CD4 T cell receptor hierarchies are stable and independent of HIV-mediated dysregulation of immune homeostasis

LT-ART and A5248 folders contain preprocessed CyTOF files (FCS format) from a 31-marker mass cytometry panel to examine all major PBMC lineages and specifically CD4 and CD8 T cell memory dynamics in people with HIV (PWH) who are durably ART suppressed for an average of 6.7 years (LT-ART, n = 10) and PWH in the first 500 days following ART initiation (A5248, n = 10). The panel also includes markers of activation (HLA-DR, CD38, CCR5), activation/exhaustion (PD-1), proliferation (Ki67), survival (Bcl-2) and long-lived memory (CD127).

Preprocessed annotated data objects (A5248_subsample.h5ad, LT-ART_subsample.h5ad) for unsupervised analysis can be accessed using the 'read_h5ad' function in Scanpy.

CD4_MSI and CD8_MSI folders contain the MSI data for the Gamma fixed-effects regression models. 

All source code for reproduction of the results can be found in the GitHub repository: https://github.com/glab-hiv/immune-recovery

LT-ART 与 A5248 文件夹内含经过预处理的CyTOF（飞行时间质谱流式细胞术，Cytometry by Time-of-Flight）文件（格式为FCS），该文件基于一套31标志物的质谱细胞术标志物组合，用于全面检测人类免疫缺陷病毒（HIV，Human Immunodeficiency Virus）感染者（PWH，People Living with HIV）体内所有主要外周血单个核细胞（PBMC，Peripheral Blood Mononuclear Cell）谱系，并专门分析两类感染者的CD4及CD8 T细胞记忆动态：一类为经抗逆转录病毒治疗（ART，Antiretroviral Therapy）持续抑制病毒平均6.7年的感染者（LT-ART组，n=10），另一类为启动ART后前500天内的感染者（A5248组，n=10）。该标志物组合还涵盖激活相关标志物（HLA-DR、CD38、CCR5）、激活/耗竭相关标志物（PD-1）、增殖相关标志物（Ki67）、存活相关标志物（Bcl-2）以及长寿记忆相关标志物（CD127）。

可通过Scanpy工具包中的`read_h5ad`函数读取用于无监督分析的预处理注释数据对象（A5248_subsample.h5ad、LT-ART_subsample.h5ad）。

CD4_MSI与CD8_MSI文件夹内含用于Gamma固定效应回归模型的MSI数据。

所有用于复现该研究结果的源代码可在以下GitHub仓库获取：https://github.com/glab-hiv/immune-recovery