bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1316: Germline genetic signals across multiple aggressive prostate cancer phenotypes
Authors: Tai Caroline G. , Emami Nima C. , Hoffmann Thomas J. , Sakoda Lori C. , Jorgenson Eric , Habel Laurel A. , Shan Jun , Ranatunga Dilrini K. , Chao Chun R. , Ghai Nirupa R. , Aaronson David , Presti Joseph , Schaefer Catherine , Risch Neil , Eeden Stephen K. Van Den , Witte John S. 
Published: July 2017

Abstract
Prostate cancer (PrCa) is documented to be highly heritable. But many known prostate cancer loci are not associated with aggressive prostate cancer phenotypes such as high-grade cancer or biochemical failure. Previous efforts have been largely underpowered or not replicated.
We conducted a study of 6,321 men with PrCa and 5,663 controls of European ancestry recruited from Kaiser Permanente (KP) matched by age and self-reported race. Phenotype data combined patient-level demographic, clinical, and tumor data from KP databases with data from 1994 to 2016. High-grade PrCa was defined using Gleason score: low-grade defined as ≤ 7 (3+4), high-grade defined as ≥ 7 (4+3). Biochemical failure was defined for cases using post-treatment prostate specific antigen (PSA) values: post-surgery failure if PSA ≥ 0.4 ng/mL; post-radiation failure if PSA value ≥ 2 ng/mL + nadir; and no failure if PSA did not reach specified threshold. Early-onset disease was defined as age &lt; 55 years at diagnosis. Men were genotyped for over 650,000 SNPs using an ethnic-specific Affymetrix Axiom array and imputed to 1000 Genomes. We tested genetic associations for multiple aggressive phenotypes (410 early-onset cases, 1324 biochemical failure cases, and 886 high grade cases) in both a case-only (e.g., high vs. low grade) and case-control (e.g., high grade vs. no prostate cancer controls) analysis using logistic regression adjusting for ancestry principal components, age, BMI, and kit for batch effects. PrCa specific mortality was too rare to be evaluated.
We identified several known and novel loci. Case-control analyses highlighted known prostate cancer loci at 8q24, 10q11, 11q13, 16q22, and 19q13. Previous reports of case-only analyses also identified 8q24, 20p13 and the gene, KLK3 in 19q13, to be associated with high-grade PrCa; we confirmed these signals in our study. Previous family-based studies identified 15q11 as a familial or early-onset prostate cancer locus.
These aggressive-specific variants could perform better in predicting clinically actionable prostate cancers than variants for overall prostate cancer and can improve the predictive ability of pre-diagnostic PSA.
Citation Format: Caroline G. Tai, Nima C. Emami, Thomas J. Hoffmann, Lori C. Sakoda, Eric Jorgenson, Laurel A. Habel, Jun Shan, Dilrini K. Ranatunga, Chun R. Chao, Nirupa R. Ghai, David Aaronson, Joseph Presti, Catherine Schaefer, Neil Risch, Stephen K. Van Den Eeden, John S. Witte. Germline genetic signals across multiple aggressive prostate cancer phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1316. doi:10.1158/1538-7445.AM2017-1316
Abstract 1319: Epigenome-wide association study reveals differential DNA methylation consistent with progression of multiple myeloma
Authors: Gragg Stephen D. , Absher Devin , Cui Xiangqin , Pillion Christina , Myers Richard , Kumar Shaji , Costa Luciano , Chiu Brian , Vachon Celine , Brown Elizabeth 
Published: July 2017

Abstract
Purpose: Multiple myeloma (MM) is the second most common hematological malignancy in the US. It is characterized by a clonal expansion of plasma cells in the bone marrow and extramedullary sites and is preceded by two precursor conditions including monoclonal gammopathy of undetermined significance (MGUS) and smoldering myeloma (SMM). Strong evidence suggests a germline and environmental etiology. However, efforts to characterize heritable changes in gene activity, such as DNA methylation, have not been widely reported.
Methods: We examined epigenome-wide DNA methylation as markers of MGUS, SMM and MM in peripheral blood obtained from treatment-naïve European American cases with heavy-chain IgG or IgA MGUS (n=60), SMM (n=31) and MM (n=54) and age- and sex-matched controls (n=79) included from the University of Alabama at Birmingham, University of Chicago and the Mayo Clinic, Rochester [54.5% males; mean age, 64 years (range, 36 to 86)]. We quantified DNA methylation of over 450,000 CpG and non-CpG loci using the Infinium HumanMethylation450 array (Illumina). Differentially methylated positions were calculated using a general linear model framework adjusted for confounders and cellular heterogeneity.
Results: A total of 6 CpGs were differentially methylated in MM cases compared to controls at a level of genome-wide statistical significance. MM was associated with hypomethylation at differentially methylated positions inside SBNO2 (P=3.37x10-10), WIZ (P=1.12x10-8), CA6 (P=4.29x10-8) and ADORA1 (P=3.68x10-8) as well as intergenic positions proximal to TNFRSF8 (Chr 1p36.22; P=2.24x10-9) and ENDOV (Chr 17q25.3; P=2.74x10-8). Each of these loci, with the exception of CA6 and ADORA1, were hypomethylated in each of the 3 plasma cell dyscrasia phenotypes including MGUS and SMM and MM cases compared to controls (P&lt;0.03), albeit not at a level of genome-wide statistical significance.
Conclusions: These preliminary findings suggest that differences in DNA methylation may contribute to altered risk of MM, as well as its precursor conditions, and may play a role in plasma cell dyscrasia progression as a consequence of heritable changes in gene activity due to past exposures. Replication in a large yet similarly well-characterized population is warranted.
Citation Format: Stephen D. Gragg, Devin Absher, Xiangqin Cui, Christina Pillion, Richard Myers, Shaji Kumar, Luciano Costa, Brian Chiu, Celine Vachon, Elizabeth Brown. Epigenome-wide association study reveals differential DNA methylation consistent with progression of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1319. doi:10.1158/1538-7445.AM2017-1319
Abstract 1320: Non-additive and interaction effects of HLA class 2 polymorphism contributing to risk of glioma
Authors: Zhang Chenan , Walsh Kyle 
Published: July 2017

Abstract
Although genome-wide association studies have identified a number of susceptibility loci for adult glioma, little is still known regarding whether polymorphisms in the human leukocyte antigen (HLA) region contribute risk. HLA associations have previously been reported for a number of malignancies, with selected HLA polymorphisms investigated in a subset of glioma studies. However, no systematic analysis has been conducted to date, and no investigation into potential non-additive effects of such associations has been described. In this study, we conducted comprehensive genetic analyses of HLA variants in the major histocompatibility complex (MHC) region among 1,746 adult glioma patients and 2,312 controls from the GliomaScan Consortium. Genotype data were generated with the Illumina 660-Quad array, containing 1,822 SNP probes across the MHC region. We imputed HLA alleles using a reference panel of 5,225 individuals in the Type 1 Diabetes Genetics Consortium who underwent high-resolution HLA typing via next-generation sequencing. Subjects were of European-ancestry, and case-control comparisons were adjusted for population stratification using ancestry-informative principal components. Because alleles in different loci across the MHC region are linked, we created multi-locus haplotypes consisting of genes DRB1, DQA1, and DQB1. Although none of the haplotypes were associated with glioma in additive models, DRB1*15:01-DQA1*01:02-DQB1*06:02 showed an improvement in model fit after the inclusion of a non-additive term, which was significant after Bonferroni correction (P = 2.5x10-3). Furthermore, the interaction of DRB1*15:01-DQA1*01:02-DQB1*06:02 with haplotype DRB1*04:01-DQA1*03:01- DQB1*03:01 resulted in a 3.80-fold increase in the odds of glioma (P = 8.8x10-3). Our results indicate that the DRB1*15:01-DQA1*01:02-DQB1*06:02 haplotype contributes to the risk of glioma via a dominant effect, with heterozygosity conferring greater risk of glioma than expected from homozygote disease risk in an additive model.
Citation Format: Chenan Zhang, Kyle Walsh. Non-additive and interaction effects of HLA class 2 polymorphism contributing to risk of glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1320. doi:10.1158/1538-7445.AM2017-1320
Abstract 1325: Genome-wide association study of thyroid nodule in Korean population
Authors: Lee Eun Kyung , Hwangbo Yul , Park Young Joo , Kim Jong-Il , Jung Yuh-Seog , Ryu Jun Sun 
Published: July 2017

Abstract
Thyroid nodule is very common. Several autopsy surveys reported that 30% or more of patients had thyroid nodule. However, inherited genetic risk factors for thyroid nodule remain unknown. Genome-wide association studies (GWAS) are widely used in human genetics to identify genes associated with various diseases. We aimed to find genetic factors for thyroid nodule and conducted case-control GWAS.
Objective: To identify genetic variants associated with susceptibility to thyroid nodules
Methods: We performed a two-stage GWAS for thyroid nodule. The discovery stage involved a genome-wide scan of 713 subjects with thyroid nodule and 591 subjects with normal thyroid from a population-based cohort. replication testing was conducted in an additional 600 cases and 600 controls from the participants of a health check-up.
Results In discovery stage, 21 candidate single nucleotide polymorphisms (SNP) in 20 loci including NKX2-1, ITGB1 and ZBTB25 were selected for replication. The strongest signal located in NKX2-1 (P = 9x10-7), which is known susceptibility locus for differentiated thyroid cancer. However, no SNP showed significant association in replication test. In joint analysis, no association signals reaching genome-wide significance (P &lt;5x10-8) were detected.
Conclusion GWAS for thyroid nodule have failed to identify susceptibility locus. Therefore, genetic effect for development of thyroid nodule could be negligible.
Citation Format: Eun Kyung Lee, Yul Hwangbo, Young Joo Park, Jong-Il Kim, Yuh-Seog Jung, Jun Sun Ryu. Genome-wide association study of thyroid nodule in Korean population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1325. doi:10.1158/1538-7445.AM2017-1325
Abstract 1327: CD147 contributes to extracellular matrix remodeling and degradation
Authors: Tan Tiffany , Kosmider Beata , Marchetti Nathaniel , Bolla Sudhir , Mandapati Chenna , Criner Gerard , Bahmed Karim 
Published: July 2017

Abstract
Chronic obstructive pulmonary disease (COPD) is an incurable, progressive lung disease characterized by shortness and difficulty in breathing. Patients with COPD are at higher risk of developing lung cancer and often are associated with poor outcome of lung cancer diagnosis and treatment. Extracellular matrix (ECM) remodeling and degradation is one of the common hallmarks between cancer and COPD. It contributes to degradation of air sacs (emphysema) or small airways (obstructive bronchiolitis). It is also involved in cancer initiation and progression to assist tumor expansion and cancer cell migration. In this study, we analyzed lung tissue and primary alveolar type II (ATII) cells isolated from patients with emphysema and control organ donors. ATII cells secrete and store pulmonary surfactant and restore the epithelium after damage. We performed RNA sequencing in ATII cells to identify dysregulated proteins, which are involved in ECM degradation in emphysema. To further study the mechanism involved in the ECM degradation in this disease, we analyzed the expression of selected proteins and we focused on the role of extracellular matrix metalloproteinase inducer (CD147). CD147 is a cell membrane protein involved in inducing the production of extracellular matrix metalloproteinases (MMPs). First, we found that cells isolated from patients with emphysema have higher expression of CD147 in ATII cells in comparison with controls as detected by western blotting and RT-PCR. This may explain high ECM degradation in this disease. Second, we observed higher MMPs levels in plasma obtained from individuals with this disease. Third, we found significantly higher expression of cathepsin B in ATII cells isolated from emphysema in comparison with controls. Cathepsin B is an enzyme that facilitates a direct degradation of ECM proteins and activate other proteases capable of degrading ECM. Fourth, our data indicate that CD147 interacts with cathepsin B, which may lead to the activation of MMPs and emphysema progression. In summary, our results show for the first time the important role of CD147 in emphysema development. Moreover, we found that cathepsin B may contribute to CD147-mediated disease progression. Further studies will elucidate its role in lung cancer development in patients with emphysema.
Note: This abstract was not presented at the meeting.
Citation Format: Tiffany Tan, Beata Kosmider, Nathaniel Marchetti, Sudhir Bolla, Chenna Mandapati, Gerard Criner, Karim Bahmed. CD147 contributes to extracellular matrix remodeling and degradation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1327. doi:10.1158/1538-7445.AM2017-1327
Abstract 1332: NOTCH - HEY1 pathway induces EMT in head and neck squamous cell carcinoma
Authors: Fukusumi Takahito , Guo Theresa W. , Ren Shuling , Sakai Akihiro , Ando Mizuo , Haft Sunny , Liu Chao , Califano Joseph A. 
Published: July 2017

Abstract
Background
Head and neck squamous cell carcinoma (HNSCC) is noted to have a NOTCH mutation rate of 20% within the Cancer Genome Atlas (TCGA) dataset consistent with tumor suppressor gene status. However, NOTCH genes are also upregulated in wild type HNSCC and show signs of downstream activation in a substantial proportion of HNSCC. In this study, we aimed to further explore the potential for NOTCH pathways to be activated in HNSCC.
Material and Methods
mRNA sequence of TCGA data includes 520 HNSCC tumors and 46 normal tissues. We used 447 HNSCC excluding 73 tumors with NOTCH mutations. The activated groups of NOTCH downstream genes were defined as tumors with expression 1 standard deviation above the mean of normal tissue. We used four HNSCC cell lines (SKN3, Cal27, SCC61, SCC090) to ascertain the results of the TCGA analysis in vitro.
Result
In TCGA analysis, HEY1 activated HNSCC had significant more expression of NOTCH pathway genes. In particular NOTCH4 had the most significant correlation with HEY1 activation among NOTCH receptors. To confirm this result in vitro, HEY1 expression was compared between si-control and si-NOTCH4 of SKN3, Cal27, SCC61 and SCC090. As expected, HEY1 expression in all si-NOTCH4 treated cell lines were significant decreased. Next, we examined the relationship about NOTCH4 and an epithelial mesenchymal transition phenotype (EMT). Using TCGA data, we found that mesenchymal marker genes were significantly increased in high NOTCH4 group. In vitro experiments, si-NOTCH4 cells decreased mesenchymal marker gene expression such as Fibronectin and TWIST1. We also examined HEY1 function. Similar to NOTCH4, it was found that HEY1 is significantly related to EMT in silico and in vitro.
Conclusion
The NOTCH4-HEY1 pathway is significantly upregulated in HNSCC and induces EMT.
Citation Format: Takahito Fukusumi, Theresa W. Guo, Shuling Ren, Akihiro Sakai, Mizuo Ando, Sunny Haft, Chao Liu, Joseph A. Califano. NOTCH - HEY1 pathway induces EMT in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1332. doi:10.1158/1538-7445.AM2017-1332
Abstract 1334: Mesenchymal cell sub-populations selectively modulate paracrine hedgehog signaling in triple negative breast cancer
Authors: Ramos Karla P. , Domenech Maribella 
Published: July 2017

Abstract
Recent studies correlate Hedgehog (Hh) signaling with reduced survival rates in triple negative breast cancer (TNBC) patients. Activation of hedgehog signaling in the adjacent mesenchyme has been shown to promote tumor growth and it is a poor prognosis factor for TNBC. We developed a novel tumor-mesenchymal in vitro model of hedgehog signaling in TNBC to evaluate the role of mesenchymal cell sub-populations in the proliferative potential and stem cell markers of breast cancer cells using a custom designed multiwell array. As a source of mesenchymal cell sub-populations we evaluated myofibroblasts, mesenchymal stem cells derived from bone marrow or adipose tissue and tumor cells that undergo epithelial-mesenchymal transition (EMT). Tumor cells were culture with 1 or 2 mesenchymal cell sub-populations in adjacent compartments +/- SHH ligand for 72-96hrs. Active Hh signaling was confirmed by up-regulation of main Hh target genes (e.g. Gli1, Patch1). Paracrine Hh signaling only in bone marrow-derived mesenchymal stem cell and EMT significantly increased proliferation (10-15%) of TNBC and normal breast cancer cell lines. Addition of adipose-derived mesenchymal stem cells or pharmacological Hh inhibitors (Cyclopamine and Gant61) partially abolished tumor growth indicating that other non-canonical signals are involve in paracrine Hh-driven tumors. Cancer stem cell markers were selectively modulated in co-cultures. Our results suggest that paracrine Hh signaling-driven by bone marrow and EMT mesenchymal are potential therapeutic targets to treating TNBC.
Citation Format: Karla P. Ramos, Maribella Domenech. Mesenchymal cell sub-populations selectively modulate paracrine hedgehog signaling in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1334. doi:10.1158/1538-7445.AM2017-1334
Abstract 1335: Deubiquitinase OTUD6B isoforms are important regulators of growth and proliferation
Authors: Bocchetta Maurizio , Osipo Clodia , Sobol Anna 
Published: July 2017

Abstract
Deubiquitinases (DUBs) are increasingly linked to the regulation of fundamental processes in normal and cancer cells, including DNA replication and repair, programmed cell death, and oncogenes and tumor suppressors signaling. Here evidence is presented that the deubiquitinase OTUD6B regulates protein synthesis in non-small cell lung cancer (NSCLC) cells, operating downstream from mTORC1. OTUD6B associates with the protein synthesis initiation complex and modifies components of the 48S preinitiation complex. The two main OTUD6B splicing isoforms seem to regulate protein synthesis in opposing fashions: the long OTUD6B-1 isoform is inhibitory, while the short OTUD6B-2 isoform stimulates protein synthesis. These properties affect NSCLC cell proliferation, since OTUD6B-1 represses DNA synthesis while OTUD6B-2 promotes it. Mutational analysis and downstream mediators suggest that the two OTUD6B isoforms modify different cellular targets. OTUD6B-2 influences the expression of cyclin D1 by promoting its translation while regulating (directly or indirectly) c-Myc protein stability. This phenomenon appears to have clinical relevance as NSCLC cells and human tumor specimens have a reduced OTUD6B-1/OTUD6B-2 mRNA ratio compared to normal samples. The global OTUD6B expression level does not change significantly between non-neoplastic and malignant tissues, suggesting that modifications of splicing factors during the process of transformation are responsible for this isoform switch. Because protein synthesis inhibition is a viable treatment strategy for NSCLC, these data indicate that OTUD6B isoform 2, being specifically linked to NSCLC growth, represents an attractive, novel therapeutic target and potential biomarker for early diagnosis of malignant NSCLC.
Note: This abstract was not presented at the meeting.
Citation Format: Maurizio Bocchetta, Clodia Osipo, Anna Sobol. Deubiquitinase OTUD6B isoforms are important regulators of growth and proliferation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1335. doi:10.1158/1538-7445.AM2017-1335
Abstract 1348: GDC-0032, a p110 beta sparing PI3K inhibitor is highly efficient on PIK3CA-mutated and HER2-amplified breast cancer model
Authors: De Pradip , Sun Yuliang , Carlson Jennifer , Friedman Lori , Williams Casey , Dey Nandini , Leyland-Jones Brian 
Published: July 2017

Abstract
Background: HER2 amplification/overexpression frequently co-occurs with PI3K pathway activation in breast tumors. Mutations in PIK3CA are known to be involved in a wide range of human cancers including HER2+ breast cancer, and mutant PIK3CA is thought to act as an oncogene. Here, we evaluate the efficacy of GDC0032, a p110 beta-sparing PI3K inhibitor against HER2+ or HER2+/PIK3CA mutated breast cancer cells. MATERIALS AND METHODS: Four HER2+ breast cancer (BC) cell lines consisting of three activating (either helical or kinase domain) PIK3CA mutation (HER2+/ER+ and HER2+/ER-) were analyzed for proliferation, apoptosis, cell cycle and signaling pathway activation assays. Preclinical efficacy of GDC-0032 was also evaluated in vivo in a mouse model. RESULTS: 1) All HER2+ and HER2+/PIK3CA mutant cell lines exhibited low IC50 values (ranging from 0.1 µM-1.5 µM) irrespective of ER-positive or not. 2) GDC-0032 caused a strong differential growth inhibition in both HER2+ and HER2+/ /PIK3CA mutated breast cancer cell lines when compared to lines that were HER2- and PIK3CA wild type by 3D-ON-TOP clonogenic assay. 3) Administration of GDC-0032 induced cell cycle G0/G1 arrest and resulted in increased apoptosis in a dose-dependent manner. Furthermore, induction of apoptosis was more with GDC-0032 when combined with RAD001. 4) GDC0032 also blocked expression of CYCLIN D1. 5) Investigation of the signal transduction revealed that the treatment of GDC-0032 reduced the level of p-AKT (Ser473 and Thr308), and p-S6 expression is indicating the down-regulation of downstream signaling of PI3K and mTOR pathway. 6) GDC-0032 was highly active at reducing established tumor growth in vivo in BC mouse xenografts harboring PIK3CA mutation and HER2 amplification. CONCLUSION: Our in vitro or in vivo data showed that GDC-0032 was highly efficient either as a single agent as well as with RAD001 in HER2+/PIK3CA mutated breast cancer cell lines. Our data suggest that GDC-0032 represents a novel therapeutic option in patients harboring PIK3CA mutations and/or HER2/neu gene amplification in breast cancer.
Citation Format: Pradip De, Yuliang Sun, Jennifer Carlson, Lori Friedman, Casey Williams, Nandini Dey, Brian Leyland-Jones. GDC-0032, a p110 beta sparing PI3K inhibitor is highly efficient on PIK3CA-mutated and HER2-amplified breast cancer model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1348. doi:10.1158/1538-7445.AM2017-1348