bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2404: Quality assessment of circulating cell-free DNA using multiplexed droplet-digital PCR
Authors: Contente-Cuomo Tania , Murtaza Muhammed 
Published: August 2015

Abstract
Recent proof-of-principle studies have demonstrated potential utility of sequencing cell-free DNA in cancer diagnostics. However, little is understood about the effect of fragment size distributions in plasma DNA on the performance of sequencing-based assays. We developed a multiplexed assay to perform one-step analysis of DNA quantity and integrity from minute amounts of cell-free DNA using picoliter droplet digital PCR. Primers were designed to amplify 5 short PCR products (67-71 bp) and 4 long PCR products (439-522 bp) from independent quiescent regions of the human genome. Oligonucleotide probes targeting each of the short and long products were labeled with fluorescent dyes FAM and TET respectively. We evaluated the performance of our assay using control human genomic DNA sheared using sonication to an average of 150 bp, 300 bp, 500 bp and 1000 bp fragment sizes. We observed that relative quantities of short and long PCR products reflect integrity of sheared input DNA. We further observed that accurate quantification and assessment of integrity could be achieved using picogram amounts of cell-free DNA (as few as 200 pg in current assessments). Finally, our results were predictive of diversity and obtainable depth-of-coverage in next-generation sequencing libraries made from cell-free DNA samples.
Citation Format: Tania Contente-Cuomo, Muhammed Murtaza. Quality assessment of circulating cell-free DNA using multiplexed droplet-digital PCR. [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 2404. doi:10.1158/1538-7445.AM2015-2404
Abstract 241: A novel tumor suppressor miRNA co-regulating EMT and p53-independent cell survival in breast cancer
Authors: Raza Umar , Uhlmann Stefan , Yurdusev Emre , Wiemann Stefan , Sahin Ozgur 
Published: August 2015

Abstract
Breast cancer is the most common cancer and the second leading cause of cancer-related deaths among women. MicroRNAs (miRNAs) have been shown to be key regulators of cancer-related processes including cell proliferation, survival, migration and invasion. Here, we performed a small scale miRNA mimic screen to identify miRNAs leading to inhibition of cell survival and epithelial-mesenchymal transition (EMT), both of which are key parameters for tumor growth and metastasis. We identified a miRNA (miR-644) which leads to apoptosis in p53-mutated breast cancer cell lines, but not in p53-wild type ones. Furthermore, in vitro migration and invasion assays revealed that miR-644 inhibits both migration and invasion by interfering with the EMT process. Then, we combined whole genome mRNA profiling with target prediction algorithms to determine the potential targets of this miRNA, and identified transcriptional co-repressor CTBP1 as a novel direct target which is already known for limiting apoptosis by repressing Bax transcription. CTBP1 has also been reported to bind ZEB transcription factors and assists EMT by enhancing ZEB-mediated downregulation of E-Cadherin. We showed that silencing of CTBP1 phenocopies the effects of miR-644 in induction of p53-independent apoptosis and blocking EMT and cell invasion. Currently, we are testing the role of miR-644 and its target CTBP1 in tumor growth and metastasis in in vivo assays. Overall, our results suggest that miR-644 is a novel tumor suppressor miRNA co-regulating EMT and cell survival and it could be a potential target for breast cancer therapy.
Note: This abstract was not presented at the meeting.
Citation Format: Umar Raza, Stefan Uhlmann, Emre Yurdusev, Stefan Wiemann, Ozgur Sahin. A novel tumor suppressor miRNA co-regulating EMT and p53-independent cell survival in breast cancer. [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 241. doi:10.1158/1538-7445.AM2015-241
Abstract 2410: Cell-free DNA derived from ascites: Detection of copy number and somatic mutations using OncoScan FFPE® Assay
Authors: Husain Hatim , Venkatapathy Sumathi , Gomez German , Woodward Brian , Lee Suzanna , Khambaty Lubena , Chen Lily , Duttagupta Radha , Fung Eric T. , Kurzrock Razelle 
Published: August 2015

Abstract
Background: There is increased interest in molecular analysis of cell-free DNA isolated from body fluids for the evaluation of tumor progression. These “liquid” biopsies are usually obtained from blood. Their advantages include the fact that they can be repeatedly accessed, are less invasive, and may be sensitive to changes in tumor profile from multiple metastatic sites.
Materials and Methods: Eleven ascites samples from patients with metastatic epithelial neoplasms (gastric, N = 3; pancreas, N = 3; ovarian, N = 2; breast, N = 2; and lung cancer, N = 1) were investigated. Cell-free DNA was isolated from supernatant of ascites fluid (50 ml) after centrifugation using commercially available DNA purification kits (Norgen Bioteck Corp and Qiagen), and analyzed using the OncoScan FFPE Assay kit.
Results: Cell-free DNA yields ranged from 1.7 ng to 230 ng per mL of ascites fluid, indicating wide variability in DNA content. Of the 11 patients, all had detectable aberrations, including copy number alterations affecting from &lt;1%- 37% of the genome. A sample from a patient with metastatic breast cancer had apparent chromosome 12 chromothripsis (chromosome breakage with numerous clustered chromosomal rearrangements). Another sample (metastatic lung cancer) had high overall genomic stability (T); the lung tumor tissue did not show these alterations though the patient has never smoked. Other aberrations were seen in genes including: p53 (N = 4 patients), EGFR (N = 3), ERBB2 (N = 2), PI3KCA (n = 2).
Conclusions. Combined copy number and somatic analysis of ascites cell-free DNA revealed clinically relevant aberrations, including ones not found in primary tumor tissue. Comparison to circulating cells in ascites, cell-free DNA in blood, as well as tumor molecular profile is ongoing.
Citation Format: Hatim Husain, Sumathi Venkatapathy, German Gomez, Brian Woodward, Suzanna Lee, Lubena Khambaty, Lily Chen, Radha Duttagupta, Eric T. Fung, Razelle Kurzrock. Cell-free DNA derived from ascites: Detection of copy number and somatic mutations using OncoScan FFPE® Assay. [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 2410. doi:10.1158/1538-7445.AM2015-2410
Abstract 2430: Treatment sequence and molecular biomarker in EGFR mutant lung cancer cells
Authors: Motes Hannah , Reyes Emma Borrego-Diaz , Kevern Jared , Huang Chao H. , Van Veldhuizen Peter J. 
Published: August 2015

Abstract
Introduction
Lung cancer is the leading cause of cancer related death in the US. A subset of patients with lung cancer has a mutation in the Epidermal Growth Factor Receptor (EGFR) which makes them extremely responsive to EGFR tyrosine kinase inhibitor (TKI) erlotinib. The emergence of EGFR TKI resistance is new challenge in the management of these patients. We conducted a study to determine the best treatment sequence after resistance to EGFR TKI, testing the use of chemotherapy Pemetrexed (P), Afatinib (A), Rociletinib (R) and the combination of these agents in lung cancer cell lines with EGFR mutation that were pretreated with erlotinib.
Material and methods
Lung cancer cell lines with EGFR mutation CRL-2868 (E746 - A750 deletion) and CRL-2871 (L747 - E749 deletion, A750P) mutation were treated with 5 nM erlotinib for 24h and 72 h.
The erlotinib resistance cells were then treated with 10nM of A or 10nM of P, or 21.5 nM of R, or the combination AP or the combination of RP. As control, we used lung cancer HTB-177 which does not have EGFR mutation. MTT proliferation assay was performed after 24, 48, 72 and 144h after the treatment. microRNA profiling was done by real time PCR in all cells after erlotinib treatment to find potential biomarkers as hallmark of erlotinib resistance cells.
Results
Rociletinib induced the maximum inhibition of cell proliferation at 144h in both cell lines with EGFR mutation. The RP also induced decreased cell proliferation in both cell lines with EGFR mutation. RP combination was more effective then R alone in CRL 2871. The use of A alone, P alone or AP combination was not different in CRL2871 but P had antagonistic effect when combined with A or R in CRL 2868. microRNA 10b, 27a and 27b were upregulated in the erlotinib resistant cells.
Conclusion.
EGFR resistance arises after treatment with erlotinib in lung cancer cell lines with EGFR mutation. Treatment with R and the combination of RP induced greater inhibition of proliferation compared to A, P alone. The combination of AP was antagonistic. This may have implications in the management of patients resistant to EGFR TKI. microRNA analysis showed up-regulation of several microRNA that should be tested in clinical setting.
Citation Format: Hannah Motes, Emma Borrego-Diaz Reyes, Jared Kevern, Chao H. Huang, Peter J. Van Veldhuizen. Treatment sequence and molecular biomarker in EGFR mutant lung 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 2430. doi:10.1158/1538-7445.AM2015-2430
Abstract 2433: A novel MDM2 inhibitor suppresses breast cancer growth and metastasis
Authors: Qin Jiang-Jiang , Wang Wei , Voruganti Sukesh , Zhang Ruiwen 
Published: August 2015

Abstract
The MDM2 oncogene is amplified and/or overexpressed in many human cancers, including breast cancer, and it has been suggested as a molecular target for treating human cancers. MDM2 is a major negative regulator of tumor suppressor p53. Most MDM2 inhibitors under development are targeting the MDM2-p53 binding, and have little or no effects on cancers without functional p53, such as advanced breast cancer. Therefore, new strategies to target MDM2 are desirable. The present study was designed to develop a new class of MDM2 inhibitors that exert anti-breast cancer activity, regardless of p53 status in the cancers. The selective MDM2 inhibitors were discovered by a computational structure-based screening, yielding a lead compound, termed JapA. Fluorescence polarization (FP)-based binding assay and cellular thermal shift assay were performed to determine the binding between MDM2 and JapA. Its cytotoxicity was initially evaluated in breast cancer cell lines (MCF-7, MCF-7/p53−/−, MDA-MB-231, and MDA-MB-468) and normal human breast cells (MCF-10A). Its anti-breast cancer activities were further assessed in in vitro and in vivo MCF-7 and MDA-MB-231 models. The molecular mechanisms for its targeting effects on MDM2 were elucidated in various cell models in vitro and in vivo. We further found that JapA selectively inhibited breast cancer cell growth, decreased cell proliferation, and induced G2/M phase arrest and apoptosis in breast cancer cells through an MDM2-dependent mechanism, regardless of p53 status. In MCF-7 and MDA-MB-231 xenograft models, JapA inhibited MDM2 and suppressed tumor growth and lung metastasis in a dose-dependent manner, without host toxicity. Furthermore, JapA directly bound to MDM2 protein and reduced MDM2 levels in cancer cells in vitro and in vivo by promoting MDM2 protein degradation and inhibiting MDM2 transcription, which is distinct from the existing MDM2 inhibitors. In conclusion, JapA represents a new class of MDM2 inhibitor that exerts its anticancer activity through directly down-regulating MDM2, and might be developed as a novel cancer therapeutic agent. (Supported by the NIH R01 CA112029, R01 CA121211, and R01 CA186662)
Citation Format: Jiang-Jiang Qin, Wei Wang, Sukesh Voruganti, Ruiwen Zhang. A novel MDM2 inhibitor suppresses breast cancer growth and metastasis. [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 2433. doi:10.1158/1538-7445.AM2015-2433
Abstract 2605: The geranylgeranyltransferase I inhibitor GGTI-2418 suppresses multiple myeloma malignancy in the 5TMG1 mouse model
Authors: Yang Hua , Emmons Michael F. , Cubitt Christopher , Shain Ken , Coppola Domenico , Sullivan Daniel , Lynch Conor C. , Hazlehurst Lori , Sebti Said M. 
Published: August 2015

Abstract
Little is known about the contributions of geranylgeranylated proteins to multiple myeloma (MM) malignancy, and whether targeting geranylgeranyltransferase I (GGT-1) is a viable therapeutic approach in myeloma is yet to be explored. In this study, we investigated the effects of GGTI-2418, a GGT-1 inhibitor that has reached phase I clinical trials, on MM malignancy in the 5TMG1 mouse model, where GGTI-2418 effects were assessed in the confines of the bone microenvironment that recapitulates the clinical disease in humans. GGTI-2418 treatment significantly decreased the serum levels of the MM biomarker IgG2B (M-protein) as well as the percentage of MM tumors within the tibia as demonstrated by H&E staining. X-ray and micro-CT analyses also identified that GGTI-2418 prevented MM induced bone disease with significantly lower tumor induced osteolysis and trabecular bone volume loss noted. Furthermore, treatment of mice with GGTI-2418 resulted in a significant activation of caspase 3 (apoptosis induction), accumulation of nuclear p27Kip in MM tumors (a positive prognostic biomarker for MM patients), and reduction of α-SMA levels in myofibroblasts surrounding the sinusoidal vasculature, suggesting decreased vascularization of marrow blood vessels. Importantly, GGTI-2418 treatment resulted in a significant increase in mouse median survival and delay in the onset of limb paralysis. In cell culture studies, GGTI-2417, the methylester pro-drug of GGTI-2418 that is better taken up by cultured cells, inhibited MM proliferation, increased p27kip levels, induced apoptosis and sensitized MM cells to bortezomib. Taken together, our preclinical studies suggest targeting GGT-1 as a viable therapeutic approach in MM, and warrant the investigation of GGTI-2418 in the clinic.
Citation Format: Hua Yang, Michael F. Emmons, Christopher Cubitt, Ken Shain, Domenico Coppola, Daniel Sullivan, Conor C. Lynch, Lori Hazlehurst, Said M. Sebti. The geranylgeranyltransferase I inhibitor GGTI-2418 suppresses multiple myeloma malignancy in the 5TMG1 mouse model. [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 2605. doi:10.1158/1538-7445.AM2015-2605
Abstract 285: MEDI9447: enhancing anti-tumor immunity by targeting CD73 In the tumor microenvironment
Authors: Hay Carl , Sult Erin , Huang Qihui , Hammond Scott , Mulgrew Kathy , McGlinchey Kelly , Fuhrmann Stacy , Rothstein Raymond , Poon Edmund , Stewart Ross , Hollingsworth Robert , Sachsenmeier Kris 
Published: August 2015

Abstract
MEDI9447 is a monoclonal antibody specific for the ectoenzyme, CD73. Data is presented in support of the hypothesis that targeting the extracellular production of adenosine by CD73 reduces the immunosuppressive effects of adenosine. We report a range of activities for this antibody, including inhibition of both recombinant and cellular CD73 ectonucleotidase activity, relief from AMP-mediated lymphocyte suppression in vitro, and inhibition of syngeneic tumor growth. In contrast with many other cancer immunotherapy agents such as checkpoint inhibitors or T cell agonists, MEDI9447 drives changes in both myeloid and lymphoid infiltrating leukocyte populations within the tumor microenvironment. Changes include significant increases in CD8 effector cells and activated macrophages, as well as a reduction in the proportions of myeloid-derived suppressor cells (MDSC) and regulatory T lymphocytes. Furthermore, these changes correlate directly with responder and non-responder subpopulations within the arms of animal studies using syngeneic tumors. Data showing additive activity between MEDI9447 and other immune-mediated therapy antibodies demonstrates the importance of relieving adenosine-mediated immunosuppression within tumors.
Citation Format: Carl Hay, Erin Sult, Qihui Huang, Scott Hammond, Kathy Mulgrew, Kelly McGlinchey, Stacy Fuhrmann, Raymond Rothstein, Edmund Poon, Ross Stewart, Robert Hollingsworth, Kris Sachsenmeier. MEDI9447: enhancing anti-tumor immunity by targeting CD73 In the tumor microenvironment. [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 285. doi:10.1158/1538-7445.AM2015-285
Abstract 2942: TRAIL pathway inducer ONC201/TIC10 primes multiple myeloma cells (MM) for apoptosis by downregulating X-linked inhibitor of apoptosis
Authors: Kline Christina Leah , Lulla Amriti R. , Dicker David , Allen Joshua E. , El-Deiry Wafik 
Published: August 2015

Abstract
MM cells inherently have a high protein turnover rate that makes them heavily dependent on the proteasome and uniquely sensitive to ER stress induction. Proteasome inhibitors, such as bortezomib, are used in front-line therapy for MM to elicit the ER stress response that results in apoptosis of MM cells. Despite significantly improved clinical outcomes in MM patients treated with proteasome inhibitors, resistance to therapy invariably emerges and MM remains an incurable disease. The objective of this study is to assess the utility of the TRAIL pathway inducer ONC201/TIC10 in MM due to preliminary evidence that suggests ONC201/TIC10 activates the integrated stress response (ISR) in tumor cells. We found that MM cells are uniquely sensitive to ONC201/TIC10, with EC50 values in the nanomolar range. In addition, ONC201/TIC10 was effective as a single agent against bortezomib-resistant MM cells and exhibited an additive effect with bortezomib against these cells. Sub-G1 analyses of MM cells co-treated with ONC201/TIC10 and a pan-caspase inhibitor indicated that MM cells undergo ONC201/TIC10-induced apoptosis in a caspase-dependent manner. Given that ONC201/TIC10 can inactivate both Akt and ERK signaling pathways, we assessed Akt and ERK phosphorylation in ONC201/TIC10-treated KMS18 and MM1S MM cells. These MM cell lines showed no inhibition of Akt and ERK phosphorylation or decrease in the downstream phosphorylation of Fox3a in response to ONC201/TIC10 treatment. These results suggested that alternative mechanisms of cytotoxicity are operative in myeloma cells treated with ONC201/TIC10. Given that downregulation of X-linked inhibitor of apoptosis (XIAP) has been linked to the ISR, we assessed the effect of ONC201/TIC10 treatment on XIAP expression. In agreement with ISR activation, XIAP levels were significantly downregulated in MM cells in response to ONC201/TIC10. Ongoing experiments are unraveling the mechanistic basis for lowered XIAP expression in ONC201/TIC10-treated MM cells. In summary, our results indicate that ONC201/TIC10 is highly effective in preclinical MM models by engaging antitumor mechanisms that include the ISR and downstream attenuation of XIAP expression. ONC201/TIC10 appears to have significant therapeutic potential in MM as a monoagent and in combination with bortezomib.
Citation Format: Christina Leah Kline, Amriti R. Lulla, David Dicker, Joshua E. Allen, Wafik El-Deiry. TRAIL pathway inducer ONC201/TIC10 primes multiple myeloma cells (MM) for apoptosis by downregulating X-linked inhibitor of apoptosis. [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 2942. doi:10.1158/1538-7445.AM2015-2942
Abstract 2963: 5-hydroxymethylcytosine alterations at H3K9me3 marked genomic regions serve as potential biomarker for renal cell carcinoma patients
Authors: Meng Wei , Lautenschlaeger Tim , Frankhouser David , Ye Zhenqing , Huebner Alexander , Jin Victor , Yan Pearlly , Chakravarti Arnab 
Published: August 2015

Abstract
Background: Epigenetic alterations are frequently encountered in many malignancies. Control of DNA methylation is thought to play a critical role in the global epigenetic reprogramming observed during development and carcinogenesis. DNA demethylation is initiated by the transition from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC patterns are relatively well characterized in many malignancies, not much is known about 5hmC patterns and the potential usefulness as biomarkers. We thus sought out to identify 5hmC alterations in renal cell carcinoma (RCC) and assess their potential usefulness as urine biomarkers.
Results: We performed genome-wide 5hmC MethylCap-seq on one pooled RCC tissue sample (n = 3) and the corresponding pooled matched normal kidney tissue (n = 3), as well as on one pooled urine sample obtained from RCC patients (n = 52) and one pooled urine sample obtained from control patients without malignancy (n = 65). Global 5hmC levels were dramatically reduced in RCC tissues compared to matched normal adjacent kidney tissues, and in urine samples compared to tissue samples. Assessing histone marked regions we found 5hmC levels to be highly enriched in H3K9me3 marked repressive genomic regions of RCC tissue compared to normal adjacent tissues. Given the low 5hmC signal in these regions in normal tissues, this difference was also clearly identified comparing urine samples from RCC patients to control patients without RCC.
Conclusions: We characterized the 5hmC distribution of RCC and normal human renal tissue as well as of urine samples from RCC patients and control patients without RCC. We identified dramatic genome-wide 5hmC changes to occur during carcinogenesis, which have potential for development as non-invasive urine biomarkers.
Citation Format: Wei Meng, Tim Lautenschlaeger, David Frankhouser, Zhenqing Ye, Alexander Huebner, Victor Jin, Pearlly Yan, Arnab Chakravarti. 5-hydroxymethylcytosine alterations at H3K9me3 marked genomic regions serve as potential biomarker for renal cell carcinoma patients. [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 2963. doi:10.1158/1538-7445.AM2015-2963