Unraveling the mammalian secretory pathway through systems biology and algorithm development

通过系统生物学和算法开发揭示哺乳动物的分泌途径

• 批准号: 10826657
• 负责人: Nathan Enoch Lewis
• 金额: $ 7.58万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-15 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10826657
• 关键词: Antibodies; Antiviral Agents; Biotinylation; Capsid Proteins; Cell Communication; Cells; Cirrhosis; Code; Communication; Data; Disease; Engineering; Environment; Genes; Health; Hepatitis C; Hepatitis C virus; Hepatocyte; Human Genome; Liver; Liver diseases; Measures; Membrane; Methods; Modeling; Pathway Analysis; Pathway interactions; Post-Translational Protein Processing; Process; Protein Biosynthesis; Protein Secretion; Proteins; Proteomics; Regulation; Resources; Role; Secretory Cell; Signal Transduction; Subunit Vaccines; Systems Biology; Techniques; Viral; Viral Proteins; Virus; Virus Diseases; algorithm development; extracellular; functional genomics; gene regulatory network; parent grant; particle; pathogen; programs; protein protein interaction; receptor; transcriptome; transcriptomics; transmission process

ABSTRACT The mammalian secretory pathway regulates a cell’s extracellular interactions by making most signals and receptors that moderate communication and most proteins needed for a cell to interact with its extracellular environment, which includes ~⅓ of their protein-coding genes in the human genome. Furthermore, it is frequently harnessed by pathogens, including all enveloped viruses to aid in their synthesis. To synthesize and transport these thousands of secreted, membrane, and pathogen proteins, the pathway has hundreds of machinery proteins, each with their unique role in the process. However, the regulation of this pathway is poorly understood, especially how it is tailored to the needs of each protein it produces. The parent grant is elucidating these processes by identifying all secretory pathway machinery proteins and detailing their functions, with a particular focus on liver-secreted proteins, and liver diseases. Functional genomics and systems biology techniques are deciphering the regulatory mechanisms controlling the pathway. In this supplement, we build upon the parent grant to decipher the regulatory processes that are hijacked by enveloped viruses, in particular, the Hepatitis C Virus (HCV), to facilitate the rapid synthesis, folding and post-translational modification of its coat proteins. Furthermore, the virus successfully manipulates the host cell to produce their proteins at very high levels, requiring extensive use of host cell resources and machinery. HCV, for example, primarily infects hepatocytes, and is the leading cause of liver disease including cirrhosis. To decipher how HCV regulates the host cell secretory pathway, we will leverage the Biotinylation by Antibody Recognition (BAR) method to measure protein-protein interactions between the E1E2 HCV coat protein, expressed and secreted from hepatocytes. Next we will simultaneously measure the protein secretion rates and the transcriptome for single cells. These data will be used to identify the essential host cell machinery needed for virus protein synthesis and allow the use of gene regulatory network analyses and systems biology modeling to identify how these processes are controlled by the virus. An understanding of how the HCV regulates the host secretory pathway could yield new targets for direct-acting antivirals, or even inform how to engineer cells that can produce subunit vaccines to avoid viral damage and reduce transmission.

摘要

项目成果

Single-cell A/B testing for cell-cell communication.

用于细胞间通信的单细胞 A/B 测试。

• DOI: 10.1016/j.cels.2023.05.006
• 发表时间: 2023
• 期刊: Cell systems
• 影响因子: 9.3
• 作者: Aamodt,CaitlinM;Lewis,NathanE
• 通讯作者: Lewis,NathanE

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

• DOI: 10.1016/j.cels.2016.10.020
• 发表时间: 2016-11-23
• 期刊: Cell systems
• 影响因子: 9.3
• 作者: Hefzi H;Ang KS;Hanscho M;Bordbar A;Ruckerbauer D;Lakshmanan M;Orellana CA;Baycin-Hizal D;Huang Y;Ley D;Martinez VS;Kyriakopoulos S;Jiménez NE;Zielinski DC;Quek LE;Wulff T;Arnsdorf J;Li S;Lee JS;Paglia G;Loira N;Spahn PN;Pedersen LE;Gutierrez JM;King ZA;Lund AM;Nagarajan H;Thomas A;Abdel-Haleem AM;Zanghellini J;Kildegaard HF;Voldborg BG;Gerdtzen ZP;Betenbaugh MJ;Palsson BO;Andersen MR;Nielsen LK;Borth N;Lee DY;Lewis NE
• 通讯作者: Lewis NE

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing.

• DOI: 10.1186/s12864-021-07381-z
• 发表时间: 2021-01-21
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Kellman BP;Baghdassarian HM;Pramparo T;Shamie I;Gazestani V;Begzati A;Li S;Nalabolu S;Murray S;Lopez L;Pierce K;Courchesne E;Lewis NE
• 通讯作者: Lewis NE

Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans.

建模与代谢组学的结合——WormJam 共识模型作为模式生物秀丽隐杆线虫代谢研究的基础。

• DOI: 10.3389/fmolb.2018.00096
• 发表时间: 2018
• 期刊: Frontiers in molecular biosciences
• 影响因子: 5
• 作者: Witting,Michael;Hastings,Janna;Rodriguez,Nicolas;Joshi,ChintanJ;Hattwell,JakePN;Ebert,PaulR;vanWeeghel,Michel;Gao,ArwenW;Wakelam,MichaelJO;Houtkooper,RiekeltH;Mains,Abraham;LeNovère,Nicolas;Sadykoff,Sean;Schroeder,Fran
• 通讯作者: Schroeder,Fran

An enhanced CRISPR repressor for targeted mammalian gene regulation.

• DOI: 10.1038/s41592-018-0048-5
• 发表时间: 2018-08
• 期刊: Nature methods
• 影响因子: 48
• 作者: Yeo NC;Chavez A;Lance-Byrne A;Chan Y;Menn D;Milanova D;Kuo CC;Guo X;Sharma S;Tung A;Cecchi RJ;Tuttle M;Pradhan S;Lim ET;Davidsohn N;Ebrahimkhani MR;Collins JJ;Lewis NE;Kiani S;Church GM
• 通讯作者: Church GM