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  • American Association for Cancer Research (AACR)  (17)
  • 2015-2019  (17)
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  • American Association for Cancer Research (AACR)  (17)
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  • 2015-2019  (17)
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  • 1
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2017
    In:  Cancer Research Vol. 77, No. 13_Supplement ( 2017-07-01), p. 376-376
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 376-376
    Abstract: The Biospecimen Preanalytical Variables (BPV) Program was initiated by the National Cancer Institute’s Biorepositories and Biospecimen Research Branch to evaluate the impact of preanalytical factors on the molecular integrity of biospecimens. Selected preanalytical factors including cold ischemic time (delay to formalin fixation (DTF)), time in formalin (TIF), freezing methods, and storage temperatures and durations were examined for their potential effects on molecular profiles from surgical resection tissues and matched blood from four cancer types (kidney, ovary, colon and lung). The BPV program has collected tumor specimens from 364 cancer patients. Each specimen was annotated with 300+ data elements that cover steps in the collection, handling, and processing procedures, pathology review, and clinical information. NCI conducted multiple studies using these specimens to evaluate the preanalytical impacts on different analytical platforms including gene expression profiling, copy number variation, proteomics and metabolomics profiling. The program invites interested organizations to work with NCI through collaboration to further evaluate preanalytical effects on molecular analyses (https://techtransfer.cancer.gov/availabletechnologies/e-000-2013). The remaining specimens are available to support relevant research focusing on biospecimen science and/or clinical biomarker assay development (https://specimens.cancer.gov/search/). The IT infrastructure that was developed to support BPV biospecimen collection and management has been further developed into open source products (https://github.com/NCIP/CDR and https://github.com/NCIP/CDR-Lite). The controlled vocabulary that records the terms and definitions used in describing the overall biospecimen collection efforts has been refined and published at publicly accessible CDE repositories: NCI’s caDSR (https://cdebrowser.nci.nih.gov/CDEBrowser/ ) and NIH’s CDE portal (https://cde.nlm.nih.gov/cde/search ). An ongoing collaboration with an academic ontology consortium will map the CDEs to existing biobanking ontology frameworks and make them publicly available. The BPV program has generated a wide range of ~omics data. We are preparing a BPV data compendium to be submitted to dbGaP at NCBI. These data will be used as the experimental evidence to develop evidence-based best practices for fit-for-purpose collection, processing, and storage of biospecimens for cancer research. Citation Format: Ping Guan, Helen M. Moore. Biospecimen and data resources for cancer research from NCI’s BPV program [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 376. doi:10.1158/1538-7445.AM2017-376
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 14 ( 2017-07-15), p. 3758-3765
    Abstract: Gastrointestinal stromal tumor (GIST) is the most common subtype of sarcoma. Despite clinical advances in the treatment of KIT/PDGFRA–mutant GIST, similar progress against KIT/PDGFRA wild-type GIST, including mutant BRAF-driven tumors, has been limited by a lack of model systems. ETV1 is a master regulator in the intestinal cells of Cajal (ICC), thought to be the cells of origin of GIST. Here, we present a model in which the ETV1 promoter is used to specifically and inducibly drive Cre recombinase in ICC as a strategy to study GIST pathogenesis. Using a conditional allele for BrafV600E, a mutation observed in clinical cases of GIST, we observed that BrafV600E activation was sufficient to drive ICC hyperplasia but not GIST tumorigenesis. In contrast, combining BrafV600E activation with Trp53 loss was sufficient to drive both ICC hyperplasia and formation of multifocal GIST-like tumors in the mouse gastrointestinal tract with 100% penetrance. This mouse model of sporadic GIST model was amenable to therapeutic intervention, and it recapitulated clinical responses to RAF inhibition seen in human GIST. Our work offers a useful in vivo model of human sporadic forms of BRAF-mutant GIST to help unravel its pathogenesis and therapeutic response to novel experimental agents. Cancer Res; 77(14); 3758–65. ©2017 AACR.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 3
    In: Cancer Immunology Research, American Association for Cancer Research (AACR), Vol. 5, No. 1 ( 2017-01-01), p. 42-51
    Abstract: Radiotherapy is the primary treatment for nasopharyngeal carcinoma (NPC). Patients with intermediate and advanced stage NPC receiving only radiotherapy have limited survival, so newer immunotherapeutic approaches are sought. The major impediment to better clinical outcomes is tumor immune tolerance. Indoleamine 2,3-dioxygenase (IDO), an IFNγ-inducible enzyme, is a major inducer of immune tolerance during tumor development; therefore, inhibition of the IDO pathway is an important modality for cancer treatment. We show that bortezomib, a proteasomal inhibitor, inhibited the pathways leading to STAT1 and IRF-1 activation, both of which are necessary for IDO expression. Bortezomib downregulated IFNγ-induced IDO expression via inhibition of STAT1 phosphorylation and nuclear translocation, thereby suppressing STAT1-driven IDO transcription in NPC cells. Bortezomib also promoted IκB-α phosphorylation-ubiquitination, which released NF-κB from IκB-α. However, the released NF-κB could not enter the nucleus to conduct its biological effects and accumulated in the cytoplasm. Negative feedback inhibited the transcription of NF-κB, which is important for activating IRF-1 expression. IDO expression is regulated by two important transcription factor binding sites, ISREs, which bind STAT1 and IRF-1, and GASs, which binds STAT1. Bortezomib upregulated IRF-1 protein by inhibiting its proteasome-dependent degradation, but it also inhibited STAT1 phosphorylation, which directly inhibited the activation of GAS and indirectly inhibited the activation of ISRE, which needs both STAT1 and IRF-1. These discoveries provide a mechanism for the antitumor action of bortezomib and have implications for the development of clinical cancer immunotherapy for preventing and treating NPC. Cancer Immunol Res; 5(1); 42–51. ©2016 AACR.
    Type of Medium: Online Resource
    ISSN: 2326-6066 , 2326-6074
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 4
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 24, No. 2_Supplement ( 2018-01-15), p. B13-B13
    Abstract: Aberrant activation of the mitogen activate kinase (MAPK) pathway is highly prevalent in cancer and therapies targeting the pathway are approved or under active investigation in multiple malignancies. MAPK signaling leads to activation of a transcriptional program that includes general growth promoting genes, negative feedback regulators of the MAPK pathway, and lineage-specific genes. While the mechanisms of upstream signal transduction that leads to MAPK activation have been studied in detail, how MAPK activation is dynamically coupled with downstream nuclear transcriptional response is not fully understood. In gastrointestinal stomal tumor (GIST) and melanoma, two malignancies with aberrant MAPK activation, we find that Pea3 family ETS transcription factors ETV1, ETV4, and ETV5 are critical nuclear effectors of MAPK signaling. We find that the primary mechanism linking MAPK and Pea3 activity is through protein stability via the COP1 E3 ligase. The loss of COP1 leads to decoupling between upstream MAPK signaling and downstream transcription with constitutively stabilized Pea3 protein levels, constitutively high MAPK transcriptome, yet decreased upstream signaling due to Pea3-mediated transcription of negative feedback regulators. This leads to decreased therapeutic sensitivity to MAPK pathway inhibition in vitro and in vivo. These observations indicate that MAPK signaling-dependent regulation of Pea3 ETS protein stability is a crucial pathway that couples downstream transcriptional response to MAPK signaling and can shape the therapeutic sensitivity to MAPK pathway inhibition in cancer. Citation Format: Yuanyuan Xie, Zhen Cao, Wai Pung Wong, Youxin Guan, Jenny Zhang, Edward Walczak, Devan Murphy, Leili Ran, Inna Sirota, Shangqian Wang, Shipra Shukla, Dong Gao, John Wongvipat, Simon Knott, Kenneth Chang, Cristina Antonescu, Gregory Hannon, Ping Chi, Yu Chen. COP1-ETS axis regulates ERK transcriptional output and modulates sensitivity to MAPK inhibitors [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B13.
    Type of Medium: Online Resource
    ISSN: 1078-0432 , 1557-3265
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 5
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 13_Supplement ( 2018-07-01), p. 4763-4763
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 4763-4763
    Abstract: High quality human biospecimens are essential to clinical diagnosis and treatment and serve as a vital foundation for medical research. Substantial variation in procedures for biospecimen collection, processing, and storage exists within and between institutions. Such variation can have a substantial effect on the quality of biospecimens and the accuracy of downstream analytical results, and is of particular concern at a time of high demand for biospecimens for large-scale studies. Recognizing the need for harmonization of biospecimen practices, the National Cancer Institute (NCI)'s Biorepositories and Biospecimen Research Branch (BBRB) began developing a series of documents known as Biospecimen Evidence-Based Practices (BEBPs). The first of NCI's BEBPs, “Snap-Freezing of Post-surgical Tissue Biospecimens” (https://biospecimens.cancer.gov/global/pdfs/NCI_BEBP_Snap-freezing_of_Post-surgical_Tissue_Biospecimens.pdf), was released in 2014. BBRB will soon release two new expert-reviewed BEBPs. The first expert-vetted BEBP, “Formalin-Fixation and Paraffin Processing of Tissue Biospecimens”, is a fit-for-purpose guide for formalin fixation, paraffin impregnation, and embedding of human tissues that was reviewed by more than 40 experts as part of a BBRB-sponsored workshop. The second, entitled “DNA and RNA Extraction from Formalin-fixed Paraffin-embedded Tissue Biospecimens”, categorizes steps in the extraction of DNA and RNA that may affect the quality of nucleic acids obtained from FFPE specimens and was reviewed by five experts. Each BEBP has been developed in close partnership with scientists having state-of-the art biospecimen science expertise and a strong publication record. BEBP documents contain step-by-step recommendations and procedural guidelines as well as a summary of supporting literature and expert-derived evidence. Development of each BEBP employs a stringent and thorough analysis of literature indexed in the National Library of Medicine's PubMed database and curated in NCI's publicly accessible Biospecimen Research Database (BRD; http://biospecimens.cancer.gov/brd), a free database of peer-reviewed biospecimen science articles. The database also houses over 400 SOPs searchable by numerous parameters including specimen type, preservation, diagnosis, analyte, pre-analytical factors, and technology platform. Given the nuanced requirements for each individual step in biospecimen collection, NCI's BEBPs serve as a framework to inform the development of Standard Operating Procedures (SOPs) by individual institutions while providing room for flexibility and adaptation. NCI's BBRB continues to add to its BEBP series to improve the reproducibility of molecular data derived from biospecimens. Experts interested in contributing to future BEBPs are encouraged to contact BBRB at ncibbrb@nih.gov. Citation Format: Esmeralda Casas-Silva, Lori D. Campbell, Kelly Engel, Sarah Greytak, Ping Guan, Helen Moore. NCI's Expert-Vetted Biospecimen Evidence-Based Practices (BEBP): A resource for harmonization of biospecimen collection procedures [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 4763.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 79, No. 13_Supplement ( 2019-07-01), p. 2780-2780
    Abstract: The interleukin-13 receptor alpha2 (IL13RA2), which is known to overexpressed in glioblastoma multiforme, plays a role in various cellular processes such as cell migration that may contribute to tumor progression. Studies have attributed IL13RA2 to invasion and metastasis in cancers of the ovary, breast, and pancreas but the pathological role of IL13RA2 in thyroid cancer is still unclear. This study aims to evaluate the expression of IL13RA2 in thyroid carcinomas and examine the role of IL13RA2 in progression of papillary thyroid cancer (PTC). We performed IL13RA2 immunochemical staining on tissue microarrays of 137 thyroid carcinomas and observed that IL13RA2 expression was significantly correlated with advanced tumor stage (pT3 / pT4; p=0.001) and regional lymph node metastasis (pN1; p & lt;0.001). Moreover, the staining scores of IL13RA2 were significantly higher in PTC compared to follicular and anaplastic subtypes (p & lt;0.02) and correlated with advanced tumor stage amongst PTC samples (pT3 / pT4; p=0.028). This differential profile of IL13RA2 in PTC was further validated in thyroid cancer cell lines overexpressing IL13RA2 to assay the effects on cell proliferation, cell migration and epithelial-mesenchymal transition (EMT) using CCK-8, transwell migration assay, qRT-PCR and western blot analyses. Knockdown of IL13RA2 in the PTC subtype B-CPAP cell line showed significantly reduced cell viability, cell migration and EMT markers including N-cadherin, Vimentin and Snail. Exogenous overexpression of IL13RA2 in another PTC cell line, K1 increased cell migration and EMT although cell proliferation was not affected. In summary, we demonstrated that IL13RA2 is differentially regulated in PTC and is involved in cell migration by enhancing EMT. The underlying molecular mechanisms on how IL13RA2 drives progression of thyroid cancer remains to be further investigated. Citation Format: Siao Ting Chong, Catherine Y. Kok, Khee Ming Tan, Shou Ping Guan, Siang Hui Lai, Cindy Lim, Jiancheng Hu, Charles Sturgis, Charis Eng, Paula Y. Lam, Joanne Ngeow. IL13RA2 is differentially regulated in papillary thyroid carcinoma versus follicular thyroid carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2780.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2019
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. 1821-1821
    Abstract: Variations in how human biospecimens are collected, processed and stored have been shown to significantly affect downstream molecular analyses. FFPE (formalin-fixed, paraffin-embedded) specimens are valuable resources for biospecimen based research, since many such samples are routinely collected and stored in biobanks. With an aim to evaluate the impact of delay to fixation on total protein and phosphoprotein profiles, we used a label free mass spectrometry based proteomic and phosphoproteomic analysis on FFPE renal cell carcinoma (RCC) tumor tissues from 20 patients at four “delay to fixation” time points (1h, 2h, 3h and 12h delay to fixation), collected under the National Cancer Institute's (NCI) Biospecimen Pre-analytical Variables (BPV) program. In addition, we compared tumor and adjacent normal kidney tissue at the four delay to fixation time points. This comparison was performed using both FFPE and frozen (OCT) tissue from case-matched tumor specimens to assess the relative impact of the two biospecimen preservation methods. We employed a label-free intensity based quantitation for the proteome profiling using high resolution Orbitrap mass spectrometry. A total of 3475 proteins and 1690 phosphoproteins were quantitated in the FFPE specimens and 3728 proteins and 1817 phosphoproteins in the OCT (frozen) tumor specimens. Very few significant changes were observed at the proteome level with different delay to fixation times. However, at the phosphoprotein level, significant numbers of phosphopeptides were observed to change and these changes were observed across the majority of patients. Approximately 8% of the phosphopeptides were significantly changed after a 12 h delay in time to fixation (vs. 1 h) compared to just 0.5% of the nonphosphopeptides. The observed changes to the phosphoproteome do not appear to be completely random. The phosphopeptides that are differentially expressed are enriched in proteins associated with renal cell death. In the tumor versus normal tissue comparison, large numbers of changes were observed at both the proteome and phosphoproteome level. These changes were consistent between the FFPE and OCTtumor specimens. In general, however, greater magnitude fold changes were observed in OCT versus the FFPE tumor specimens. Many of the differentially expressed proteins observed in this study have previously been identified in urine. These findings could potentially lead to the development of a urine-based biomarker assays for renal cell carcinoma that could aid in the early detection of this cancer. This work is funded by NCI Contract No. HHSN261200800001E. Citation Format: Fiona E. McAllister, Rachana Agarwal, Bich Nguyen, Yiyong Zhou, Sushmita Roy, Daniel Chelsky, Ping Guan, Mary Barcus, Hana Odeh, Lararsha Carithers, Helen Moore. FFPE preanalytical variables: Investigating the effect of delayed times to fixation on the proteome and phosphoproteome for FFPE kidney tumor samples and a comparison of tumor versus normal for matching FFPE and OCT frozen tissue. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1821. doi:10.1158/1538-7445.AM2015-1821
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
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  • 8
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. LB-139-LB-139
    Abstract: The activity of a previously identified hematopoietic stem cell marker, Runx1 enhancer element (eR1) (Ng et al, Stem Cells 28, 1869-1881, 2010), was found to mark tissue stem cells of multiple organs. In corpus of stomach, stem cells are known to reside at isthmus, upper part of gastric unit. They are undifferentiated cells. However, molecular approach to these stem cells has not been described. Recently, fully differentiated Pepsinogen expressing chief cells at the bottom of gastric unit were shown to have tissue regeneration activity, and these cell were named reserve stem cells (Stange et al, Cell 155, 357-368, 2013). In our study, eR1 was shown to mark stem cells of both types. Lineage tracing experiments demonstrated that both types of stem cells continuously gave rise to mature cells to maintain the gastric unit. Manipulation of gene expression in a stem cell-specific manner in the stomach, especially in undifferentiated stem cells, is a long sought-after approach to study gastric carcinogenesis. We crossed transgenic mouse carrying eR1-CreERT2 with LSL-K-rasG12D mice. After tamoxifen treatment, rapid differentiation from the stem cells in the isthmus was observed, mainly into Muc5ac+ cells (surface epithelial cells). As a result, pseudo-pyloric metaplasia was induced which is similar to that observed in human gastritis. Acid-producing parietal cells were eliminated during this process. Rapid generation of Muc5ac+ cells and other phenotype are similar, but not identical, to the phenotype described in Menetrier disease which is known to be caused by excessive production of TGF-α and hyper-stimulation of EGF receptor (Reviewed in Coffey et al, J Clin Invest. 117:70-80, 2007). Menetrier disease is considered to be pre-malignant state. Activation of K-rasG12D in eR1+ chief cells also induced metaplastic lesions. In this case, pepsinogen producing chief cells robustly expressed the marker of mucous neck cells that are considered to be a precursor to chief cells. Therefore, chief cells appeared to be de-differentiated to precursor cells and acquired the stem cell property. We are using eR1 to study step-wise carcinogenesis in stomach and other organs. Citation Format: Junichi Matsuo, Shunichi Kimura, Cai Ping Koh, Md Zakir Hossain, Akihiro Yamamura, Kazuyoshi Kohu, Michiaki Unno, Jimmy Bok Yan So, Feng Zhu, Supriya Srivastava, Teh Meng, Nicholas Barker, Khay Guan Yeoh, Motomi Osato, Yoshiaki Ito. Tissue stem cell specific enhancer element identifies two types of stem cells in the corpus epithelium of the stomach. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-139. doi:10.1158/1538-7445.AM2015-LB-139
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 9
    In: Cancer Discovery, American Association for Cancer Research (AACR), Vol. 7, No. 11 ( 2017-11-01), p. 1284-1305
    Abstract: Protein-coding mutations in clear cell renal cell carcinoma (ccRCC) have been extensively characterized, frequently involving inactivation of the von Hippel–Lindau (VHL) tumor suppressor. Roles for noncoding cis-regulatory aberrations in ccRCC tumorigenesis, however, remain unclear. Analyzing 10 primary tumor/normal pairs and 9 cell lines across 79 chromatin profiles, we observed pervasive enhancer malfunction in ccRCC, with cognate enhancer-target genes associated with tissue-specific aspects of malignancy. Superenhancer profiling identified ZNF395 as a ccRCC-specific and VHL-regulated master regulator whose depletion causes near-complete tumor elimination in vitro and in vivo. VHL loss predominantly drives enhancer/superenhancer deregulation more so than promoters, with acquisition of active enhancer marks (H3K27ac, H3K4me1) near ccRCC hallmark genes. Mechanistically, VHL loss stabilizes HIF2α–HIF1β heterodimer binding at enhancers, subsequently recruiting histone acetyltransferase p300 without overtly affecting preexisting promoter–enhancer interactions. Subtype-specific driver mutations such as VHL may thus propagate unique pathogenic dependencies in ccRCC by modulating epigenomic landscapes and cancer gene expression. Significance: Comprehensive epigenomic profiling of ccRCC establishes a compendium of somatically altered cis-regulatory elements, uncovering new potential targets including ZNF395, a ccRCC master regulator. Loss of VHL, a ccRCC signature event, causes pervasive enhancer malfunction, with binding of enhancer-centric HIF2α and recruitment of histone acetyltransferase p300 at preexisting lineage-specific promoter–enhancer complexes. Cancer Discov; 7(11); 1284–305. ©2017 AACR. See related commentary by Ricketts and Linehan, p. 1221. This article is highlighted in the In This Issue feature, p. 1201
    Type of Medium: Online Resource
    ISSN: 2159-8274 , 2159-8290
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 10
    In: Cancer Discovery, American Association for Cancer Research (AACR), Vol. 7, No. 6 ( 2017-06-01), p. 630-651
    Abstract: Promoter elements play important roles in isoform and cell type–specific expression. We surveyed the epigenomic promoter landscape of gastric adenocarcinoma, analyzing 110 chromatin profiles (H3K4me3, H3K4me1, H3K27ac) of primary gastric cancers, gastric cancer lines, and nonmalignant gastric tissues. We identified nearly 2,000 promoter alterations (somatic promoters), many deregulated in various epithelial malignancies and mapping frequently to alternative promoters within the same gene, generating potential pro-oncogenic isoforms (RASA3). Somatic promoter–associated N-terminal peptides displaying relative depletion in tumors exhibited high-affinity MHC binding predictions and elicited potent T-cell responses in vitro, suggesting a mechanism for reducing tumor antigenicity. In multiple patient cohorts, gastric cancers with high somatic promoter usage also displayed reduced T-cell cytolytic marker expression. Somatic promoters are enriched in PRC2 occupancy, display sensitivity to EZH2 therapeutic inhibition, and are associated with novel cancer-associated transcripts. By generating tumor-specific isoforms and decreasing tumor antigenicity, epigenomic promoter alterations may thus drive intrinsic tumorigenesis and also allow nascent cancers to evade host immunity. Significance: We apply epigenomic profiling to demarcate the promoter landscape of gastric cancer. Many tumor-specific promoters activate different promoters in the same gene, some generating pro-oncogenic isoforms. Tumor-specific promoters also reduce tumor antigenicity by causing relative depletion of immunogenic peptides, contributing to cancer immunoediting and allowing tumors to evade host immune attack. Cancer Discov; 7(6); 630–51. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 539
    Type of Medium: Online Resource
    ISSN: 2159-8274 , 2159-8290
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
    detail.hit.zdb_id: 2607892-2
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