Konigshofer, Bharathi Anekella. Development of well characterized breast, lung, and brain cancer copy number variation reference materials [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4540.
Abstract 4543: Combined analysis of cell-free DNA methylation in plasma for early detection of NSCLC
Authors: Cao Li , Wang Hao , Dong Xu , Zhong Li 
Published: August 2018

Abstract
Introduction: Detection of cell-free DNA (cfDNA) methylations in plasma samples may provide diagnostic information for non-small lung cancer (NSCLC). Here, we evaluated 5 preselected genes for methylation analysis from patient and control plasma samples.
Method: Plasma samples were collected from 91 patients who were diagnosed with primary NSCLC with pathological or cytological confirmation. All the cases did not received any surgery or chemotherapy treatments when blood samples were collected. Meanwhile, 58 cases of healthy blood samples were collected as the control group. Methylation specific PCR (methylation specific-PCR, MS-PCR) was used to detect RUNX3, RASSF1A, 3-OST-2, DAPK, PTPRO genes methylation. Data was analyzed individually as well as jointly for the optimal diagnostic accuracy.
Results: The DNA methylation rates for the 5 genes RUNX3, RASSF1A, 3-OST-2, DAPK, PTPRO were 47.25% (43/91), 51.65% (47/91), 27.47% (25/91), 36.26% (33/91), and 41.76% (38/91) respectively in patient plasma samples. In the normal control group, only PTPRO gene methylation was detected with the methylation rate of 5.2% (3/58), and the rest of 4 genes were not detected. Methylation of RUNX3 gene was found to have higher frequencies in adenocarcinoma than other cell types of NSCLC (P &lt; 0.05). DAPK gene methylation was found to be associated with the stages of lung cancer, and methylation rate was higher in stage III/IV than in stage I/II (P &lt; 0.05). Combined analysis of the 5 genes methylation rates was achieved the sensitivity 86.81% (79/91) and the specificity 79.31% (46/58).
Conclusion: The combined DNA methylation analysis of RUNX3, RASSF1A, 3-OST-2, DAPK, and PTPRO genes with MS-PCR achieved a satisfied sensitivity and specificity in NSCLC diagnosis.
Citation Format: Li Cao, Hao Wang, Xu Dong, Li Zhong. Combined analysis of cell-free DNA methylation in plasma for early detection of NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4543.
Abstract 4551: Thyroid hormone induces PD-L1 expression in oral cancer cells
Authors: Chin Yu-Tang , Su Kwan-Wei , Lim Yee-Tang , Shih Ya-Jung , Chen Yi-Ru , Lee Sheng-Yang , Davis Paul J. , Lin Hung-Yun , Fu Earl 
Published: August 2018

Abstract
Oral cancer is a fatal disease, which accounts for the fourth highest incidence of malignancy in males and the seventh highest in the general population of Taiwan. Oral cancer is increasing in Taiwan. About 95% of oral cancer in Taiwan is oral squamous cell carcinoma (OSCC). With the development of cancer molecular biology and immunology, targeted therapy for immune checkpoints of programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) has shown enormous development prospects for treatment of head and neck cancer. The PD-1/PD-L1 checkpoint is a critical regulator of activated T cell-cancer cell interactions which defend tumor cells against immune surveillance. Thyroid hormone induces PD-L1 expression in human oral cancer cells. Human oral cancer OEC-M1 and SCC-25 cells were treated with different concentrations of T4 (10-8 to 10-6M) for 24 h and cells were harvested and total RNA was extracted. qPCR of PD-L1 revealed that PD-L1 mRNA was significantly induced by thyroid hormone on a concentration-dependent basis. Parallel studies were conducted to study the effect of thyroid hormone on PD-L1 protein accumulation. Cancer cells were treated with different concentrations of T4 for 24 h. Total proteins were extracted and western blot analysis of PD-L1 was conducted. Thyroid hormone-activated ERK1/2 and STAT3 were companied with PD-L1 expression. Inhibition of ERK1/2 and consequently STAT3 activation also blocked PD-L1 induced by thyroid hormone. Knockdown of PD-L1 expression by siRNA also inhibits thyroid hormone-induced proliferation of oral cancer cells which indicated that PD-L1 expression is involved in thyroid hormone-induced cancer growth via an ERK1/2-STAT3 signal transduction pathway in oral cancer cells.
Citation Format: Yu-Tang Chin, Kwan-Wei Su, Yee-Tang Lim, Ya-Jung Shih, Yi-Ru Chen, Sheng-Yang Lee, Paul J. Davis, Hung-Yun Lin, Earl Fu. Thyroid hormone induces PD-L1 expression in oral cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4551.
Abstract 4552: Tumor-restricted immune modulation by multispecific molecules from the DARPin toolbox
Authors: Fiedler Ulrike , Reichen Christian , Taylor Joanna , Schildknecht Patricia , Barsin Sophie , Metz Clara , Schlegel Anja , Fontaine Simon , Villemagne Denis , Ahlskog Julia , Kaufmann Yvonne , Link Alexander , Rigamonti Nicolo , Hepp Julia , Stumpp Michael T. 
Published: August 2018

Abstract
During the last years, immune-modulating drugs became an important cornerstone in the treatment of cancer patients. In particular, the PD1/PDL-1 and CTLA-4 antagonists revolutionized the field. However, only a limited number of patients benefit from these antagonistic molecules and more combination therapies are on the way to increase the number of patients benefiting from these novel therapies. Among the combinations, drugs that are T-cell or myeloid cell agonists belonging to the TNFR-superfamily show first promising clinical results. However, systemic immune activation bears the risk of severe side effects that will not allow using these powerful drugs at an effective dose. We have developed a new class of DARPin molecules that enable tumor-restricted immune cell activation of TNFR-superfamily agonists in the tumor only, thereby preventing systemic immune-activation. We generated DARPin molecules that bind with high affinity to TNFR-superfamily members (CD134, CD137 and CD40) and DARPin molecules that bind to tumor-specific antigens such as HER2 and EGFR or targets restricted to the tumor stroma compartment like FAP and extra-domain B of fibronectin (ED-B). Using these building blocks from our DARPin toolbox, we constructed a variety of multi-specific molecules consisting of a TNFR-superfamily receptor targeting DARPin molecule and a tumor-localizing DARPin molecule. In reporter cell assays the multi-specific DARPin molecules activate the respective TNF-superfamily receptor only in the presence of a cell expressing the tumor-localizer; e.g. the FAP-CD134 molecule activates CD134 only in the presence of a stromal cell expressing FAP and not in its absence. Moreover, activation of CD134 was dependent on the density of FAP expression on cells, showing that CD134 only becomes activated if a certain level of the tumor-localizing target is expressed. These finding were confirmed in experiments with primary immune cells where we see immune-cell activation only upon binding to the tumor-localizing target. This could be shown for multiple combinations (&gt;8) and supports the concept that multi-specific DARPin molecules are powerful drug-candidates allowing tumor-restricted immune cell activation.
Citation Format: Ulrike Fiedler, Christian Reichen, Joanna Taylor, Patricia Schildknecht, Sophie Barsin, Clara Metz, Anja Schlegel, Simon Fontaine, Denis Villemagne, Julia Ahlskog, Yvonne Kaufmann, Alexander Link, Nicolo Rigamonti, Julia Hepp, Michael T. Stumpp. Tumor-restricted immune modulation by multispecific molecules from the DARPin toolbox [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4552.
Abstract 4556: Phagocytosis response of macrophage to CD47 expression of tumor cells in anti-CD47 therapy
Authors: Yang Huajun , Li Zhongliang , Wang Phillip , Tang Beibei , Ma Qinyun , Xing Frank , Shi Qian 
Published: August 2018

Abstract
Macrophage as an important surveillance system is escaped by human cancer cells expressing CD47. To reinstate macrophage functionality in clearing tumor cells targeting CD47 and thereby blocking phagocytosis inhibitory CD47-SIRPalpha interaction has been an important strategy in immune-oncology therapy. We profiled a large panel of tumor cell lines, Crown's proprietary PDX models and clinical lung cancer tumors for CD47 expression. Although it has been reported as a ubiquitously expressed immune-escape marker in cancer cells, the expression levels of CD47 vary among different tumor cell lines and models when the cells were examined by flow cytometry. It is of interest that a portion of tumor cells in fact do not present CD47. To tackle the cause for the loss of CD47 expression, whole-exome sequencing was performed to examine the intactness of the gene in the CD47 loss models. The results will be presented. We next established a robust and reproducible in vitro assay platform to support anti-CD47 drug research. We applied a macrophage differentiation system using isolated CD14+ monocytes as starting material, and were able to achieve &gt;80% of M1 and M2 populations, respectively, through the 6-day differentiation. Differentiated macrophage was co-cultured with target tumor cells labeled for flow cytometry analysis. In the presence of blocking anti-CD47 antibody BRICK126, steady and specific phagocytosis effect was observed when target tumor cells express high level of CD47 markers. BRIC126 antibody blocks the CD47-SIRPalpha interaction. In contrast, aCD274 antibody did not yield more than background phagocytosis effect in the same assay. To prove the CD47-specific effect, we constructed isogenic cell models from a couple of parental cell models in that CD47 gene is knocked out in one sub-cell line and overexpressed in another sub-cell line. The isogenic systems were then subject to the CD47 biology assay and more profound changes in phagocytosis responses were observed. Furthermore, the in vitro findings were validated in in vivo setting.
Citation Format: Huajun Yang, Zhongliang Li, Phillip Wang, Beibei Tang, Qinyun Ma, Frank Xing, Qian Shi. Phagocytosis response of macrophage to CD47 expression of tumor cells in anti-CD47 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4556.
Abstract 4583: Combined analysis of circulating tumor cells, fecal occult blood test and serum carcinoembryonic antigen for early detection and monitoring recurrence of patients with colorectal cancer
Authors: Hung Wei-Shan , Tsai Wen-Sy , Wang Tzu-Min , Hsu Hsueh-Ling , Liu Hsuan , Yang Chia-Yu , Tseng Ching-Ping , Cheng Ju-Chien 
Published: August 2018

Abstract
Current methods for clinical early detection and disease monitoring of patients with colorectal cancer (CRC) are immunochemical fecal occult blood test (iFOBT) and serum levels of carcinoembryonic antigen (CEA), which are known with low sensitivity. There is an unmet need to seek for additional molecular tools for early detection and disease monitoring of patients with CRC. Whether enumeration of circulating tumor cells (CTCs) supplements current clinical tests and facilitates early detection and monitoring disease progression was investigated. A total of 109 pre-operative patients with CRC (including early and advanced stages) and 65 non-cancerous controls were enrolled in this study. CTCs were enriched from the peripheral blood of these individuals by using the PowerMag negative selection system. Immunofluorescence staining of epithelial cell adhesion molecule (EpCAM), and podoplanin (PDPN, a marker related to poor cancer progression) was performed to define the two distinct subtypes of CTCs. Heterogeneous CTCs expressing PDPN or EpCAM are defined in the peripheral blood of patients with CRC. Regardless clinical stages in patients, the number of both EpCAM+-CTCs and PDPN+-CTCs explicitly differentiated non-cancerous controls and patients with CRC, and were also correlated with clinicopathological diagnosis. Receiver operating characteristic analysis demonstrated that the sensitivity and specificity of EpCAM+-CTCs was 86.32% and 78.46%, respectively, when the cutoff value was 23 EpCAM+-CTCs/mL. Using 7 PDPN+-CTCs/mL as the cutoff value, the sensitivity and specificity of PDPN+-CTCs was 77.98% and 75.38%, respectively. 84.2% and 80.3% of patients with serum CEA &lt; 5 ng/mL were found to have higher EpCAM+-CTCs and PDPN+-CTCs counts, respectively. In addition, simultaneous measurements of iFOBT and CTCs could compromise the false-positive rate of iFOBT, while measurements of CEA and CTCs are applicable to monitor cancer recurrence after surgery. This study implicates that CTC testing supplements the current clinical methods to facilitate early detection and disease monitoring in CRC.
Citation Format: Wei-Shan Hung, Wen-Sy Tsai, Tzu-Min Wang, Hsueh-Ling Hsu, Hsuan Liu, Chia-Yu Yang, Ching-Ping Tseng, Ju-Chien Cheng. Combined analysis of circulating tumor cells, fecal occult blood test and serum carcinoembryonic antigen for early detection and monitoring recurrence of patients with colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4583.
Abstract 4586: Evaluation of available blood collection tubes for use in stabilizing concentrations of extracellular vesicles / exosomes and associated cell-free RNA
Authors: George Nicholas 
Published: August 2018

Abstract
Introduction: Liquid Biopsy has revolutionized the detection and the monitoring of cancer disease states. In addition to the widely utilized circulating cell-free DNA (ccfDNA), cell-free RNAs (cfRNA) and the extracellular vesicles (EV's) / exosomes they are stored in, is drawing significant interest in cancer diagnostics. Analysis of disease-specific EV's / exosomes or cfRNA requires that collected samples maintain draw-time concentrations of these analytes in order to remain relevant. Blood components, such as platelets, red, and white blood cells, are unstable when stored in normal blood collection tubes (BCT's), thus leading to increases of EVs and associated cfRNA concentration. We undertook an analysis of currently available commercial BCT's to determine whether any of these sufficiently stabilize EV / exosome and cfRNA concentration. Materials and Methods: Healthy consenting adult donors were drawn into blood collection tubes per approved protocol. Samples were either processed immediately (Day-0) or allowed to incubate at room temperature for the indicated times. Cleared plasma was isolated and subsequently frozen at -80oC until use. Assay of extracellular vesicle concentration utilized the Nanosight-300 (Malvern Instruments) per manufactures protocol. Isolation of cell-free RNA utilized the Circulating Nucleic Acid Isolation Kit (Qiagen) per manufacturer's protocol with the exception of the lysis step; this was extended from 30 minutes to 60 minutes. Digital PCR (ddPCR) utilized the Bio-Rad workflow (QX200 Droplet Generator and Reader). Conclusion: Stabilization of EV's and cfRNA was assayed for blood samples drawn into a variety of Streck nucleic acid stabilizing BCT's, non-Streck nucleic acid stabilizing BCT's, and a traditional K3EDTA BCT. A majority of the assayed tubes led to time-dependent increases in EV concentration with the most robust increases occurring between Day-3 and Day-7. Time-dependent increases in cfRNA concentration mirrored the increases observed in EV's, and based on ddPCR analysis; the majority of this increase was likely the result of erythrocyte membrane shedding. One type of Streck BCT was found to stabilize both EV and cfRNA concentration as a function of blood storage time. Incorporation of this tube into the Liquid Biopsy workflow will maximize assay target sensitivity by preventing the deleterious effects of excess cfRNA from non-specific release of EV's / exosomes.
Citation Format: Nicholas George. Evaluation of available blood collection tubes for use in stabilizing concentrations of extracellular vesicles / exosomes and associated cell-free RNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4586.
Abstract 4587: ESR1 methylation in primary tumors and paired circulating tumor DNA of patients with high-grade serous ovarian cancer
Authors: Giannopoulou Lydia , Mastoraki Sofia , Strati Areti , Chebouti Issam , Pavlakis Kitty , Kasimir-Bauer Sabine , Lianidou Evi 
Published: August 2018

Abstract
Background: The estrogen receptor is highly expressed in epithelial ovarian cancer and represents the main target for endocrine therapy. The ESR1 gene is frequently methylated in many types of gynecological malignancies and previous studies have shown an inverse correlation between ESR1 methylation and gene expression. Few studies attempted to investigate the role of ESR1 methylation in ovarian cancer so far, and the clinical significance of ESR1 methylation status is not as yet clear.
Methods: The ESR1 methylation status was examined in primary tumors and corresponding circulating tumor DNA (ctDNA) samples of patients with high-grade serous ovarian cancer. For the detection of methylation we applied a novel highly specific and sensitive real-time methylation specific PCR (real-time MSP) assay. Two groups of primary tumor samples were recruited (training group, n=66 and validation group, n=61), along with the corresponding plasma samples (n=58) for the validation group. ESR1 methylation was also analyzed in a small group of 16 normal fallopian tube samples.
Results: ESR1 was found methylated in both groups of primary tumor samples and in the corresponding plasma samples of the validation group. More specifically, ESR1 methylation was detected in 32/66 (48.5%) and 17/61 (27.9%) primary tumor samples of the training and the validation group, respectively, and in 23/58 (39.7%) corresponding plasma samples. A significant agreement between ESR1 methylation in primary tumors and paired ctDNA was observed in 40/56 (71.4%) samples of the validation group (P=0.004, k=0.360). Almost all normal fallopian tube samples (15/16) were found methylated. Interestingly, the presence of ESR1 methylation in the primary tumor samples of the validation group was nearly significantly correlated (P=0.057) with a better overall survival.
Conclusions: We detected for the first time ESR1 methylation in ctDNA of patients with high-grade serous ovarian cancer. The agreement between ESR1 methylation in the primary tumors and paired ctDNA is statistically significant. Our results indicate a potential correlation between ESR1 methylation and better overall survival in high-grade serous ovarian cancer patients.
Citation Format: Lydia Giannopoulou, Sofia Mastoraki, Areti Strati, Issam Chebouti, Kitty Pavlakis, Sabine Kasimir-Bauer, Evi Lianidou. ESR1 methylation in primary tumors and paired circulating tumor DNA of patients with high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4587.