Biodefense Proteomics Collaboratory

生物防御蛋白质组学实验室

• 批准号: 7780782
• 负责人: David G Gorenstein
• 金额: $ 63.84万
• 依托单位: UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-04-15 至 2010-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7780782
• 关键词: Applied Research; Arenavirus; Arts; Binding; Bioinformatics; Biological Markers; Biological Models; Biotechnology; Bioterrorism; Cell model; Cells; Centers for Disease Control and Prevention (U.S.); Class; Collaborations; Complex; Computer Analysis; Computer software; Data; Development; Diagnostic; Drug Design; Early Diagnosis; Electrophoresis; Ensure; Flow Cytometry; Gel; Gene Expression; Genes; Genomics; Genus Lynx; Gold; Human; Image; Immune response; Immunologist; In Vitro; Industry; Infection; Inflammation; Inflammatory; Inflammatory Response; Inflammatory Response Pathway; Laboratories; Libraries; Mass Spectrum Analysis; Medical; Methodology; Methods; NF-kappa B; Natural Immunity; Nuclear Envelope; Oligonucleotides; Pathway interactions; Performance; Pharmacologic Substance; Pichinde; Process; Promoter Regions; Protein Databases; Protein Family; Proteins; Proteome; Proteomics; Research Personnel; Resolution; Resources; Rodent; Rodent Model; Schedule; Scientist; Screening procedure; Secure; Shock; Signal Transduction; Solutions; Sorting - Cell Movement; Standards of Weights and Measures; Structural Biologist; Technology; Texas; Therapeutic; United States National Institutes of Health; Universities; Vertebral column; Viral; Virus; Virus Diseases; base; biodefense; biosafety level 4 facility; cell type; chemical synthesis; collaboratory; combinatorial; cost; data management; immunological intervention; novel; outcome forecast; pathogen; phosphorothioate; protein expression; response; surface enhanced laser desorption ionization; tool; transcription factor; two-dimensional

DESCRIPTION (provided by applicant): In vitro enzymatic combinatorial selection and split-synthesis chemical combinatorial methods will be used to develop a "ThioAptamer Chip" (TACh) for proteomics - a diagnostic tool to identify and quantify the differential expression of key proteins in response to pathogens of concern for bioterrorism threat (BT). This new proteomics technology will utilize our proprietary thioselection and phosphorothioate-modified oligonucleotide "thioaptamers," combined with the surface enhanced laser desorption/ionization (SELDI) mass spectroscopy technology of our collaborating partner, Ciphergen, to target both rodent and human proteomes. In particular we will study the inflammatory response of cytokines and key transcription factors (e.g., NF-kappaB) challenged with BT agents. The five NF-?B/Rel family proteins can combine to form 15 homo- and heterodimers, each performing a specific signaling function upon translocation across the cell nuclear membrane and binding to a gene's promoter region. In partnership with Ciphergen, we will also develop new, massively parallel, thioaptamer bead-based screening of the proteome with SELDI mass-spectrometric methods to identify uncharacterized proteins involved in the immune response to BT viruses. Our results from the TACh/SELDI approaches will be validated by 2D gel mass spectrometric proteomic methods. We will also apply bioinformatic analyses to correlate changes in protein expression with available genomic data on changes in gene expression as a result of inflammation after viral infection or shock. Elucidating these protein expression changes will allow early diagnosis and enhanced prognosis of viral disease, and subsequent development of effective pharmacological and immunological interventions. Specific initial viral targets include arenaviruses, Pichinde and Lassa (the latter on both the NIH and CDC class A lists).

描述（由申请人提供）：体外酶促组合选择和分割合成化学组合方法将用于开发用于蛋白质组学的“ThioAptamer芯片”（TACh）——一种诊断工具，用于识别和量化针对生物恐怖主义威胁（BT）关注的病原体的关键蛋白质的差异表达。这种新的蛋白质组学技术将利用我们专有的硫代选择和硫代磷酸酯修饰的寡核苷酸“硫适体”，结合我们合作伙伴 Ciphergen 的表面增强激光解吸/电离 (SELDI) 质谱技术，以靶向啮齿动物和人类蛋白质组。特别是，我们将研究 BT 制剂激发的细胞因子和关键转录因子（例如 NF-kappaB）的炎症反应。五种 NF-κB/Rel 家族蛋白可以结合形成 15 个同源二聚体和异源二聚体，每种二聚体在跨细胞核膜易位并与基因启动子区域结合时执行特定的信号传导功能。我们还将与 Ciphergen 合作，开发新的大规模并行、基于硫代适体珠的蛋白质组筛选方法，采用 SELDI 质谱方法来识别参与 BT 病毒免疫反应的未表征蛋白质。我们的 TACh/SELDI 方法结果将通过 2D 凝胶质谱蛋白质组学方法进行验证。我们还将应用生物信息学分析，将蛋白质表达的变化与病毒感染或休克后炎症导致的基因表达变化的可用基因组数据关联起来。阐明这些蛋白质表达变化将有助于病毒性疾病的早期诊断和增强预后，以及随后开发有效的药理学和免疫学干预措施。具体的初始病毒目标包括沙粒病毒、Pichinde 病毒和拉沙病毒（后者均位于 NIH 和 CDC A 类列表中）。

项目成果

Thioaptamers targeting dengue virus type-2 envelope protein domain III.

• DOI: 10.1016/j.bbrc.2014.09.053
• 发表时间: 2014-10-24
• 期刊: BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
• 影响因子: 3.1
• 作者: Gandham, Sai Hari A.;Volk, David E.;Lokesh, Ganesh L. R.;Neerathilingam, Muniasamy;Gorenstein, David G.
• 通讯作者: Gorenstein, David G.

X-aptamers: a bead-based selection method for random incorporation of druglike moieties onto next-generation aptamers for enhanced binding.

• DOI: 10.1021/bi300471d
• 发表时间: 2012-10-23
• 期刊: Biochemistry
• 影响因子: 2.9
• 作者: He W;Elizondo-Riojas MA;Li X;Lokesh GL;Somasunderam A;Thiviyanathan V;Volk DE;Durland RH;Englehardt J;Cavasotto CN;Gorenstein DG
• 通讯作者: Gorenstein DG

NMR structure of human thymosin alpha-1.

• DOI: 10.1016/j.bbrc.2011.11.041
• 发表时间: 2011-12-16
• 期刊: Biochemical and biophysical research communications
• 影响因子: 3.1
• 作者: Elizondo-Riojas MA;Chamow SM;Tuthill CW;Gorenstein DG;Volk DE
• 通讯作者: Volk DE

Blocking the adhesion cascade at the premetastatic niche for prevention of breast cancer metastasis.

• DOI: 10.1038/mt.2015.45
• 发表时间: 2015-06
• 期刊: Molecular therapy : the journal of the American Society of Gene Therapy
• 作者: Shin-Ae Kang;Nafis Hasan;Aman P Mann;Wei Zheng;Lichao Zhao;Lynsie Morris;Weizhu Zhu;Yan D Zhao;K Stephen Suh;William C Dooley;D. Volk;D. Gorenstein;M. Cristofanilli;H. Rui;Takemi Tanaka

Structure of the envelope protein domain III of Omsk hemorrhagic fever virus.

鄂木斯克出血热病毒包膜蛋白结构域III的结构。

• DOI: 10.1016/j.virol.2006.03.030
• 发表时间: 2006
• 期刊: Virology.
• 作者: Volk,DavidE;Chavez,Leonard;Beasley,DavidWC;Barrett,AlanDT;Holbrook,MichaelR;Gorenstein,DavidG
• 通讯作者: Gorenstein,DavidG