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Moffitt K, Einarsson G, Walker B, Elborn J, Martin S. The effects of bacterial stimulation on prostasin levels within the cystic fibrosis lung. J Cyst Fibros 2010. [DOI: 10.1016/s1569-1993(10)60068-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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77
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Walker B. Enigma Number 1601. New Sci 2010. [DOI: 10.1016/s0262-4079(10)61553-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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78
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Walker B. Enigma Number 1596. New Sci 2010. [DOI: 10.1016/s0262-4079(10)61263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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79
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Yang F, Bilke S, Pineda M, Walker B, Zhu J, Meltzer P. Abstract 4612: Analysis of transcriptional regulation by progesterone receptor in ER-positive breast cancer cells by ChIP-Seq. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancer is among the most common malignancies in women. It is well established that progesterone receptor (PR) is a major determinant in the development and progression of breast tumor, as well as in diagnosis and treatment of breast cancer. However, it is still not fully understood how PR affects downstream signaling pathways and cross talks with other intracellular signal transduction pathways. To better define the role played by PR in estrogen receptor (ER)-dependent gene regulation, we have used chromatin immunoprecipitation coupled with next generation sequencing (ChIP-Seq) to examine the in vivo DNA binding by PR. Whole-Genome ChIP-Seq analysis has identified large number of PR binding sites in T-47D breast cancer cells, which are ER-positive and PR-positive. PR binding sites were detected in proximal promoter regions as well as distal regions, with most located in non-proximal regions. The comparison of PR and ER binding sites revealed that a significant of portion of the PR binding sites overlaps with the ER binding sites, indicating a close relationship between PR and ER in ER-dependent gene regulation. The PR motifs were found to be among the most enriched sequence motifs within the PR binding sites. Further analysis using the chromosome conformation capture assay revealed that progesterone induces changes to the chromatin structures of known PR-regulated genes. The ChIP-Seq data, together with the expression profiling and other results, indicate that PR may cooperate with ER and play an important role in ER-dependent gene regulation, mammary epithelial differentiation and breast cancer development.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4612.
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Walker B. Enigma Number 1591. New Sci 2010. [DOI: 10.1016/s0262-4079(10)60928-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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81
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Walker B. Enigma Number 1586. New Sci 2010. [DOI: 10.1016/s0262-4079(10)60592-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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82
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Walker B. Enigma Number 1578. New Sci 2010. [DOI: 10.1016/s0262-4079(10)60109-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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83
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Tay A, Walker B, Lim H, Subbiah R, Kuchar D, Thorburn C. Cardiac Device and Lead Displacement Secondary to Significant Weight Loss in the Obese Patient. Heart Lung Circ 2010. [DOI: 10.1016/j.hlc.2010.06.897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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84
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Phan J, Hayward C, Tay A, Subbiah R, Kuchar D, Thorburn C, Walker B. The CRT Learning Curve: A Single Centre Experience. Heart Lung Circ 2010. [DOI: 10.1016/j.hlc.2010.06.929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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85
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Walker B. Enigma Number 1572. New Sci 2009. [DOI: 10.1016/s0262-4079(09)63066-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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86
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87
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Henn MR, Boutwell C, Lennon N, Power K, Malboeuf C, Charlebois P, Gladden A, Levin J, Casali M, Philips L, Berlin A, Berical A, Erlich R, Anderson S, Streeck H, Kemper M, Ryan E, Wang Y, Green L, Axten K, Brumme Z, Brumme C, Russ C, Rosenberg E, Jessen H, Altfeld M, Nusbaum C, Walker B, Birren B, Allen TM. P09-20 LB. Ultra-deep sequencing of full-length HIV-1 genomes identifies rapid viral evolution during acute infection. Retrovirology 2009. [PMCID: PMC2767916 DOI: 10.1186/1742-4690-6-s3-p400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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88
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Chevalier M, Pyo A, Jolin JS, Addo M, Kwon DS, Toth I, Walker B, Streeck H. P16-31. Skewed HIV-1-specific CD4+ Th2 helper cell contribution in progressive HIV-1 infection. Retrovirology 2009. [PMCID: PMC2767760 DOI: 10.1186/1742-4690-6-s3-p260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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89
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Boutwell CL, Schneidewind A, Brumme Z, Brockman M, Streeck H, Brumme C, Dudek T, Kane K, Kemper M, Walker B, Altfeld M, Allen T. P09-19 LB. CTL escape mutations in gag epitopes restricted by protective HLA class I alleles cause substantial reductions in viral replication capacity. Retrovirology 2009. [PMCID: PMC2767913 DOI: 10.1186/1742-4690-6-s3-p399] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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90
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Jia M, Chen J, Hong K, Liu S, Zhang X, Zhao H, Altfeld M, Walker B, Yu X, Shao Y. P16-12. Relative dominance of Gag-specific cytotoxic T lymphocytes is associated with viral load inversely in HIV-1 clade B' infected Chinese. Retrovirology 2009. [PMCID: PMC2767739 DOI: 10.1186/1742-4690-6-s3-p241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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91
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Walker B. Enigma Number 1569. New Sci 2009. [DOI: 10.1016/s0262-4079(09)62873-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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92
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Moodley ES, Thobakgale C, Ramkalawon P, Vanderstok M, Mncube Z, Bishop K, Reddy S, Chonco F, Walker B, Goulder P, Ndung'u T. P07-02. Cytotoxic T lymphocyte-mediated immune responses in HIV-1 clade C infected mother-child pairs. Retrovirology 2009. [PMCID: PMC2767583 DOI: 10.1186/1742-4690-6-s3-p100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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93
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94
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Walker B. Enigma Number 1561. New Sci 2009. [DOI: 10.1016/s0262-4079(09)62336-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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95
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Kauer M, Ban J, Kofler R, Walker B, Davis S, Meltzer P, Kovar H. A molecular function map of Ewing's sarcoma. PLoS One 2009; 4:e5415. [PMID: 19404404 PMCID: PMC2671847 DOI: 10.1371/journal.pone.0005415] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 03/27/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND EWS-FLI1 is a chimeric ETS transcription factor that is, due to a chromosomal rearrangement, specifically expressed in Ewing's sarcoma family tumors (ESFT) and is thought to initiate the development of the disease. Previous genomic profiling experiments have identified EWS-FLI1-regulated genes and genes that discriminate ESFT from other sarcomas, but so far a comprehensive analysis of EWS-FLI1-dependent molecular functions characterizing this aggressive cancer is lacking. METHODOLOGY/PRINCIPAL FINDINGS In this study, a molecular function map of ESFT was constructed based on an integrative analysis of gene expression profiling experiments following EWS-FLI1 knockdown in a panel of five ESFT cell lines, and on gene expression data from the same platform of 59 primary ESFT. Out of 80 normal tissues tested, mesenchymal progenitor cells (MPC) were found to fit the hypothesis that EWS-FLI1 is the driving transcriptional force in ESFT best and were therefore used as the reference tissue for the construction of the molecular function map. The interrelations of molecular pathways were visualized by measuring the similarity among annotated gene functions by gene sharing. The molecular function map highlighted distinct clusters of activities for EWS-FLI1 regulated genes in ESFT and revealed a striking difference between EWS-FLI1 up- and down-regulated genes: EWS-FLI1 induced genes mainly belong to cell cycle regulation, proliferation, and response to DNA damage, while repressed genes were associated with differentiation and cell communication. CONCLUSIONS/SIGNIFICANCE This study revealed that EWS-FLI1 combines by distinct molecular mechanisms two important functions of cellular transformation in one protein, growth promotion and differentiation blockage. By taking MPC as a reference tissue, a significant EWS-FLI1 signature was discovered in ESFT that only partially overlapped with previously published EWS-FLI1-dependent gene expression patterns, identifying a series of novel targets for the chimeric protein in ESFT. Our results may guide target selection for future ESFT specific therapies.
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Walker B. Enigma No. 1520. New Sci 2008. [DOI: 10.1016/s0262-4079(08)62884-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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97
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Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, Carrington M, Goulder P, Heckerman D. 168-P: In silico resolution of ambiguous HLA typing data. Hum Immunol 2008. [DOI: 10.1016/j.humimm.2008.08.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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98
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Young PG, Beresford-West TBH, Coward SRL, Notarberardino B, Walker B, Abdul-Aziz A. An efficient approach to converting three-dimensional image data into highly accurate computational models. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2008; 366:3155-3173. [PMID: 18573757 DOI: 10.1098/rsta.2008.0090] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Image-based meshing is opening up exciting new possibilities for the application of computational continuum mechanics methods (finite-element and computational fluid dynamics) to a wide range of biomechanical and biomedical problems that were previously intractable owing to the difficulty in obtaining suitably realistic models. Innovative surface and volume mesh generation techniques have recently been developed, which convert three-dimensional imaging data, as obtained from magnetic resonance imaging, computed tomography, micro-CT and ultrasound, for example, directly into meshes suitable for use in physics-based simulations. These techniques have several key advantages, including the ability to robustly generate meshes for topologies of arbitrary complexity (such as bioscaffolds or composite micro-architectures) and with any number of constituent materials (multi-part modelling), providing meshes in which the geometric accuracy of mesh domains is only dependent on the image accuracy (image-based accuracy) and the ability for certain problems to model material inhomogeneity by assigning the properties based on image signal strength. Commonly used mesh generation techniques will be compared with the proposed enhanced volumetric marching cubes (EVoMaCs) approach and some issues specific to simulations based on three-dimensional image data will be discussed. A number of case studies will be presented to illustrate how these techniques can be used effectively across a wide range of problems from characterization of micro-scaffolds through to head impact modelling.
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99
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Einarsson G, Martin S, Walker B, Elborn J, McDowell A. Degradation of host defence molecules by CF-related pathogens grown as biofilms. J Cyst Fibros 2008. [DOI: 10.1016/s1569-1993(08)60165-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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100
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Minkis K, Kavanagh D, O'Neill D, Alter G, Sunderji S, Adams S, Walker B, Pavlick AC, Gandhi R, Bhardwaj N. Transfection of dendritic cells (DCs) with mRNA encoding IL-12p70 enhances anti-tumor immunity in melanoma patients. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.22217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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