bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 429: Optimization of an RNA sequencing method for low-quantity degraded samples
Authors: Su Dan , Powers Jason G. , Halsey Thomas A. , Hurban Patrick 
Published: August 2018

Abstract
RNA-sequencing (RNA-seq) is an effective tool for gene expression analysis, promising to be a diagnostic tool for patient stratification and individualized therapy. However, it has been challenging to apply RNA-seq to low-quantity and degraded RNA derived from formalin fixed paraffin embedded clinical samples. The Illumina TruSeq® RNA Access approach, utilizing capture probes targeting known exons to enrich for coding RNAs, has shown high performance to profile poor quality RNA samples at input amounts at or above 20 ng. Here, we have further optimized the Illumina TruSeq® RNA Access method for samples with low quality and low quantity, and have compared results to those obtained with libraries prepared with SMARTer® Stranded Total RNA-Seq- Pico Input Kit. Libraries were prepared using 1 ng and 10 ng of degraded RNA from Banked FFPE liver specimens, and were compared to libraries prepared using the standard RNA Access method with an input of 100 ng. With the optimized low-input RNA Access method, the alignment rate was consistently high (95-97%) across both input amounts, with 82-84% of aligned reads mapped to the transcriptome. This is comparable to results obtained with the standard 100 ng input. Gene detection however, changed as a function of input, with ~ 15,900 genes detected at an input of 10 ng, and ~ 13,500 detected at 1 ng of input. In contrast, the SMARTer method detected a relatively constant number of genes (~ 14,500 genes) at both input amounts, albeit with a lower % aligned reads to transcriptome (46-47%), and an increased % reads aligned to Ribosomal RNA when compared to RNA Access. Thus, while both methods are capable of comparable levels of performance, the RNA Access method is more cost-effective from a sequencing standpoint. These characteristics were maintained across a group of additional FFPE-derived samples tested by both methods.
Taken together, these results demonstrate that an optimized RNA Access method has consistent mapping performance and a high gene detection rate, and is thus suitable for the analysis of low-quantity degraded RNA.
Citation Format: Dan Su, Jason G. Powers, Thomas A. Halsey, Patrick Hurban. Optimization of an RNA sequencing method for low-quantity degraded samples [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 429.
Abstract 4291: Oncogenic ALK regulates cell cycle progression via CDK1: Implications for therapy
Authors: Scorsone Kathleen A. , Gahlawat Sonal , Tyagi Siddhartha , Orellana Mayra C. , Westbrook Thomas F. , Bernardi Ronald J. 
Published: August 2018

Abstract
Pharmacologic inhibition of oncogenic ALK can yield clinical responses in a variety of cancer types, including non-small cell lung cancer, anaplastic large-cell lymphoma, and neuroblastoma; however, de novo and acquired resistance remain major problems. As is seen with inhibition of other oncogenic receptor tyrosine kinases, ALK inhibition primarily induces G1 cell cycle arrest. However, we and others have also observed a role for receptor tyrosine kinases in regulating G2/M progression. For instance, oncogenic HER2 has been shown to directly phosphorylate tyrosine 15 of CDK1, the mitosis promoting factor. This tyrosine is also the well-known substrate of WEE1 and serves to inactivate CDK1 kinase activity as a critical component of the G2-M checkpoint. In the current study, we aimed to determine if oncogenic ALK functions in a similar capacity. We used recombinant proteins to demonstrate that ALK is also capable of directly phosphorylating tyrosine 15 of CDK1. Further, combined inhibition of ALK and WEE1 with crizotinib and AZD-1775 leads to greater reduction in pY15-CDK1 than either agent alone in ALK-amplified neuroblastoma cells. These findings suggest a model where oncogenic ALK and WEE1 provide redundant regulation of the G2-M checkpoint, which may be critical in cancer cells that have lost some of the usual complement of checkpoint controls, such as p53. Consequently, either ALK or WEE1 activity would be sufficient to maintain appropriate cell cycle regulation, while dual blockade would allow mitosis to proceed unchecked. In agreement with these predictions, we performed live cell imaging and observed that combined inhibition of ALK and WEE1 leads to aberrant mitotic progression and mitotic catastrophe. Further, this combination yields greater anti-proliferative activity than either agent alone in ALK-driven models. Thus, this therapeutic strategy holds great promise for ALK-driven cancers.
Citation Format: Kathleen A. Scorsone, Sonal Gahlawat, Siddhartha Tyagi, Mayra C. Orellana, Thomas F. Westbrook, Ronald J. Bernardi. Oncogenic ALK regulates cell cycle progression via CDK1: Implications for 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 4291.
Abstract 4295: ASF1B promotes cell proliferation and regulates cell cycle in human benign prostate hyperplasia (BPH)
Authors: Rani Nisha Dahiya , Ankem Dr. Murali , Damodaran Dr. Chendil 
Published: August 2018

Abstract
Background
Benign Prostate Hyperplasia (BPH) is enlargement of the prostate, which occurs in 50% men above 50 years of age. Alpha-adrenergic blockers and 5-alpha-reductase inhibitors are the standard medical therapy for BPH. However, these treatments are not only partially effective but also cause significant toxicity in patients. Understanding the molecular pathogenesis of BPH may reveal novel preventive or therapeutic targets for BPH.
Methods
Normal Human Prostate Epithelial Cells (HPrEpC), RWPE-1 and Benign Prostate Hyperplasia (BPH) were utilized for global sequencing and molecular studies. Western blot analysis was performed to determine the expression of G0/G1 and S-phase and M phase regulators of the cell cycle in BPH and RWPE-1 lysates. Cell cycle and western blot analysis was performed at successive time-points post starvation to understand the dynamics of cell cycle progression in both the cell lines. Knock out experiments were conducted to understand the function ASF1B in normal and BPH cells.
Results
RNA sequencing analysis revealed that the level of ASF1b (Anti-Silencing Function 1B Histone Chaperone) was over 80 times upregulated in BPH cells as compared to healthy prostate epithelial cells. Induction of ASF1B is specific to BPH as confirmed at protein levels. Induction of ASF1B expression correlated in a time-dependent manner with the increased expression of G1 (cdk4, 6 and cyclin D), G1-S (cdk2) and S-phase (cdk2 and cyclin-A) regulators at both transcription and translation levels. The G1-S phase transcriptional enhancers such as E2-F1 were also upregulated with successive time-points. The cell cycle analysis at sequential time-points revealed that the BPH cells entry to S phase was achieved earlier and by higher fraction of cells than the healthy prostate epithelial cells. Knocking down ASF1B expression by siRNA inhibited the proliferation of BPH cells by 30%. The findings so far suggest that ASF1B might be related to hyper-proliferation in BPH cells. The results indicate that ASF1B might be a novel therapeutic target for preventing hyper-proliferation in BPH. Studies are ongoing to validate the expression of ASF1B in clinical samples along with screening of small molecules targeting ASF1B expression specifically. Current study may lead to identification of a novel preventive and/or therapeutic target and related treatment for BPH.
Conclusion
Our studies suggest that ASF1b is a G1 and S phase regulator which are critical phases for hyper-proliferative BPH cells.
Citation Format: Nisha Dahiya Rani, Dr. Murali Ankem, Dr. Chendil Damodaran. ASF1B promotes cell proliferation and regulates cell cycle in human benign prostate hyperplasia (BPH) [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 4295.
Abstract 4298: Targeting the DNA damage checkpoint kinase Chk1 induces multiple pathways of cytotoxicity
Authors: Warren Nicholas , Ditano Jennifer , Eastman Alan 
Published: August 2018

Abstract
DNA damaging agents are standard therapies for many cancers, but result in limited long-term clinical benefit. DNA damage checkpoints arrest DNA synthesis and provide time for repair and recovery. Using DNA checkpoint inhibitors to sensitize cancer cells to traditional chemotherapeutics is an emerging strategy. However, clinical trials involving Checkpoint Kinase 1 inhibitors (Chk1i) plus DNA-damaging chemotherapies have shown little clinical benefit. This may be due to sub-optimal scheduling of combinations. We have published that delaying Chk1i until 18 h after gemcitabine confers the greatest sensitization of cancer cells. We have now characterized the mechanisms by which the Chk1i, MK-8776, sensitizes human cancer cells to gemcitabine and SN38. SN38, the active metabolite of irinotecan, traps topoisomerase I on DNA resulting in S phase arrest. Chk1i re-activates replication and drives cells into mitosis before the damage from SN38 is repaired. Co-incubation with a CDK1/2 inhibitor surprisingly failed to prevent S phase progression, but did block mitotic entry and prevented further DNA damage. Conversely, the replication-associated kinase, CDC7, is essential for Chk1i-mediated S phase abrogation. CDC7 is presumably required to activate dormant origins of replication. Gemcitabine inhibits ribonucleotide reductase, thus preventing production of deoxyribonucleotides. Addition of Chk1i 18 h following gemcitabine causes aberrant activation of DNA helicases, but without deoxyribonucleotides, this results in excessive single-stranded DNA. Eventually, the level of single-stranded DNA exceeds cellular stores of the protective protein, RPA, which leads to nucleolytic cleavage and double-strand DNA breaks. Chk1i-mediated helicase activation is again dependent on CDC7, but insensitive to a CDK1/2 inhibitor. Concurrent incubation with gemcitabine plus MK8776 does not activate DNA helicases. These data provide a rationale for a delayed administration of Chk1i when patients are receiving gemcitabine. These investigations have detailed how Chk1i elicits distinct mechanisms of cytotoxicity depending on the context of DNA damage. Understanding of these mechanisms may help identify biomarkers to predict patient response. Furthermore, the clinical development of several Chk1i have been terminated due to unfavorable toxicity, but the cause of toxicity remains unknown. The work described here may help the clinical development by determining whether the observed toxicities are due to on- or off-targets.
Citation Format: Nicholas Warren, Jennifer Ditano, Alan Eastman. Targeting the DNA damage checkpoint kinase Chk1 induces multiple pathways of cytotoxicity [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 4298.
Abstract 4299: Mutual influence of ROS, pH and CLIC1 membrane protein in the regulation of G1/S phase progression in human glioblastoma stem cells
Authors: Verduci Ivan , Peretti Marta , Raciti Federica Maddalena , Carlini Valentina , Patarozzi Alessandra , Barozzi Sara , Garrè Massimiliano , Sertic Sarah , Costa Alex , Daga Antonio , Barbieri Federica , Florio Tullio , Mazzanti Michele 
Published: August 2018

Abstract
Glioblastoma (GB) is the most lethal, aggressive and diffuse brain tumor. The main challenge of successful treatment is targeting the cancer stem cell (CSC) sub-population responsible for tumor origin, progression and recurrence. Chloride Intracellular Channel 1 (CLIC1), highly expressed in CSCs, is constitutively present in the plasma membrane where it is associated with chloride ion permeability. In vitro, CLIC1 inhibition leads to a significant arrest of GB CSCs in G1 phase of the cell cycle. Furthermore, CLIC1 knockdown impairs tumor growth in vivo. Here we demonstrate that CLIC1 membrane localization and function is specific for GB CSCs. Mesenchymal stem cells (MSCs) do not show CLIC1-associated chloride permeability and inhibition of CLIC1 protein function has no influence on MSC cell cycle progression. Investigation of the basic functions of GB CSCs reveals a constitutive state of oxidative stress and cytoplasmic alkalinization compared with MSCs. We now report that these three elements are temporally linked during CSC G1/S transition. Impeding CLIC1-mediated chloride current prevents both intracellular ROS accumulation and pH changes. CLIC1 membrane functional impairment results in GB CSCs resetting from an allostatic tumorigenic condition to a homeostatic steady state. In contrast, inhibiting NADPH oxidase and the NHE1 proton pump results in cell death of both GB CSCs and MSCs. Our results show that CLIC1 membrane protein is crucial and specific for GB CSC proliferation, and is a promising pharmacological target for successful brain tumor therapies.
This work was supported by grant n.16713, IG 2015 to MM Italian Association for Cancer Research (AIRC).
Citation Format: Ivan Verduci, Marta Peretti, Federica Maddalena Raciti, Valentina Carlini, Alessandra Patarozzi, Sara Barozzi, Massimiliano Garrè, Sarah Sertic, Alex Costa, Antonio Daga, Federica Barbieri, Tullio Florio, Michele Mazzanti. Mutual influence of ROS, pH and CLIC1 membrane protein in the regulation of G1/S phase progression in human glioblastoma stem 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 4299.
Abstract 4309: SPCIP2 enhances breast cancer cell proliferation, cell cycle and tumor formation by expression and interaction with Y1
Authors: Byun Hyunjung , Lee Changhoon 
Published: August 2018

Abstract
SPCIP2 is a member of the serine/threonine protein kinase family. However, the working mechanism of SPCIP2 in cellular functions has not yet been properly understood. In this study, we found that SPCIP2 directly interacts with Y1, a multifunctional protein that can act as a regulator of transcription and translation. Furthermore, we determined the binding domains required for the interaction between SPCIP2 and Y1. The ectopic expression of SPCIP2 activates cell growth by inducing Y1. Binding activates is confirmed by SPCIP2-dependent increase of Y1 expression, as well as by the induced cell proliferation and tumor formation. Also, expression of siSPCIP2 and siY1 is found to induce cell cycle arrest and apoptotic activity in breast cancer cells. These insights provide evidence that SPCIP2 induces cell proliferation and tumor formation via expression and interaction with Y1.
Citation Format: Hyunjung Byun, Changhoon Lee. SPCIP2 enhances breast cancer cell proliferation, cell cycle and tumor formation by expression and interaction with Y1 [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 4309.
Abstract 4312: 3-Hydroxyterphenyllin induces S phase arrest in ovarian cancer cells
Authors: Chen Yi C. 
Published: August 2018

Abstract
Epithelial ovarian cancer is the fifth most common cause of cancer-related death among women in the United States. 3-Hydroxyterphenyllin is a secondary metabolite of Aspergillus fungi. In this study, we evaluated 3-hydroxyterphenyllin as a potential anti-cancer agent using human ovarian cancer cells. The cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37°C in a humidified incubator with 5% CO2. The [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay, flow cytometry and western blot analysis were used to confirm that 3-hydroxyterphenyllin exhibited a potent growth inhibitory effect against human ovarian cancer OVCAR-3 and A2780/CP70 cells. 3-hydroxyterphenyllin (2, 4, 8, 12 and 16 μM) reduced the viability of OVCAR-3 and A2780/CP70 cells in a concentration-dependent manner. 3-hydroxyterphenyllin (2, 4 and 8 μM) induced S phase cellular arrest for OVCAR-3 and A2780/CP70 cells by upregulating CyclinB1 and Cdc25A expression and inhibiting Cdk4, CyclinA2 and CyclinE1 expression. These results suggest that 3-hydroxyterphenyllin has the potential to fight ovarian cancer cell growth by preventing progression past the S phase of the cell cycle.
Citation Format: Yi C. Chen. 3-Hydroxyterphenyllin induces S phase arrest in ovarian 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 4312.
Abstract 4324: Systematic characterization of A-to-I RNA editing in cancer development
Authors: Liang Han 
Published: August 2018

Abstract
Adenosine (A) to inosine (I) RNA editing, mediated by ADAR enzymes, is a well-established RNA modification mechanism. Recent studies show that A-to-I RNA editing introduces a large number of nucleotide changes in both coding and noncoding regions in cancer transcriptomes. First, to elucidate the contribution of RNA editing to proteomic diversity in human cancer, we performed an integrated analysis of The Cancer Genome Atlas (TCGA) genomic data and proteomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). We detected a considerable contribution of RNA editing in terms of amino acids changes induced per tumor sample in breast cancer. We validated some of these editing events at both RNA and protein levels, and further experimentally demonstrated the functional effects of some edited protein (e.g., increased proliferation, migration, and invasion of cancer cells in vitro). Second, we systematically characterized the miRNA editing hotspots across 20 cancer types from TCGA miRNA sequencing data and independently validated the vast majority of them by perturbation experiments in several cancer cell lines. These miRNA editing events show extensive correlations with key clinical variables and other molecular drivers. Focusing on the RNA editing hotspot in miR-200b, a key tumor metastasis suppressor, we found that the miR-200b editing level correlates with patient prognosis opposite to that pattern for the wild-type miR-200b expression. We further experimentally showed that in contrast to wild-type miRNA, the edited miR-200b can promote cell invasion and migration through its impaired ability to inhibit ZEB1/ZEB2 and acquired concomitant ability to repress new targets including LIFR, a well-characterized metastasis suppressor. Our results highlight the contribution of A-to-I RNA editing in cancer development and suggest its translational potential as both biomarkers and therapeutic targets.
Citation Format: Han Liang. Systematic characterization of A-to-I RNA editing in cancer development [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 4324.
Abstract 4325: Cisplatin treatment of testicular cancer introduces long-term changes to the epigenome
Authors: Rounge Trine B. , Bucher-Johannessen Cecilie , Page Christian M. , Haugen Trine B. , Fosså Sophie D. , Haugnes Hege S. , Grotmol Tom 
Published: August 2018

Abstract
Testicular cancer (TC) survival rates have increased substantially over the last decades, largely due to the introduction of cisplatin (CP) chemotherapy. This treatment is, however, associated with increased risk of developing metabolic syndrome (MetS), defined according to the National Cholesterol Education Program. We aimed to investigate if CP treatment were associated with epigenetic changes, and whether these changes render TC survivors susceptible for developing MetS later in life.
We included 279 Norwegian TC survivors with and without CP treatment and MetS, matched on age at blood sampling (Table 1). The TC survivors were re-examined on average 16 years after the orchiectomy, and for some patients, CP treatment. Whole genome DNA methylation profiles were measured with MethylationEPIC BeadChip and analyzed with the R package minfi. We used a linear regression model adjusting for smoking, age and cell type composition to identify CP differentially methylated CpG sites and logistic regression adjusting for smoking and age to identify differentially methylated CpG sites associated with MetS. Gene enrichment analyses were based on Fisher's exact test using KEGG and Reactome pathways.
32 and 15 differentially methylated CpG sites were associated with CP treatment after adjusting for multiple testing with False Discovery Rate (FDR) and Bonferroni correction, respectively. The PTK6-RAS-MAPk pathway was significantly enriched with the FDR significant CpGs (p-value &lt; 0.1). We could not identify FDR significant differentially methylated CpGs associated with MetS with our sample size.
In conclusion, our results suggest that CP treatment has long-term effects on the epigenome. Genes involved in double-strand break repair, consistent with the cytotoxicity of CP treatment, are among the differentially methylated CpGs. Our top list of differentially methylated CpGs associated with MetS (lowest unadjusted p-values), should be further explored in a larger sample set of TC survivors.
Table 1: Overview of sample characteristicsCP+ MetS+CP- MetS+CP+ MetS-CP- MetS-N613411569Mean age at surgery31312730Mean age at sample collection49484443Time between surgery and sample collection17181714
Citation Format: Trine B. Rounge, Cecilie Bucher-Johannessen, Christian M. Page, Trine B. Haugen, Sophie D. Fosså, Hege S. Haugnes, Tom Grotmol. Cisplatin treatment of testicular cancer introduces long-term changes to the epigenome [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 4325.