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颖的遗传平台，在选定的条件下对整个 HIV 基因组进行功能分析，并在每个核苷酸位置上进行突变。 HIV基因组的遗传相互作用将由选定的宿主限制因素决定。遗传平台将定量识别区域 基因组（和相应的编码氨基酸）对于功能相互作用至关重要，并且代表着识别宿主-病原体相互作用的重要一步。利用该研究小组开发并成功论证的新型高分辨率基因分析方法，该研究将定量评估 HIV-1 基因组内每个核苷酸位置的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结合将用于同时监测基因组所有位置的突变。为了实现研究目标，该研究将旨在建立初始谱来衡量每个核苷酸位置对 HIV-1 复制的重要性，并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 (IFITM3) 的抵抗和补偿作用的核苷酸位置。将使用一种充分表征的限制因子载脂蛋白 B mRNA 编辑酶催化多肽样 3G (APOBEC3G) 作为比较。更重要的是，所提出的功能分析方法将证明能够评估跨所有基因组空间中整个病毒基因组的大型且多样化的病毒突变体群体，以参与单个实验平台上的复制过程或致病过程，这不仅会影响HIV-1研究，还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，详细描述了每个核苷酸位置对所有可能的碱基变化的突变耐受性，这对 HIV/AIDS 疫苗的开发非常有益。病毒-细胞相互作用的鉴定提供了 大量新的潜在有用的治疗药物设计靶点。