Fitness Profile of HIV-1 Genome with Host Cofactor Selection Pressure

HIV-1 基因组与宿主辅因子选择压力的适应度概况

• 批准号: 8731701
• 负责人: REN SUN
• 金额: $ 19.25万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-02-01 至 2016-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8731701
• 关键词: AIDS/HIV problem; Amino Acids; Anti-Retroviral Agents; Attenuated; Blood Circulation; Catalysis; Cell Line; Cells; Code; Community Health; Coupled; Data; Development; Drug Design; Drug resistance; Engineering; Enzymes; Epidemic; Essential Amino Acids; Event; Generations; Genetic; Genetic Recombination; Genetic Variation; Genome; Genomics; Goals; HIV Genome; HIV-1; Health; Human; Immune; Interferons; Knowledge; Libraries; Maps; Mediating; Membrane Proteins; Methods; Monitor; Mutagenesis; Mutate; Mutation; Nucleic Acids; Nucleotides; Outcome; Output; Pathogenesis; Patients; Pharmaceutical Preparations; Phenotype; Planets; Plasmids; Point Mutation; Population; Positioning Attribute; Prevention therapy; Process; Protease Gene; RNA; RNA-Directed DNA Polymerase; Replication-Associated Process; Research; Resistance; Resolution; Reverse Transcription; Sequence Analysis; Site; Stretching; Surveys; T-Lymphocyte; Technology; Therapeutic; Time; Vaccines; Variant; Viral; Viral Genome; Virion; Virus; apolipoprotein B mRNA editing enzyme; base; cofactor; design; fitness; genetic profiling; innovation; mutant; new technology; next generation sequencing; novel; overexpression; pathogen; polypeptide; pressure; prevent; protein protein interaction; public health relevance; research clinical testing; research study; therapeutic target; transmission process; vaccine candidate; vaccine development; vector

DESCRIPTION (provided by applicant): The proposed research will utilize a novel genetic platform to functionally profile the entire HIV genome at selected conditions with mutation at every single nucleotide position. The genetic interaction of HIV genome will be determined with selected host restriction factors. The genetic platform will quantitatively identify regions of the genome (and the corresponding coded amino acids) that are essential for the functional interaction, and represents a major step forward to identify host-pathogen interactions. Using the novel high-resolution genetic profiling approach that the research group has developed and successfully demonstrated, the study will quantitatively assess mutational impact for all possible nucleic acid base changes for every nucleotide position within the HIV-1 genome. The combination of saturation mutagenesis with next generation sequence will be applied to monitor mutations at all positions of the genome simultaneously. In accomplishing the research goals, the study will aim to establish the initial profile gauging the essentialness of each nucleotide position for HIV-1 replication, and subsequently identify nucleotide positions in the genome for resistance and compensatory effects to host restriction factor interferon-induced trans-membrane protein 3 (IFITM3). A well-characterized restriction factor apolipoprotein B mRNA-editing enzyme, catalytic polypeptide- like 3G (APOBEC3G) will be used as a comparison. More importantly, the proposed functional profiling method will demonstrate the ability to evaluate a large and diverse viral mutant population spanning an entire viral genome in all genomic space for the involvement in a replication process or pathogenic process on a single experimental platform, which will impact not just HIV-1 research, but the study of many other viral pathogens. From the obtained high resolution map of the entire HIV-1 genome detailing mutational tolerability at each nucleotide position for all possible base changes, which should prove highly beneficial for HIV/AIDS vaccine development. Identification of viral-cellular interactions provides a great wealth of new potentially useful targets for therapeutic drug design.

描述（由申请人提供）：拟议的研究将利用一种新的遗传平台，在选定的条件下对整个HIV基因组进行功能分析，每个核苷酸位置都有突变。HIV基因组的遗传相互作用将用选定的宿主限制因子来确定。基因平台将定量识别 基因组（和相应的编码氨基酸）的功能相互作用是必不可少的，并代表了一个重大的一步，以确定宿主-病原体相互作用。使用该研究小组开发并成功证明的新型高分辨率遗传分析方法，该研究将定量评估HIV-1基因组内每个核苷酸位置所有可能的核酸碱基变化的突变影响。饱和诱变与下一代序列的组合将用于同时监测基因组所有位置的突变。在实现研究目标的过程中，该研究的目标是建立初始图谱，衡量每个核苷酸位置对HIV-1复制的必要性，随后确定基因组中对宿主限制因子干扰素诱导的跨膜蛋白3（IFITM 3）的抗性和补偿效应的核苷酸位置。将使用充分表征的限制因子载脂蛋白B mRNA编辑酶催化多肽样3G（APOBEC 3G）作为比较。更重要的是，提出的功能分析方法将证明能够在单个实验平台上评估跨越整个病毒基因组的大型和多样化的病毒突变群体参与复制过程或致病过程，这不仅会影响HIV-1研究，而且会影响许多其他病毒病原体的研究。从获得的整个HIV-1基因组的高分辨率图谱中，详细说明了每个核苷酸位置对所有可能的碱基变化的突变耐受性，这应该证明对HIV/AIDS疫苗开发非常有益。病毒-细胞相互作用的鉴定提供了 为治疗药物设计提供了大量新的潜在有用的靶点。