bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2559: Genome-wide haplotype association tests identified three candidate loci associated with sporadic colorectal cancer risk in Singapore Chinese
Authors: Cheah Peh Yean , Thean Lai Fun , Teo Yik Ying , Koh Woon-Puay , Yuan Jian-Min , Chew Min Hoe , Tang Choong Leong 
Published: July 2016

Abstract
Colorectal cancer (CRC) is one of the most frequent cancers and leading cause of cancer mortality in the developed world. Twin study has attributed about 35% of the etiology of sporadic CRC to genes. Hitherto, more than 20 single nucleotide polymorphism (SNP) loci from genome-wide association studies (GWAS) were associated with CRC risk. Most of these index SNPs however have small effect sizes and often located in gene deserts. Thus they are unlikely to be causal. Haplotype-based methods may offer a more powerful approach to disease gene mapping. We previously performed a GWAS on 2,000 ethnicity-, age-, and gender-matched Singapore Chinese CRC patients and healthy controls using the Affymetrix SNP 6 platform. Sporadic patients were defined as aged 50 or more at the time of surgery and with no dominant family history of CRC. Haplotype block detection was performed in Golden Helix SVS after this SNP6 dataset was filtered for genotype call rate (&gt;95%), Hardy-Weinberg equilibrium in the controls and principal component analysis. Block detection was performed requiring strong linkage disequilibrium between block pairs, minor allelic frequencies (MAF) of SNPs more than 0.01, the maximum number of markers and length of the block at 30 and 160kb respectively. Genome-wide, 73,333 blocks were computed using 336, 466 markers on 22 autosomes. Haplotype frequencies were estimated using the EM algorithm. Chi-Squared and logistic regression with odds ratio tests of haplotype association were performed using these pre-computed blocks on a per-haplotype basis. Three candidate loci at chromosomes 3, 15 and 20, each with 6 to 9 SNPs and sizes ranging from 4 to 15 kb achieved genome-wide significance and encompass potential novel disease genes. These loci are currently being validated in an independent replication panel using the Fluidgm SNPtype assays and pooled analyses will be performed.
Citation Format: Peh Yean Cheah, Lai Fun Thean, Yik Ying Teo, Woon-Puay Koh, Jian-Min Yuan, Min Hoe Chew, Choong Leong Tang. Genome-wide haplotype association tests identified three candidate loci associated with sporadic colorectal cancer risk in Singapore Chinese. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2559.
Abstract 2563: Analysis of a novel gene in relation to bladder cancer GWAS signals within the 20p12.2 region
Authors: Banday Rouf , Yan Wusheng , Middlebrooks Candace D. , Kiss Eniko , Prokunina-Olsson Ludmila 
Published: July 2016

Abstract
Background: Genome-wide association studies (GWAS) of bladder cancer risk recently identified several signals on chromosome 20p12.2 marked by single nucleotide polymorphisms (SNPs) rs6104690, rs62185668 and rs6108803 (Figueroa et al, HMG, 2015). Interestingly, associations of SNPs rs62185668 and rs6108803 were significantly stronger for the risk of muscle-invasive (stages T2-T4) compared to non-muscle-invasive (stages Ta and T1) bladder cancer, suggesting that detailed analysis of these signals could further our understanding of aggressive bladder cancer.
Methods: We used data from The Cancer Genome Atlas (TCGA) bladder cancer set (n = 412) and an independent RNA-seq dataset for 12 bladder tissues. qRT-PCR analysis was performed with custom TaqMan assays in an additional set of 40 tumor and 40 adjacent normal bladder tissue samples. RNAscope in situ hybridization analysis with custom probes was used to evaluate mRNA expression in bladder tissue microarrays that included 7 pairs of normal-tumor bladder tissues.
Results: At a distance of more than 300 and 800 Kb, JAG1 and BTD3 are the closest genes to the GWAS signals in the 20p12.2 region. Analysis of TCGA data did not show significant association of JAG1 and BTD3 expression with genotypes of 20p12.2 GWAS markers analyzed through TCGA-genotyped proxies SNPs rs6040291 and rs6074214. Using RNA-seq data in an independent set of 12 bladder tissue samples, we discovered a novel putative gene in the 20p12.2 region. Cloning of this gene from bladder tumor tissue and annotation by several methods showed two alternative splicing forms, designated as major and minor transcripts. Expression of the major transcript in bladder tumors was significantly increased with the rs6104690-A allele (P = 0.014), which is associated with increased risk of bladder cancer. SNPs with stronger association with muscle-invasive bladder cancer (rs62185668 and rs6108803) showed weaker or non-significant associations with expression of this novel transcript (P = 0.037 and P = 0.42, respectively). This transcript might be protein-coding as it is predicted to have several open reading frames for short peptides, or it may be a long non-coding RNA (lncRNA). RNAscope analysis in bladder tumors showed nuclear expression of the major transcript. Functional analysis of this novel gene in relation to bladder cancer is underway.
Conclusions: A novel gene might be related to the GWAS signals within the 20p12.2 region and the risk of bladder cancer.
Citation Format: Rouf Banday, Wusheng Yan, Candace D. Middlebrooks, Eniko Kiss, Ludmila Prokunina-Olsson. Analysis of a novel gene in relation to bladder cancer GWAS signals within the 20p12.2 region. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2563.
Abstract 2568: Meta-analysis of genome-wide association studies identifies multiple lung cancer susceptibility loci in never-smoking Asian women
Authors: Lan Qing , Wang Zhaoming , Seow Wei Jie , Shiraishi Kouya , Shen Hongbing , Hsiung Chao A. , Matsuo Keitaro , Liu Jie , Chen Kexin , Yamji Taiki , Yang Yang , Chang I-Shou , Wu Chen , Yeager Meredith , Kohno Takashi , Zheng Wei , Shu Xiao-Ou , Yang Pan-Chyr , Wu Tangchun , Lin Dongxin , Zhou Baosen , Yu Jinming , Kubo Michiaki , Chanock Stephen J. , Rothman Nathaniel 
Published: July 2016

Abstract
Background: The incidence rates of lung cancer among never-smoking females in some parts of East Asia are among the highest in the world. Genome-wide association studies (GWAS) of lung cancer in Asian never-smoking women have previously identified six susceptibility loci associated with lung cancer risk including 3q28, 5p15.33, 6p21.32, 6q22.2, 10q25.2 and 17q24.3. This study aims to discover additional lung cancer susceptibility loci among never-smoking Asian females.
Methods: We imputed data from four GWAS of Asian non-smoking female lung cancer (6,877 cases and 6,277 controls) using the 1,000 Genomes Project (Phase 1 Release 3) data as the reference and genotyped additional samples (5,878 cases and 7,046 controls) for potential replication.
Results: In our meta-analysis, three new loci achieved genome-wide significance, marked by the single nucleotide polymorphisms rs7741164 at 6p21.1 (per-allele odds ratio (OR) = 1.17; P = 5.8 × 10-13), rs72658409 at 9p21.3 (per-allele OR = 0.77; P = 1.41 ×10-10), and rs11610143 at 12q13.13 (per-allele OR = 0.89; P = 4.96 ×10-9).
Conclusions: We identified new genetic susceptibility alleles for lung cancer in never-smoking women in Asia. These findings merit follow-up to understand their biological underpinnings and potential interactions with environmental exposures.
Citation Format: Qing Lan, Zhaoming Wang, Wei Jie Seow, Kouya Shiraishi, Hongbing Shen, Chao A. Hsiung, Keitaro Matsuo, Jie Liu, Kexin Chen, Taiki Yamji, Yang Yang, I-Shou Chang, Chen Wu, Meredith Yeager, Takashi Kohno, Wei Zheng, Xiao-Ou Shu, Pan-Chyr Yang, Tangchun Wu, Dongxin Lin, Baosen Zhou, Jinming Yu, Michiaki Kubo, Stephen J. Chanock, Nathaniel Rothman. Meta-analysis of genome-wide association studies identifies multiple lung cancer susceptibility loci in never-smoking Asian women. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2568.
Abstract 26: Sensitive step in cholesterol biosynthesis reveals role for sterol metabolites in regulating growth of EGFR/KRAS-dependent tumors
Authors: Gabitova Linara , Restifo Diana , Handorf Elizabeth , Cai Kathy Q. , Astsaturov Igor A. 
Published: July 2016

Abstract
We identified SC4MOL and NSDHL, two enzymes in the cholesterol pathway and their substrates, meiosis activating sterols (MAS), as critical regulators of receptor signaling and trafficking in normal development and in cancer. Oncogenic transformation by EGFR or RAS increases the demand for cholesterol, suggesting a possibility for metabolic interference. To test this idea in vivo, we ablated Nsdhl in adult keratinocytes expressing KRASG12D. Strikingly, Nsdhl inactivation antagonized the growth of skin tumors, while having little effect on normal skin. Loss of Nsdhl induced the expression of ATP-binding cassette (ABC) transporters ABCA1 and ABCG1, reduced the expression of low-density lipoprotein receptor (LDLR), decreased intracellular cholesterol and was dependent on the liver X receptor (LXR) α. Importantly, EGFR signaling opposed LXRα effects on cholesterol homeostasis, while an EGFR inhibitor synergized with LXRα agonists in killing cancer cells. Inhibition of SC4MOL or NSDHL, or activation of LXRα by sterol metabolites can be an effective strategy against carcinomas with activated EGFR-KRAS signaling.
Citation Format: Linara Gabitova, Diana Restifo, Elizabeth Handorf, Kathy Q. Cai, Igor A. Astsaturov. Sensitive step in cholesterol biosynthesis reveals role for sterol metabolites in regulating growth of EGFR/KRAS-dependent tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 26.
Abstract 2602: The nonclinical toxicology profile of pacritinib, a JAK2/FLT3 inhibitor with no dose-limiting clinical myelosuppression
Authors: Watson Rebecca , Al-Fayoumi Suliman 
Published: July 2016

Abstract
Pacritinib is an orally active kinase inhibitor being developed for the treatment of myelofibrosis (MF). Pacritinib is a particularly potent inhibitor of wild-type and mutant isoforms of JAK2 and FLT3 (IC50 values &lt; 15 nM), and it does not suppress JAK1 at clinically relevant concentrations. Additional kinases targeted by pacritinib include IRAK1 (IC50 = 13.6 nM) and c-fms (or CSF1R; IC50 = 39.5 nM). Pacritinib is pharmacologically active in nonclinical tumor models driven by JAK2 or FLT3 overexpression, and clinical trials have demonstrated that pacritinib can ameliorate symptoms in MF patients. A key differentiating feature of pacritinib over currently available JAK2 inhibitors is its lack of dose-limiting clinical myelosuppression, allowing for treatment of patients with cytopenias. The comparatively reduced myelosuppressive activity of pacritinib is thought to be due to its lack of pharmacological activity on JAK1, and/or its inhibition of IRAK1 and c-fms, which may contribute to anti-inflammatory activity. Nonclinical pacritinib data from rodent and canine studies were evaluated in comparison to publicly available information for other JAK2 inhibitors to determine if differences in nonclinical endpoints might correlate with the observed clinical differences in myelosuppressive effects. The qualitative nonclinical findings seen in rodents were similar for all JAK2 inhibitors, and included decreases in leukocytes, red cell mass, and reticulocytes; lymphoid depletion in the spleen, thymus, and/or lymph nodes; and hypocellularity of the bone marrow. Interestingly, platelet decreases were not observed in rodent or canine nonclinical models, even with JAK2 inhibitors associated with clinical thrombocytopenia. However, in the dog, pacritinib is unique for its minimal myelosuppressive effects in the pivotal 30-day and 39-week studies, despite being performed at higher exposure levels relative to other similar JAK2 inhibitor studies. With pacritinib, non-adverse lymphoid reduction was seen in the spleen, lymph nodes, Peyer's patches, and/or thymus; but there were no clinical pathology findings indicative of marked myelosuppression, nor were there any treatment-related findings in detailed bone marrow evaluations. Overall, these comparisons suggest that nonclinical bone marrow data and clinical pathology in the dog may be informative endpoints for estimating the myelosuppressive potential of JAK2 inhibitors in the clinic.
Citation Format: Rebecca Watson, Suliman Al-Fayoumi. The nonclinical toxicology profile of pacritinib, a JAK2/FLT3 inhibitor with no dose-limiting clinical myelosuppression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2602.
Abstract 2622: A LC-MS/MS method to quantify specific dietary isothiocyanates in human urine for epidemiological studies
Authors: Dyba Marcin , Yuan Jian-Min , Adams-Haduch Jennifer , Chung Fung-Lung 
Published: July 2016

Abstract
Epidemiological studies have demonstrated an inverse relationship between the intake of cruciferous vegetables and risk of cancers. The protective effects may be attributed to glucosinolates and glucobrassicins in these vegetables. While glucosinolates and glucobrassicins are not chemopreventive, their metabolites, isothiocyanates (ITCs), indole-3-carbinol (I3C), and 3,3′-diindolylmethane (DIM), have been shown to inhibit tumorigenesis in rodent models. In the past studies the total ITCs intake was estimated through food frequency questionnaires and/or urinary total ITC by a HPLC-based method. Self-reported intake of cruciferous vegetables has inherent limitations in estimating the intake of ITCs because of differences in the contents of their precursors present in different kinds of cruciferous vegetables, different locations and methods of cultivation, or different methods of food preparation. Animal and cell culture studies have shown that different types of ITCs have different anticancer properties and potency, suggesting that they are not equal in protecting against the development of cancers. The lack of a reliable method to quantify specific ITCs derived from dietary intake of cruciferous vegetables hinders the investigation of the role of specific ITCs against the development of cancer in human populations. To address this deficiency, we developed a flexible, highly sensitive, fast and reliable quantitative liquid chromatography mass spectrometry method (LC-MS/MS) for detecting and quantifying common dietary ITCs plus DIM in human urine. Urinary ITCs are measured as mercapturic acid conjugates (ITCs-NAC), predominant metabolite of ITCs, using multiple reaction monitoring (MRM) technique and deuterated [2H3]-ITCs-NAC as internal standards. DIM is quantified in separate experiment using [2H2]-DIM internal standard. The method was validated by a small set of previously analyzed samples from Singapore Chinese Health Study. We found an excellent correlation between previously reported total ITCs levels and sum of ITCs detected by newly developed method. The combination of minimal sample preparation, ultra-performance liquid chromatography, and highly sensitive mass spectrometer resulted in a method that is fast (below 10 min for ITCs and 12 min for DIM) and sensitive (low femtomolar LOQ) amenable to population studies.
Citation Format: Marcin Dyba, Jian-Min Yuan, Jennifer Adams-Haduch, Fung-Lung Chung. A LC-MS/MS method to quantify specific dietary isothiocyanates in human urine for epidemiological studies. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2622.
Abstract 2625A: Damnacanthal and its nanoformulation suppress cyclin D1 expression
Authors: Sukamporn Pakin , Rojanapanthu Pleumchitt , Baek Seung Joon 
Published: July 2016

Abstract
Damnacanthal is an anthraquinone isolated from the root of Morinda citrifolia L. (Noni) and exhibits many pharmacological properties including anti-cancer activity. It has been reported that Damnacanthal targets several signal transduction proteins related to cell growth inhibition or apoptosis. However, the molecular mechanisms by which Damnacanthal affects anti-cancer activity has not been elucidated in details. Cyclin D1 is the important regulatory protein in cell cycle progression and overexpressed in many cancer cells. In this study, we investigated the molecular mechanism of damnacanthal on cyclin D1 expression. We found that damnacanthal inhibited growth of several cancer cells (HCT-116, HT-29, MCF-7 and PC-3) in a dose- and time- dependent manner with decreasing in cyclinD1 protein expression. Damnacanthal did not change mRNA of cyclin D1, rather it suppressed cyclin D1 expression at the post-translational level. Subsequent experiments with dominant negative mutant cyclin D1 suggest that cyclin D1 at the lysine sites plays a pivotal role in damnacanthal-mediated cyclin D1 suppression. Furthermore, damnacanthal was encapsulated in self-assembled chitosan nanoparticle to improve both physicochemical and biological activities. Our results suggest that encapsulated damnacanthal exhibits better activity in cell growth inhibition, compared to non-encapsulated damnacanthal. Damnacanthal nanoformulation has potential to be a candidate for development of chemoprevention or therapeutic agent for cancers.
Grant support: This work was supported by grant from the University of Tennessee Center of Excellence in Livestock Diseases and Human Health and The Thailand Research Fund (TRF) and Faculty of Pharmacy, Mahidol University (IRG5780007).
Citation Format: Pakin Sukamporn, Pleumchitt Rojanapanthu, Seung Joon Baek. Damnacanthal and its nanoformulation suppress cyclin D1 expression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2625A.
Abstract 2627: Molecular analyses of histopathologic morphologic features in breast cancer
Authors: Heng Yu Jing Jan ,   TCGA Breast Cancer Expert Pathology Committee, Jeong Jong Cheol , Gendoo Deena M.A , Haibe-Kains Benjamin , Ciriello Giovanni , Hoadley Katherine A. , Perou Charles M. , Beck Andrew H. 
Published: July 2016

Abstract
Traditional histopathologic analysis of breast cancer phenotypes has played a central role in the diagnosis, prognosis and clinical management of breast cancer. This study integrated molecular data with breast cancer histopathologic annotations to elucidate the molecular basis of these common morphologic features.
We constructed a large, comprehensive histopathologic database of 850 invasive breast cancer cases from The Cancer Genome Atlas (TCGA). We integrated the consensus assessments of 11 morphologic features (nuclear pleomorphism, mitotic count, epithelial tubule formation, inflammation, DCIS, LCIS, lymphovascular invasion, necrosis, fibrotic focus, apocrine features and proportion of epithelium in invasive portion by area) with TCGA's genomic, transcriptomic and proteomic data. Using this highly annotated dataset, we identified molecular profiles associated with morphologic features, constructed Omics-based multivariate models to predict morphologic features and provided insights into their molecular etiology. The association of morphologic features’ signatures with survival in ER-positive and ER-negative breast cancer was assessed using six independent datasets. All data are publicly accessible at http://pathology.ai/tcga_breast.
Morphologic features were associated with PAM50 subtypes, PAM50 proliferation scores, genomic alterations and gene expression (p&lt;0.05). Clustering of morphologic features and genomic alterations produced two clusters of morphologic features and their separate were driven by TP53, CDH1 and PIK3CA mutations and chr12p13.3, ch8q24.21 and chr3q26.3 amplifications. The clustering of morphologic features and gene sets/pathways also produced two clusters of morphologic features characterized by “proliferation” or “inflammation”. The transcriptomic signatures of nuclear pleomorphism and epithelial tubule formation were independently prognostic in ER-positive breast cancer. No signatures were prognostic in ER-negative.
Our detailed morphologic data enrich and complement TCGA's existing molecular data, increase our understanding of the molecular basis of breast cancer pathologic phenotypes, can facilitate the refinement of breast cancer classification, and enhance our understanding of breast cancer biology.
Citation Format: Yu Jing Jan Heng, TCGA Breast Cancer Expert Pathology Committee, Jong Cheol Jeong, Deena M.A Gendoo, Benjamin Haibe-Kains, Giovanni Ciriello, Katherine A. Hoadley, Charles M. Perou, Andrew H. Beck. Molecular analyses of histopathologic morphologic features in breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2627.