bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4327: The epigenetic effects of benzo[a]pyrene exposure
Authors: Galea Francesca , White Paul A. , Arlt Volker M. , Vineis Paolo , Flanagan James M. 
Published: August 2018

Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental carcinogens formed from the incomplete combustion of organic materials. Exposure to PAHs can be linked to at least 9 different cancer types, including lung and breast cancer. PAH are genotoxic and can form DNA adducts which can either be repaired or lead to mutations. DNA repair can lead to aberrant DNA methylation, however, few studies have investigated the link between PAH exposure and DNA methylation modifications. Here, we have used a mouse model to investigate the epigenetic consequences of PAH exposure. Mice (n=3/group) were treated by oral gavage with 0, 25, 50 and 75 mg/kg bodyweight/day of benzo[a]pyrene (BaP) for 28 days. Lung DNA from these mice was used to prepare Reduced Representation Bisulphite Sequencing (RRBS) libraries which were then sequenced using Illumina HiSeq2500to an average depth of 25x. For each mouse, DNA methylation was averaged over 500 bp tiled windows and differentially methylated regions (DMRs) were identified by comparing the controls (untreated) with all BaP-exposed mice (treated) irrespective of dose. In the treated vs untreated we identified 1815 windows (&gt;25% methylation difference, p&lt;0.05). Of these, we found that DMRs were under-represented in 5' untranslated regions (UTR), promoter, long interspersed nuclear elements (LINEs) regions and CpG islands compared with the genomic distribution of windows. DMRs were found to occur significantly more frequently in transcription termination regions. In addition, we found significantly more hypomethylation events in exon, intergenic, intronic and promoter regions, long terminal repeats (LTR) and short interspersed nuclear elements (SINE) and more hypermethylation in LINEs. Pyrosequencing validation on a selection of these DMRs is ongoing, using DNA from the same mice used in RRBS, plus mice exposed to BaP and other PAHs in lung and other tissues. In summary, these results show that PAHs have an effect on DNA methylation, and that these changes happen mostly within the gene body or intergenically, with significantly less differences observed at traditional gene expression regulators such as promoters. This
implies that the DNA methylation changes effected by BaP exposure may serve another purpose other than gene expression regulation.
Citation Format: Francesca Galea, Paul A. White, Volker M. Arlt, Paolo Vineis, James M. Flanagan. The epigenetic effects of benzo[a]pyrene exposure [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 4327.
Abstract 433: Diagnostic targeted sequencing panel for hepatocellular carcinoma genomic screening
Authors: Paradiso Viola , Garofoli Andrea , Tosti Nadia , Perrina Valeria , Lanzafame Manuela , Quagliata Luca , Matter Matthias S. , Wieland Stefan , Heim Markus H. , Piscuoglio Salvatore , Ng Charlotte K. , Terracciano Luigi M. 
Published: August 2018

Abstract
Commercially available targeted or exome panels miss some genes and regions frequently mutated in hepatocellular carcinoma (HCC); we aim to design and benchmark an HCC-specific panel as a robust high-throughput and cost-effective panel for genomic screening in HCC.
We designed an Ion AmpliSeq panel targeting all exons of 33 liver cancer protein-coding genes, recurrently mutated long non-coding RNA genes MALAT1 and NEAT1, the recurrently mutated promoter regions of TERT, WDR74, MED16 and TFPI2, as well as mutation hotspots in 7 additional cancer genes. We profiled DNA from fresh frozen tumor (FFT, n=10, median depth 1495x) and/or formalin-fixed paraffin-embedded (FFPE) tumor with low input DNA (n=36, median depth 530x), and their non-tumoral counterparts from 39 HCCs using the custom panel. We benchmarked the somatic mutations and copy number alterations (CNAs) identified against those from Illumina whole-exome sequencing (WES) of the equivalent FFT samples (median depth 112x).
At least one somatic mutation was identified in 35/39 cases using the custom panel. Median of 2.5 (0-74) and 3 (0-76) mutations were identified in FFT and FFPE samples, respectively. 98% (61/62) of the mutations identified from WES of the 10 FFT samples were successfully recovered using the custom panel, with the identification of an additional 6 and 32 mutations in coding and non-coding regions, respectively. Similarly, all 104 mutations identified from WES were also found based on the analysis of our custom panel of the 36 FFPE biopsies. We identified an additional 18 and 70 somatic mutations in coding and non-coding genes, respectively, using our custom panel, including 2 CTNNB1 activating mutations. Furthermore, copy number analysis revealed high correlation (r = 0.8) in the identification of gains/ amplifications and losses/ homozygous deletions in the genes included in the custom-panel between our custom panel and the WES.
Here, we develop a robust high-throughput and cost-effective tool for HCC genomic screening that allows the identification with high sensitivity and specificity of somatic mutations as well as copy number alterations in routine diagnostic tissue specimens.
Citation Format: Viola Paradiso, Andrea Garofoli, Nadia Tosti, Valeria Perrina, Manuela Lanzafame, Luca Quagliata, Matthias S. Matter, Stefan Wieland, Markus H. Heim, Salvatore Piscuoglio, Charlotte K. Ng, Luigi M. Terracciano. Diagnostic targeted sequencing panel for hepatocellular carcinoma genomic screening [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 433.
Abstract 4332: Meta-analysis of molecular features associated with aggressive prostate cancer
Authors: Costello James C. , Powers Rani , Goodspeed Andrew , Cramer Scott D. 
Published: August 2018

Abstract
The TMPRSS2:ERG fusion is the most common genomic alteration in prostate cancer, occurring in 40-50% of primary tumors. The frequency of the ERG fusion remains between 40-50% in metastatic tumors, supporting previous findings that the fusion can drive tumor development, but is not sufficient to drive aggressive, lethal disease. Large -omic datasets collected over thousands of patient tumors, such as The Cancer Genome Atlas (TCGA), paired with outcomes present the raw data needed to associate genetic aberrations with markers of aggressive disease. Accordingly, we performed a meta-analysis of over 2,000 patient samples to identify combinations of -omic features associated with aggressive ERG fusion-positive and ERG fusion-negative prostate cancer. The data were collected from 8 independent, publicly available prostate cancer cohorts and cover range of disease phenotypes (e.g., neuroendocrine, castration resistance). Our analysis consisted of training univariate Cox regression models separately for single genomic or pairs of genomic features within each independent dataset. Based on the availability, we explored gene expression, mutation, and copy number alterations, all used to build separate models. We then combined models for a genomic feature across all datasets by weighting individual coefficients by the inverse of their squared error in a fixed effects model; final results are reported as corrected p-values. We compared and contrasted results from combined models within data type (i.e., only gene expression) to models integrating multiple data types. Interestingly, we find that the genomic features associated with aggressive disease differed based on ERG status. We report genomic loci that are altered in all patients, but associate with aggressive disease only in patients with an ERG fusion. We also report loci that co-occur or are mutually exclusive of the ERG fusion and associated with aggressiveness. For example, SPOP mutations are known to be mutually exclusive of ERG fusions. We report a finer stratification of patients with SPOP mutations based on biochemical relapse. Our results present a compressive meta-analysis of molecular features in prostate cancer and identify novel molecular subtypes associated with aggressive disease.
Citation Format: James C. Costello, Rani Powers, Andrew Goodspeed, Scott D. Cramer. Meta-analysis of molecular features associated with aggressive prostate 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 4332.
Abstract 4338: Introduction of CALR mutations to a human erythroleukemia cell line, HEL, by CRISPR/Cas9 systems
Authors: Yasuda Shunichiro , Aoyama Satoru , Watanabe Daisuke , Kawamata Norihiko 
Published: August 2018

Abstract
[Introduction]Mutations of the calreticulin gene (CALR) are frequently found in patients with myeloproliferative neoplasms (MPN). Five-nucleotide insertion (Ins5) and 52-nucleotide deletion (Del52) in the last exon of the CALR gene are common mutations, generating an altered CALR protein with a mutated peptide sequence at the carboxy end due to the frame-shifts. Cell-lines with such CALR mutations have not been reported yet. CRISPR/Cas9 system is the novel technique commonly used in genetic engineering. CRISPR/Cas9 technology allows us to “edit” genome in mammalian cells. We introduced 46-nucleotide deletion (46Del) in the last exon of the CALR gene in a human erythroleukemia cell line, HEL. This 46Del abnormality lead to generation of an altered CALR protein with the abnormal peptide sequence at the carboxy end as seen in MPN cells with 52Del or Ins5. We compared the CALR-engineered HEL cells with the parental cells in the presence/absence of a Jak2 kinase inhibitor, ruxolitinib (RUX).
[Methods and Results]To introduce 46Del abnormality, we have designed two guide RNAs. We co-transfected vectors encoding the Cas9 with a fluorescence protein as a marker as well as the two guide RNAs into HEL cells using nucleoporation. Fluorescence protein positive cells were isolated and the single cells were cultured in 96-well plates for 3 weeks. Genomic DNA of each the clone was extracted, and genomic status of CALR was examined by PCR/sequencing. We have isolated one clone with 46Del (HEL-46DEL), of which expression of abnormal transcripts was confirmed by RT-PCR/sequencing. We also confirmed expressions of abnormal CALR protein by western blot analysis. Since the JAK2-STAT5 pathway is known to be activated in MPN cells, phosphorylation status of STAT5 in HEL and HEL-DEL46 was examined, showing comparable levels in each the line. Proliferation of HEL and HEL-DEL46 was examined with XTT assay, showing that the two lines proliferated similarly. RUX inhibited proliferation of HEL cells as well as HEL-DEL46. HEL cells have a JAK2 mutation which causes constitutive activation of the JAK2-STAT5 pathway. Introduction of the Del46 mutation into HEL cells might not enhance activation of the pathway because the JAK2 mutation already activates the pathway at the maximum level.
Citation Format: Shunichiro Yasuda, Satoru Aoyama, Daisuke Watanabe, Norihiko Kawamata. Introduction of CALR mutations to a human erythroleukemia cell line, HEL, by CRISPR/Cas9 systems [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 4338.
Abstract 4354: Molecular signature of multiple myeloma progression through single-cell RNA-seq
Authors: Jang Jin Sung 
Published: August 2018

Abstract
Multiple myeloma (MM) is a malignant plasma cell disorder with well-defined primary genetic/cytogenetic abnormalities. Investigating genetic heterogeneity in the MM cells, may have an impact on therapeutic approaches and assessment of response to treatment. Single cell genomic profiling technology provides an opportunity for us to identify genetic heterogeneity during the pathogenesis of MM progression and select the most appropriate clinical interventions. We performed single cell whole transcriptome analysis in 597 CD138 positive cells derived from 15 patients at different stages of MM progression. Using Coefficient of Variation (CV) approach, we identified 790 genes and defined four main groups reflective of increasing levels of aggressiveness at the single cell level. Differential gene expression and gene set enrichment analyses showed that protein homeostasis pathways, unfolded protein response and mTORC1 related gene sets were significantly enriched at the most aggressive level consistent with the MM cell progression and predicts the overall survival. Our results provide novel insights into the cellular heterogeneity within each MM patient and a foundation for therapeutic opportunities including proteasome inhibitors.
Citation Format: Jin Sung Jang. Molecular signature of multiple myeloma progression through single-cell RNA-seq [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 4354.
Abstract 4356: SIRT2-deacetylase activity is a potential predictive and prognostic marker in lung cancer patients
Authors: Guo Yang , Song Ha Yong , Raparia Kirtee , Vassilopoulos Athanassios 
Published: August 2018

Abstract
Background: SIRT2 has been described as a tumor suppressor, whereas our previous study using an LSL-KRASG12D mouse model showed that Sirt2 loss induced lung tumorigenesis in vivo through increased KRAS acetylation (K147) and activity. However, there is limited information about the clinical significance of SIRT2 expression and/or activity in lung cancer patients.
Purpose: The aim of this study was to investigate the associations between SIRT2 levels and activity with clinical-pathological characteristics and patient outcomes in lung cancer.
Materials and Methods: SIRT2 expression and activity was analyzed using a tissue microarray of 162 resected lung cancer samples from Northwestern Memorial Hospital. To assess SIRT2 expression, we used an antibody against SIRT2 for immunohistochemistry. To assess SIRT2 activity, we evaluated acetylated levels of two specific deacetylation targets, α-tubulin (K40) and KRAS (K147). For all tested markers, staining intensity of each tissue sample was scored as 0 (no signal), + 1 (weak), + 2 (distinct), + 3 (strong). The percentage of each positive staining was categorized as A (&lt;25%), B (25~50%), C (&gt;50%). Following statistical analysis, it was determined whether SIRT2 expression and activity were associated with several clinical parameters or outcomes. p &lt; 0.05 was assumed statistically significant.
Results: Acetylated α-tubulin and acetylated KRAS in lung tumor samples were significantly correlated with each other (p&lt;0.05), but not with SIRT2 expression. Of note, acetylated α-tubulin was significantly associated with TTF1 expression (p&lt;0.05), staging (p&lt;0.005), pleural metastasis (p&lt;0.005), surgery (p&lt;0.001), and chemotherapy (p&lt;0.005). Acetylated KRAS had significant associations with surgery (p&lt;0.005), lymph nodal status (p&lt;0.05) and pleural metastasis (p&lt;0.05). Kaplan-Meier analysis further indicated that both TTF1 and acetylated α-tubulin were independent predictors of patient survival (p=0.005 and p=0.028, respectively).
Conclusions: Our data implicated that SIRT2 deacetylation activity, but not SIRT2 expression levels, could represent an optimal predictive and prognostic factor in lung cancer. Based on this finding, strategies to increase SIRT2 activity might be favorable in clinical treatment protocols for lung cancer.
Citation Format: Yang Guo, Ha Yong Song, Kirtee Raparia, Athanassios Vassilopoulos. SIRT2-deacetylase activity is a potential predictive and prognostic marker in lung cancer patients [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 4356.
Abstract 4361: Role of Rab GTPases and endosomal adaptor proteins in oncogenic RAS induced formation of perinuclear signaling complexes (PSCs)
Authors: Basu Srikanta , Basu Sandip K. , Salotti Jacqueline , Johnson Peter F. 
Published: August 2018

Abstract
Oncogenic RAS signaling leads to neoplastic transformation in immortalized cells and oncogene induced senescence in primary cells. Our laboratory has found that in both primary and immortalized cells oncogenic RAS induces constitutive perinuclear re-localization of p-ERK, CK2, and the MAPK scaffolding protein, KSR1. KSR1 binds to p-ERK and CK2, forming assemblies that we call “perinuclear signaling complexes” (PSCs). We observe PSCs in all cancer cell lines tested and in KRasG12V-driven mouse lung tumors, indicating that PSC formation is an important and integral characteristic of tumor cells. Our results show that KSR1 is essential for PSCs, as RNAi-mediated depletion of KSR1 or knockout of KSR1 disrupted their formation. We also demonstrated a key role for endosomal trafficking in this localized RAS signaling, as pharmacological inhibition of endocytosis prevented PSC formation. Furthermore, Rab11A, a Rab GTPase involved in trafficking of recycling endosomes, is required for establishment of PSCs and co-localizes with a pool of cellular CK2 and KSR1, but not p-ERK. Moreover, Rab11A knockdown caused decreased proliferation and survival of A549 cells (human KRAS mutant non-small cell lung adenocarcinoma). Our results demonstrate that there may be at least two classes of PSC-containing endosomes, p-ERK bound endosomes and CK2 bound endosomes. We are currently attempting to identify Rab GTPases that may differentiate these two kinds of PSC containing endosomes. Jongsma et al. (Cell, 2016) have shown that endosomes associated with the ubiquitin adaptor proteins EPS15, Tollip or TAXBP1 localize to the perinuclear region via the signaling adaptor, SQSTM1 (p62), which is tethered to the ER. We found that Tollip knockdown in A549 cells disrupted the CK2 bound endosomes but not p-ERK bound endosomes. Tollip knockdown also decreased cell proliferation and cell survival, while increasing apoptosis and autophagy. Whether other adaptor proteins are involved in RAS-mediated PSC formation remains to be determined. Growth factors (GF) also transiently induced PSCs in normal cells with delayed kinetics (4-6 hr). Our findings indicate that transformed cells sustain this novel late phase of GF signaling, localizing RAS pathway kinases to a nuclear-proximal compartment to drive tumorigenesis. We propose that PSCs are hallmarks of cancer cells and may represent useful biomarkers for cancer diagnosis and therapeutic responses.
Citation Format: Srikanta Basu, Sandip K. Basu, Jacqueline Salotti, Peter F. Johnson. Role of Rab GTPases and endosomal adaptor proteins in oncogenic RAS induced formation of perinuclear signaling complexes (PSCs) [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 4361.
Abstract 4367: The small GTPase ARF6 is necessary for melanomagenesis
Authors: Acosta Lehi , Rogers Aaron , Peng Jingfu , Mueller Alan , Tong Zongzhong , Shin Donghan , Yoo Jae Hyuk , Li Dean Y. , Odelberg Shannon J. , Holmen Sheri L. , Grossmann Allie H. 
Published: August 2018

Abstract
ARF6 is a member of the adenosine diphosphate (ADP)-ribosylation factor (ARF) family of small GTPases and is part of the RAS superfamily. We have shown that pharmacologic inhibition of ARF6 can inhibit proliferation of uveal melanoma and invasion/metastasis of cutaneous melanoma. Most cutaneous melanomas are defined by mutually-exclusive driver mutations in BRAF, NRAS, or NF1. These subtypes share similar mechanisms of oncogenesis because they align along a continuum of RAS signaling. Mutations in the PI3K pathway occur in a fraction of all melanoma subtypes, indicating a selective advantage for PI3K/AKT activation beyond BRAF or RAS activation. We and others have reported ARF6-dependent ERK activation occurring upon either extracellular ligand stimulation or mutant oncoprotein signaling. Recently, ARF6 has also been shown to be upstream of PI3K signaling. Based on these findings, we hypothesized that ARF6 is critical for both the RAF and PI3K arms of the RAS pathway and that loss of ARF6 will impede tumor growth driven by these oncogenes. We tested this hypothesis using human melanoma cell lines and with an inducible, genetically engineered mouse model (GEMM) of melanoma. Our data reveal that pharmacologic inhibition of ARF6 can reduce proliferation of BRAF, NRAS and NF1-mutated melanoma cells. Furthermore, loss of Arf6 causes a reduction in mean tumor size and improves survival in BRAFV600E/CDKN2ANULL/PTENNULL/AKTE17K and BRAFV600E/CDKN2ANULL/PTENNULL mice. These results indicate that ARF6 is necessary for melanomagenesis and for oncogenic BRAF and/or PI3K signaling. Our data suggest that ARF6 may be an actionable node in the RAS pathway and that therapeutic targeting of ARF6 has the potential to improve current treatment methods for progressive disease.
Citation Format: Lehi Acosta, Aaron Rogers, Jingfu Peng, Alan Mueller, Zongzhong Tong, Donghan Shin, Jae Hyuk Yoo, Dean Y. Li, Shannon J. Odelberg, Sheri L. Holmen, Allie H. Grossmann. The small GTPase ARF6 is necessary for melanomagenesis [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 4367.
Abstract 4369: Functional role of RhoGEF FGD4 in promotion of aggressive prostate cancer
Authors: Bossan Alexia , Ottman Richard , Coppola Domenico , Chakrabarti Ratna 
Published: August 2018

Abstract
Hyperactivation of Rho family of GTPases including Rac, Cdc42 and Rho, as a result of deregulation of Rho guanine nucleotide exchange factors (GEF) is commonly noted in various cancers including prostate cancer. A number of GEFs are overexpressed in prostate and breast cancer cells and tissues, and show an association with poor prognosis. Earlier, we showed that a prolonged treatment with androgen receptor antagonist Casodex resulted in up regulation of a GEF FGD4, traditionally associated with hereditary motor and sensory neuropathies including Charcot-Marie-Tooth disease. FGD4 is a Cdc42 specific GEF and contains an actin binding domain FAB, in addition to the conserved FYVE domain, a DH domain for catalytic activity and two PH domains for targeting proteins to the membranes through phosphoinositide binding. Our study revealed that Casodex treatment of prostate cancer cells lead to down regulation of a microRNA cluster miR-17-92a that targets FGD4. Here we show that FGD4 is upregulated in cancerous prostate tissues compared to benign prostatic hyperplasia and PIN. FGD4 protein expression and altered localization gradually increase with increasing tumor grade and aggressiveness. Inhibition of FGD4 expression using siRNAs, reduced cell proliferation, resulted in a G2/M arrest, inhibited cell migration and reduced Cdc42 activity. Inhibition of FGD4 also improved sensitivity of androgen sensitive LNCaP cells to Casodex and PC-3 cells to the microtubule stabilizing drug docetaxel. Our data demonstrate a tumor promoting function of FGD4 in prostate cancer cells and that inhibition of FGD4 expression has a therapeutic benefit for both androgen-dependent and -independent prostate cancer cells.
Citation Format: Alexia Bossan, Richard Ottman, Domenico Coppola, Ratna Chakrabarti. Functional role of RhoGEF FGD4 in promotion of aggressive prostate 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 4369.