Use of clonal genotyping to predict resistance development in ART-naive IDU

使用克隆基因分型预测未接受 ART 的 IDU 的耐药性发展

• 批准号: 7625170
• 负责人: Richard B. Markham
• 金额: $ 56.87万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-06-01 至 2013-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7625170
• 关键词: Affect; Age; Anti-Retroviral Agents; CD4 Lymphocyte Count; Caring; Cells; Clinical; Cost Savings; Data; Data Analyses; Detection; Development; Dideoxy Chain Termination DNA Sequencing; Disease; Disease Progression; Drug usage; Drug user; Employee Strikes; Event; Face; Failure; Frequencies; Genotype; HIV-1; Haplotypes; Health; Health Care Costs; Highly Active Antiretroviral Therapy; Illicit Drugs; Incidence; Individual; Injecting drug user; Injection of therapeutic agent; Laboratory Study; Light; Medical; Methods; Minority; Mutation; Mutation Detection; NNRTI-resistance; Nucleosides; Patients; Pattern; Peptide Hydrolases; Persons; Pharmaceutical Preparations; Pharmacotherapy; Plasma; Population; Process; Protease Inhibitor; RNA; Recording of previous events; Relapse; Reporting; Research Design; Research Personnel; Resistance; Resistance development; Resistance profile; Retrospective Studies; Reverse Transcriptase Inhibitors; Risk; Sampling; Sequence Analysis; Site; Social Impacts; Techniques; Technology; Testing; Time; Treatment Protocols; Variant; Viral; Virion; Virus; Visit; Woman; antiretroviral therapy; base; case control; clinical research site; clinically relevant; cohort; cost; design; experience; high risk; interest; medical schools; new technology; non-compliance; non-nucleoside reverse transcriptase inhibitors; novel; pol Gene Products; pol genes; pressure; resistance mutation; response; standard of care; therapy development

DESCRIPTION (provided by applicant): Failure of antiretroviral therapy (ART) has been a particular problem among HIV-1 infected illicit drug users. This failure has primarily been attributed to poor compliance with antiretroviral drug regimens. Studies from this laboratory have indicated that a higher viral mutation frequency that we have documented in injection drug users (IDU) and the resulting higher frequency of primary resistance mutations in pol might contribute to the poor response in this group. Genotypic resistance analysis using population sequencing has proved useful in guiding selection of antiretroviral therapy in individuals who have developed viral relapse after initial treatment. Our preliminary data analyzing up to 10 viral clones from protease inhibitor (PI) and non-nucleoside reverse transcriptase inhibitor (NNRTI) naive IDU have indicated that a strikingly and significantly high proportion of IDU subject-visits (28%) carry PI resistance mutations compared to the much lower proportion (8%) found in non-IDU. Almost none of these resistance mutations were detected using standard population genotyping techniques. Similar high levels of primary resistance have been found in a cohort of non-injection illicit drug users followed by investigators at Vanderbilt Medical School. This proposal hypothesizes that use of sensitive sequencing techniques prior to initiation of HAART will be predictive of rapid development of resistance, therefore enabling the development of personalized and more effective initial HAART regimens. Specifically in cohorts from the Johns Hopkins and Vanderbilt Schools of Medicine of 150 HAART-naive drug users who rapidly failed HAART and 150 comparable subjects for whom therapy was successful we will 1) Determine whether identification of resistance mutations by standard clonal analysis using the Sanger sequencing method to study the pol region from 20 HIV-1 clones from a single visit predicts risk of subsequent therapy failure better than population genotyping from that same visit 2) evaluate whether identification of resistance mutations by high throughput clonal analysis of relatively short sequences from the RT and protease regions (454 sequencing) predicts risk of subsequent therapy failure better than: i) standard population genotyping and ii) analysis of 20 clones (sequenced using the Sanger method) in which both NRTI and NNRTI or PI resistance mutations can be identified on the same viral clone and 3) Evaluate, using 454 sequencing technology, the frequency of clonal resistance needed for clones with PI or NNRTI resistance to predict increased risk of rapid development of therapy failure. The results of this study could provide a new standard of care for initiation of HAART and could greatly reduce the financial and social impact of HAART failure. This study is designed to evaluate new technologies that will render anti-HIV-1 drug therapy more effective. This new technology will permit better characterization of the viral strains that are infecting an individual so that the therapy can be specifically targeted to those viruses.

描述（由申请人提供）：抗逆转录病毒治疗（ART）失败一直是感染 HIV-1 的非法吸毒者面临的一个特殊问题。这一失败主要归因于抗逆转录病毒药物治疗方案依从性差。该实验室的研究表明，我们在注射吸毒者 (IDU) 中记录的病毒突变频率较高，以及由此导致的 pol 中原发性耐药突变频率较高，可能是导致该群体反应不佳的原因。事实证明，使用群体测序进行的基因型耐药性分析有助于指导初次治疗后出现病毒复发的个体选择抗逆转录病毒疗法。我们对来自蛋白酶抑制剂 (PI) 和非核苷逆转录酶抑制剂 (NNRTI) 的初次 IDU 的多达 10 个病毒克隆进行分析的初步数据表明，与相比，IDU 受试者就诊中携带 PI 抗性突变的比例惊人且显着较高 (28%)。非注射吸毒者中的比例要低得多（8%）。使用标准群体基因分型技术几乎没有检测到这些抗性突变。范德比尔特医学院的研究人员在一组非注射非法药物使用者中也发现了类似的高水平原发性耐药性。该提议假设，在开始 HAART 之前使用敏感测序技术将预测耐药性的快速发展，从而能够开发个性化且更有效的初始 HAART 方案。具体而言，在来自约翰·霍普金斯大学和范德比尔特医学院的 150 名 HAART 初治药物使用者（HAART 快速失败）和 150 名治疗成功的类似受试者的队列中，我们将 1) 确定是否使用桑格测序通过标准克隆分析来识别耐药突变通过单次就诊研究 20 个 HIV-1 克隆的 pol 区域的方法比同次就诊的群体基因分型更好地预测后续治疗失败的风险 2) 评估是否识别出耐药性通过对来自 RT 和蛋白酶区域的相对较短序列（454 测序）进行高通量克隆分析来预测后续治疗失败的风险，比以下方法更好地预测后续治疗失败的风险：i）标准群体基因分型和 ii）20 个克隆的分析（使用 Sanger 方法测序），其中可以在同一病毒克隆上鉴定 NRTI 和 NNRTI 或 PI 抗性突变，并且 3) 使用 454 测序技术评估具有 PI 或 PI 的克隆所需的克隆抗性频率NNRTI 耐药性可预测治疗失败快速发展的风险增加。这项研究的结果可以为开始HAART提供新的护理标准，并可以大大减少HAART失败的财务和社会影响。这项研究旨在评估使抗 HIV-1 药物治疗更有效的新技术。这项新技术将允许更好地表征感染个体的病毒株，以便治疗可以专门针对这些病毒。