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Phenotypic and mechanistic analysis of the in vivo HIV latent reservoir by single-cell technologies

通过单细胞技术对体内 HIV 潜伏病毒库进行表型和机制分析

基本信息

批准号：
10448398
负责人：
Nadia R Roan
金额：
$ 84.35万
依托单位：
J. DAVID GLADSTONE INSTITUTES
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-08-01 至 2024-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10448398
关键词：
Anatomy Antigens Atlases Automobile Driving Back Bioinformatics Biological Markers Blood CD4 Positive T Lymphocytes Cell surface Cells Clinical Clonal Expansion Cytomegalovirus DNA sequencing Data Analyses Data Set Development Exhibits Face Flow Cytometry Fluorescence Frequencies Gene Expression Gene Expression Profile Genetic Transcription Genome Goals HIV HIV Genome HIV Infections Homeostasis Immunology Individual Infection Intervention Knowledge Lead Length Leukapheresis Link Location Maintenance Maps Measures Methods Molecular Patients Persons Phenotype Population Property Proteins Regression Analysis Research Research Personnel Research Priority Role Sampling Sorting - Cell Movement Specificity Surface System T-Lymphocyte T-Lymphocyte Subsets Technology Time Tissues Translations Viral Viral Proteins Virus Woman antiretroviral therapy base biological sex co-infection cohort defined contribution design experimental study high dimensionality in vivo latent HIV reservoir lymph nodes men mortality multidimensional data novel patient population receptor sex single cell analysis single cell technology single-cell RNA sequencing tool trait viral DNA

项目摘要

PROJECT SUMMARY Combination antiretroviral therapy (ART) can suppress HIV replication and lead to decreased mortality in HIV-infected individuals. However, ART does not eliminate the latent HIV reservoir, so effective viral suppression requires lifelong ART administration. Therefore, developing a way to eliminate or achieve ART-free control of the reservoir is a top research priority. One challenge to accomplishing this is that we still have limited understanding of the phenotypic and functional properties of the latently-infected cells that persist in people living with HIV. One challenge to characterizing in vivo latently-infected cells is the inability to directly phenotype these cells, due to the lack of a universal biomarker distinguishing them from uninfected cells. As a result, the only way to directly phenotype latent cells has been to stimulate a bulk population of patient-derived cells ex vivo in order to induce expression of viral proteins by the latent cells. Although this allows identification and therefore phenotyping of the reactivated cells by FACS, the measured phenotypes are different from the original phenotypes of the latently-infected cells since ex vivo stimulation alters gene expression. Here, by applying a pseudotime-based bioinformatics approach called PP-SLIDE on paired sets of unstimulated and stimulated patient cells deep-phenotyped by high-dimensional single-cell analytical approaches (CyTOF, single-cell RNAseq), we infer the phenotypes of latently-infected cells in their original pre-stimulation state, and use this approach to chart the in vivo latent reservoir. In Aim 1, we will use PP-SLIDE on CyTOF-phenotyped cells to compare the latently-infected cells present in the blood and tissues of clinically-matched men and women. In Aim 2, we will characterize the extent to which markers identified in Aim 1, as well as markers identified from an unbiased approach implementing PP-SLIDE on cells analyzed by single-cell RNAseq, enrich for reservoir cells harboring HIV with genetically-intact replication-competent HIV, for these are the cells that are likely the most important to control or eliminate for ART-free viral control. In Aim 3, we will characterize the mechanisms that allow the latently-infected cells to persist, focusing on the role of antigen- and homeostasis-driven clonal expansion of CD4+ T cells. By combining cutting-edge single-cell analysis tools with high-dimensional data analysis methods to map the “atlas” of in vivo latent cells, our studies will provide an unprecedented definition of the features of reservoir cells that persist, reveal whether any reservoir cell traits associate with anatomy (blood vs. tissues) or biological sex (men vs. women), and inform on the mechanisms driving reservoir maintenance. This knowledge that will be important for designing targeted methods to achieve a universal HIV cure.

项目总结