bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2278: Scalability and reliability improvements to the Iso-Seq analysis pipeline enables higher throughput sequencing of full-length cancer transcripts
Authors: Tseng Elizabeth , Clark Tyson , Ashby Meredith H. 
Published: August 2018

Abstract
The characterization of gene expression profiles via transcriptome sequencing has proven to be an important tool for characterizing how genomic rearrangements in cancer affect the biological pathways involved in cancer progression and treatment response. More recently, better resolution of transcript isoforms has shown that this additional level of information can be useful in stratifying patients into cancer subtypes with different outcomes and responses to treatment. The Iso-Seq protocol developed at PacBio is uniquely able to deliver full-length, single molecule cDNA sequences, allowing for the unambiguous, direct determination of splice variants. This has led to the identification of novel cancer biomarker candidates and has yielded new insights into gene fusion events that contribute to cancer progression.1,2,3
Recent improvements to the Iso-Seq bioinformatics pipeline increases the speed and scalability of data analysis while boosting the reliability of isoform detection and cross-platform usability. Here we report evaluation of Iso-Seq runs of human UHRR samples with spiked-in synthetic RNA controls on the Sequel System and show that the new pipeline recovers both more human and synthetic isoforms while reducing the number of false positives. We also share the results of sequencing the well-characterized HCC-1954 breast cancer and matched normal cell lines, which will be made publicly available. Combined with the recent simplification of the Iso-Seq sample preparation protocol, the new analysis pipeline completes a streamlined workflow for revealing the most comprehensive picture of transcriptomes at the throughput needed to characterize cancer samples.
1. Kohli M, et. al. (2017) Androgen Receptor Variant AR-V9 Is Coexpressed with AR-V7 in Prostate Cancer Metastases and Predicts Abiraterone Resistance. Clin Cancer Res. ePub ahead of print. doi: 10.1158/1078-0432.CCR-17-0017
2. Komor MA, et. al. (2017) Identification of differentially expressed splice variants by the proteogenomic pipeline Splicify. Mol Cell Prot. ePub ahead of print. doi: 10.1074/mcp.TIR117.000056
3. Weirather JL, et. al. (2015) Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing. Nucleic Acids Res, 43 (18), e116.
Citation Format: Elizabeth Tseng, Tyson Clark, Meredith H. Ashby. Scalability and reliability improvements to the Iso-Seq analysis pipeline enables higher throughput sequencing of full-length cancer transcripts [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 2278.
Abstract 2287: Precise common and rare germline CNV calling with GATK
Authors: Babadi Mehrtash , Lee Samuel K. , Smirnov Andrey , Lichtenstein Lee , Gauthier Laura D. , Howrigan Daniel P. , Poterba Timothy 
Published: August 2018

Abstract
We propose, implement, and evaluate a novel method (GATK gCNV) for accurate discovery of rare and common copy-number variations (CNVs) from read-depth data obtained from whole genome sequencing (WGS), whole exome sequencing (WES), or custom gene panels. GATK gCNV utilizes a sophisticated Bayesian model to learn bias factors arising from sequencing and library preparation. This model accounts for ploidy of sex chromosomes and autosomal aneuploidies, treats GC bias probabilistically, and automatically determines the necessary level of model complexity in a data-driven manner. Unlike most existing read-depth methods, GATK gCNV maintains a high level of sensitivity in common CNV regions, due to a hierarchical hidden Markov model used for accurate genotyping of multi-allelic loci. Furthermore, GATK gCNV performs bias modeling and CNV discovery simultaneously and self-consistently, resulting in significantly improved sensitivity and precision. Our implementation utilizes the PyMC3/Theano framework for performing automatic differentiation variational inference (ADVI). In addition, GATK gCNV automatically scatters large tasks across multiple machines using the Cromwell/WDL framework, enabling the scalable processing of large cohorts.
We use GATK gCNV to compute copy-number transmission and de novo rates in a cohort of WES trios and observe consistency with observed population metrics. Furthermore, we benchmark GATK gCNV for sensitivity, precision, and reproducibility of both rare and common CNV calls. Using a cohort of WES blood normal samples from The Cancer Genome Atlas (TCGA), we show that GATK gCNV calls are in remarkable concordance with Genome STRiP calls on matched WGS data and gCNV substantially outperforms XHMM and CODEX. We also validate GATK gCNV calls on WGS data against calls made using PacBio long reads.
Citation Format: Mehrtash Babadi, Samuel K. Lee, Andrey Smirnov, Lee Lichtenstein, Laura D. Gauthier, Daniel P. Howrigan, Timothy Poterba. Precise common and rare germline CNV calling with GATK [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 2287.
Abstract 2298A: Enhanced consideration of context dependence reveals the scope of somatic missense drivers in human cancers
Authors: Tokheim Collin J. , Nanda Neha , Roberts Nicholas J. , Karchin Rachel 
Published: August 2018

Abstract
Large-scale sequencing studies of patient cohorts have enabled identification of many driver genes whose somatic alterations confer a selective advantage to cancer cells. However, not every mutation in a driver gene is necessarily a driver of cancer. As mutation-based biomarkers are increasingly used to decide drug regimens and placement in clinical trials, it is important to distinguish specific driver mutations. Improved computational methods are necessary for identifying the particular mutations in a given cancer that are drivers, especially for rare mutations (&lt;1% of patients). We have previously developed the CHASM algorithm to identify cancer-specific driver missense mutations. Here, we present a completely re-worked version that leverages the context-dependence of driver mutations. We show that the new CHASM2 consistently outperforms comparable methods across a wide variety of benchmarks, including in vivo and in vitro experiments. Applied to 8,657 TCGA cancer samples in 32 cancer types, CHASM2 identifies 3,527 distinct driver somatic missense mutations. Our results suggest substantial heterogeneity of the driver mutation landscape across cancer types and a strikingly large prevalence of rare driver mutations. For particular cancer types driven by common mutations, current sample sizes are already saturating driver discovery. We performed validation experiments on missense mutations of rare and intermediate frequency in the tumor suppressor gene ATM and show CHASM2 distinguishes a radiosensitive phenotype in cultured cells. To our knowledge CHASM2 is the first sufficiently powered method to predict individual driver somatic missense mutations at multiple scales – whole exome, targeted gene panel, and within a single gene.
Citation Format: Collin J. Tokheim, Neha Nanda, Nicholas J. Roberts, Rachel Karchin. Enhanced consideration of context dependence reveals the scope of somatic missense drivers in human cancers [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 2298A.
Abstract 2305: Targeting 6-phosphofructo-2-kinase to increase the efficacy of ER and CDK4/6 inhibitors against breast cancer
Authors: Imbert-Fernandez Yoannis , Lanceta Lilibeth , Telang Sucheta , Chesney Jason 
Published: August 2018

Abstract
We demonstrated that estradiol stimulates the expression and activity of an enzyme, 6-phosphofructo-2-kinase (PFKFB3), that regulates glucose metabolism via allosteric stimulation of 6-phosphofructo-1-kinase. PFKFB3 expression is increased in breast cancer cells that have metastasized to lymph nodes and the combination of the anti-estrogen, fulvestrant, with a PFKFB3 inhibitor, PFK158, synergistically increases apoptosis in ER+ breast cancer cells in vitro and in vivo. Given that estradiol simultaneously increases the expression of both the regulatory subunit of CDK4/6, cyclin D1, and PFKFB3, we postulated that the combination of palbociclib with PFK158 would yield synergy against breast cancer cells. In new preliminary studies, co-treatment with palbociclib and PFK158 resulted in a marked decrease in cell proliferation in two ER+ breast cancer cell lines that was accompanied by a synergistic decrease in phospho-Retinoblastoma (Rb). Importantly, exposure of ER+ breast cancer cells to palbociclib and PFK158 causes an increase in cell cycle arrest and apoptotic cell death in vitro. Notably, this combination has no effect on cell cycle arrest or apoptosis in normal mammary cells suggesting that this therapeutic strategy may be well tolerated and selective for breast cancer.
Citation Format: Yoannis Imbert-Fernandez, Lilibeth Lanceta, Sucheta Telang, Jason Chesney. Targeting 6-phosphofructo-2-kinase to increase the efficacy of ER and CDK4/6 inhibitors against breast 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 2305.
Abstract 2312: Phospho-proteomics analysis to determine the signaling pathways affected by a novel CDC7-selective inhibitor TAK-931
Authors: Iwai Kenichi , Gotou Masamitsu , Yamanaka Kazunori , Ohashi Akihiro 
Published: August 2018

Abstract
Background: Cell division cycle 7 (CDC7) is a serine/threonine kinase, which plays important roles in initiation of DNA replication by phosphorylating MCM2. We developed the CDC7-selective small molecule inhibitor TAK-931. Treatment with TAK-931 results in delayed S phase progression, DNA replication stress (RS), centrosome disorganization, mitotic aberrations, and potent growth suppression in cancer cells. In this study, we conducted the time-dependent phospho-proteomics analysis to determine the signaling pathways affected by TAK-931.
Materials and Methods: TAK-931 was synthesized by Takeda Pharmaceutical Company, Ltd. The SILAC-labeled COLO205 cells were treated with TAK-931 at 100 nM for 0, 4, 24 hours, applying for the phospho-proteomics analysis in the PhosphoScout® Service at Evotec AG (Munich, Germany).
Results: The SILAC-labeled COLO205 cells with TAK-931 treatment were subjected to quantitative mass spectrometry, detecting 15,128 phosphorylation sites of the 4,426 phosphoproteins. At 4 h of treatment, only 2 phosphorylation sites were detected as significantly downregulated: MAX gene-associated protein (MGA) and alpha-enolase (ENO1). At 24 h of treatment, however, 51 phosphorylation sites were identified as being significantly altered, including 44 upregulation and 7 downregulation sites. The gene ontology (GO) enrichment analysis in the categories of biological process (BP) and cellular component (CC) revealed that 10 GO terms from BP and 2 GO terms from CC were significantly enriched in the treated cells after 24 h: cell cycle, cell cycle phase, cell cycle process, mitosis, nuclear division, organelle fusion, organelle organization, mitotic cell cycle, M phase of mitotic cell cycle, M phase, chromosomal part, and spindles. Network analysis on the changed phosphorylation prolife also revealed that significant network modules existed at 24 h of treatment, which included DNA replication/damage, mitotic progression/spindle assembly, nucleus assembly, GTPase activity, cell migration, cell adhesion, TP53, and protein translation.
Conclusion: The time-dependent phospho-proteomics analysis revealed the dynamics of phospho-signal transduction affected by TAK-931 in the cancer cell, which may help to provide a deeper understanding of the molecular mechanisms of TAK-931.
Citation Format: Kenichi Iwai, Masamitsu Gotou, Kazunori Yamanaka, Akihiro Ohashi. Phospho-proteomics analysis to determine the signaling pathways affected by a novel CDC7-selective inhibitor TAK-931 [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 2312.
Abstract 2318: Palbociclib, a CDK4/6 inhibitor, suppresses proliferation of triple negative breast cancer
Authors: Min Ahrum , Kim Yu Jin , Hang Hyemin , Lim Jee Min , Kim Seongyeong , Kim So Hyeon , Suh Koung Jin , Lee Kyung-Hun , Kim Tae-Yong , Im Seock-Ah 
Published: August 2018

Abstract
Background: Abnormal cell cycle progression is a characteristic of cancer and targeting the cell cycle is a strategy for cancer treatment. TCGA reported that Cyclin D1 is overexpressed in 25% to 60% of invasive breast carcinomas, and CDK4/6 and CDKN2A/B aberrations are observed in 7.6% of breast cancer cases. Palbociclib is a specific inhibitor of CDK4/6, a key regulator of the G1 checkpoint. In hormone receptor positive breast cancer, the addition of palbociclib to endocrine treatment either aromatase inhibitor or fulvestrant significantly prolonged PFS in phase III trials. However, the effects of palbociclib have not been fully examined in triple negative breast cancer (TNBC) yet, although CCND amplification and CDKN2A loss are frequently observed in TNBC. Therefore, we investigated the effects of palbociclib on TNBC cells and attempted to identify the underlying mechanisms of palbociclib.
Methods: The cytotoxicity assay, cell cycle analysis and western blotting were conducted to determine anti-tumor effect and action mechanisms of palbociclib on breast cancer cell lines. These in vitro data were validated in vivo model as well.
Results: Human breast cancer cell lines showed heterogeneous response to palbociclib. Palbociclib induced G1 cell cycle arrest by blocking Rb phosphorylation, and inhibited cell proliferative signaling. In sensitive TNBC cells, palbociclib promoted senescence rather than apoptosis. In addition, palbociclib enhanced the antitumor effect of 5-FU by modulating thymidine synthase (TS) and E2F1 expression. The anti-tumor effects of palbociclib on TNBC cells were validated in TNBC-xenograft model as well.
Conclusions: CDK4/6 inhibitor palbociclib showed anti-tumor effect in vitro and in vivo xenograft model of TNBC and acts synergistically with 5-FU by downregulating TS. Our results suggest that palbociclib has therapeutic potential for the treatment of TNBC, not limited in hormone positive breast cancer type. Our results provide a rationale for the future clinical trials of palbociclib in the treatment of breast cancers.
Citation Format: Ahrum Min, Yu Jin Kim, Hyemin Hang, Jee Min Lim, Seongyeong Kim, So Hyeon Kim, Koung Jin Suh, Kyung-Hun Lee, Tae-Yong Kim, Seock-Ah Im. Palbociclib, a CDK4/6 inhibitor, suppresses proliferation of triple negative breast 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 2318.
Abstract 2320: Heme oxygenase-1 mediates ferroptosis
Authors: Chiang Shih-Kai , Chen Shuen-Ei , Chang Ling-Chu 
Published: August 2018

Abstract
Ferroptosis is a form of oxidative cell death and has become a chemotherapeutic target for cancer treatment. BAY 11-7085 (BAY), which is a well-known IκBα inhibitor, suppressed viability in cancer cells via induction of ferroptotic death in an NF-κB-independent manner. This study was aimed to characterize the underlying mechanism by BAY and demonstrate its potential chemotherapeutic targets for cancer treatment. Reactive oxygen species scavenging, relief of lipid peroxidation, replenishment of glutathione and thiol-containing agents, as well as iron chelation, rescued BAY-induced cell death in human breast cancer cells (MDA-MB-231 and MDA-MB-468) and glioblastoma cells (DBTRG-05MG). The results from quantitative real-time PCR and western blotting analysis showed that BAY upregulated a variety of nuclear factor-E2-related factor 2 (Nrf2) target genes related to redox regulation, particularly heme oxygenase-1 (HO-1) and solute carrier family 7 membrane 1 (SLC7A11). Studies with pharmacological inhibitors and shRNA interventions suggested that the hierarchy of induction is Nrf2-SLC7A11-HO-1. The ferroptotic process induced by hHO-1 overexpression further indicated that HO-1 is a key mediator of BAY-induced ferroptosis that operates through cellular redox regulation and iron accumulation. Our study discovered that BAY induced ferroptosis via Nrf2-SLC7A11-HO-1 pathway and provided new insights to understand the mechanism of HO-1-induced ferroptosis, suggesting HO-1 as a new chemotherapeutic target for cancer treatment.
Citation Format: Shih-Kai Chiang, Shuen-Ei Chen, Ling-Chu Chang. Heme oxygenase-1 mediates ferroptosis [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 2320.
Abstract 2327: Azole antifungal drugs induce cell death by suppressing mTOR through PI3K/Akt inhibition in human breast cancer
Authors: Park Ju Ho , Kim Hyesook , Kim So Hee 
Published: August 2018

Abstract
Breast cancer is a major cancer in women and its incidence rate increases every year. So it needs a perfect treatment. Azole drugs structurally have an imidazole [clotrimazole (CTZ) and ketoconazole (KCZ)] or a triazole [fluconazole (FCZ) and itraconazole (ICZ)]. Recently, azole antifungal drugs have shown anticancer efficacy in clinical trial. However, their antitumor mechanism are vague. Here, we evaluated the effects, as apoptosis, cell arrest, and autophagy and tumor growth using human breast cancer cells. Apoptosis assay showed imidazole-induced cell death, pro-apoptosis maker, as cleaved PARP, cleaved caspase-3, Bax, increased and anti-apoptosis maker, as Bcl-2, decreased by CTZ and KCZ in both MCF-7 and MDA-MB-231 cells. We also checked imidazole of azole drugs blocked the cell cycle in G1 phage by downregulating the protein levels of cyclin D1, CDK2, and CDK6 and increased p21 and p27 in breast cancer. Further experiments showed that azole drugs also induced autophagy through the increased accumulation of LC 3B inside the cells by immunoblot analysis and immunofluorescence staining, increased beclin-1 and decreased p62 protein. With azole decreased that though 3-MA. Azole drugs inhibited PI3K/Akt/mTOR signaling pathway. Tumor growth was also inhibited in nude mice bearing MDA-MB-231 xenograft by CTZ, KCZ and ICZ through the accumulation of LC 3B in tumor xenograft. In conclusion, imidazole antifungal drugs induced apoptosis, cell cycle and autophagy by suppressing mTOR through the regulation of PI3K/Akt pathway in human breast cancer cells, suggesting azole antifungal drugs could be new potential therapeutics for breast cancer.
Citation Format: Ju Ho Park, Hyesook Kim, So Hee Kim. Azole antifungal drugs induce cell death by suppressing mTOR through PI3K/Akt inhibition in human breast 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 2327.
Abstract 2328: ADCs that induce necrosis and thwart apoptotic resistance
Authors: Prudent James R. , Marshall David 
Published: August 2018

Abstract
Purpose: We have previously shown that targeting the Na,K-ATPase (NKA) with antibody drug conjugates is a powerful method for reducing tumors at levels found to be safe in cynomolgus monkeys. Currently no approved cancer drugs induce a potent necrotic type cell death even though experimental evidence shows that necrotic cell death has many notable and untapped benefits. Therefore, we wanted to better understand the driving mechanism by which ADCs targeting NKA inhibition induce necrosis.
Experimental Design: Various cancer cell types were subjected to increasing and decreasing concentrations of Na+, K+ and Ca++, as well as various ADCs using bufalin as the warhead/payload/toxin. The cells were also subjected to siRNAs specific to the NKA and bufalin alone. The cells were then analyzed for the appearance and/or presence of necrosis, apoptosis, and markers indicating various stress pathways.
Results: Conditions found to induce necrosis included: ADCs targeting specific NKA-protein complexes, cells subjected to media containing increased concentrations of K+, the specific Na,K-ATPase siRNAs, and bufalin alone.
Conditions not found to induce necrosis included: media containing increased Na+, decreased Na+ or K+, control siRNAs, or ADCs that targeted proteins not complexed to the NKA or expressed on the cell surface.
All cells undergoing necrosis lost their actin filaments, rounded up, and adherent cells detached from the surface and lost their motility. Markers indicated initial activation of the integrated stress responses (ISR). Minimal to no annexin staining indicated that apoptosis was not the dominate pathway in any experiment.
Conclusion: Proper ion flux is important for maintaining cellular homeostasis. Cell swelling is a key process that is used to correct for changes in ion flux, induce inflammation and kill unwanted cells. The NKA is a key regulatory protein in this process and when blocked, leads to uncontrolled cells swelling and necrotic death. Precise inhibition of ion flux focused on cancer cells should be further investigated as a potential method for treating patients.
Citation Format: James R. Prudent, David Marshall. ADCs that induce necrosis and thwart apoptotic resistance [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 2328.
Abstract 2329: Noncanonical mitophagy induced by Mieap and its role in tumor suppression via ferroptosis-like cell death
Authors: Nakamura Yasuyuki , Yamamoto Makoto , Arakawa Hirofumi 
Published: August 2018

Abstract
Parkin/Pink1-mediated mitophagy plays a critical role in mitochondrial quality control, in which the damaged mitochondria are sequestered by autophagosomes, and degraded by fusion between autophagosomes and lysosomes. Here, we report Mieap-mediated noncanonical mitophagy as a new function of tumor suppressor p53. Mieap was originally identified as a p53-target gene. Overexpression of exogenous Mieap induces large vacuoles in cancer cells. Mieap-induced vacuoles are generated from the mitochondria, and directly eat and degrade the cancer mitochondria. UVRAG regulates the Mieap-mediated noncanonical mitophagy. Surprisingly, Mieap-mediated noncanonical mitophagy induces cell death via the iron-dependent production of reactive oxygen species (ROS). Introduction of exogenous Mieap strikingly suppresses in vivo tumor growth of Mieap-deficient colorectal cancer cells. Deficiency of endogenous Mieap dramatically promotes cancer development, malignancy, and aggressiveness in colorectal and gastric cancer model mice. The cell death induced by Mieap-mediated noncanonical mitophagy occurs via the ROS production in in vivo hypoxic tumor microenvironment. These results suggest that Mieap-mediated noncanonical mitophagy plays a critical role in tumor suppression via ferroptosis-like cell death.
Citation Format: Yasuyuki Nakamura, Makoto Yamamoto, Hirofumi Arakawa. Noncanonical mitophagy induced by Mieap and its role in tumor suppression via ferroptosis-like cell death [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 2329.