Commensal microbiome impact on CD4 T cell lymphopenia in HIV-1 infection

共生微生物组对 HIV-1 感染中 CD4 T 细胞淋巴细胞减少症的影响

基本信息

批准号：
10698152
负责人：
Souheil Antoine Younes
金额：
$ 76.77万
依托单位：
EMORY UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-09-15 至 2027-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10698152
关键词：
Address Adult Affect Amino Acids Apoptosis Attenuated Bacteria Bacterial Toxins Bifidobacterium Biological Assay CD3 Antigens CD4 Positive T Lymphocytes Caspase Cell Count Cell Culture System Cell Cycle Cell Death Cell Death Induction Cell Proliferation Cell Separation Cell Survival Cells Cessation of life Characteristics Circulation Citric Acid Cycle Consumption Creatinine Cresol Crista ampullaris Cytosol DNA DNA Damage Data Diet Electron Microscopy Feces Frequencies General Population Genes Genus Hippocampus Golgi Apparatus HIV HIV-1 IRF3 gene Immune Immune Plasma Immunology procedure Impairment In Vitro Incubated Indican Individual Induction of Apoptosis Infection Inflammatory Interferons Journals Kidney Lactobacillus Lymphopenia Mass Spectrum Analysis Measures Memory Metabolic Metagenomics Methods Mitochondria Mitochondrial DNA Mitochondrial Proteins Modeling Modification Monitor Morbidity - disease rate Mutation Outcome Pathway interactions Patients Peripheral Blood Mononuclear Cell Persons Phenotype Phenylalanine Plasma Probability Procedures Production Proteins Publishing Recovery Regimen Reporting Response Elements Ribosomal DNA Risk Role Ruminococcus Sampling Sorting Structure Sulfate T-Cell Activation T-Cell Proliferation T-Lymphocyte Testing Toxic effect Toxin Tyrosine aged antiretroviral therapy cell type clinical investigation clinical research site cohort commensal bacteria comorbidity cytokine dysbiosis experimental study gene induction gut bacteria gut microbiome gut microbiota in vitro testing inflammatory modulation kidney dysfunction memory CD4 T lymphocyte metabolic profile metagenomic sequencing metaproteomics microbial microbiome microbiota microscopic imaging mitochondrial dysfunction mitochondrial fitness mortality multiple omics novel nutrition prevent protein expression recruit response single-cell RNA sequencing stool sample systemic inflammatory response transcriptome sequencing transcriptomics urinary

项目摘要

Project Summary/Abstract HIV-infected Immune non-responders (INR) persons are at greater risk of comorbidity and mortality than are immune responders (IR) who restore their CD4 T cells count (IR) after anti- retroviral therapy (ART). INR have low CD4 T cell counts (<350 c/ul), heightened systemic inflammation, and increased CD4 T cell cycling (KI67+). We previously reported dysfunctional mitochondria in INR CD4 T cells by transcriptomic and flow cytometric assays. In here we report the metabolic profiles of sorted memory CD3+CD4+CD45RO+T cells from healthy controls (HC), IR, and INR and found dysregulation of the tricarboxylic acid cycle (TCA) intermediates suggestive of mitochondrial dysfunction confirmed by Electron Microscopy Imaging (EMI). Disrupted Golgi structure, reduced mitochondrial numbers, inactive mitochondrial cristae, and evidence of mitophagy were detected in INR EMI sections. We report the novel observation that memory CD4 T cells and plasma samples of INR from several cohorts are enriched for levels of the gut-derived bacterial toxins p- cresol-sulfate (PCS) and indoxyl sulfate (IS) that both negatively correlate with CD4 T cell counts. Incubation of peripheral blood mononuclear cells (PBMCs) from HC with PCS or IS blocks CD4 T cell proliferation in vitro, induces apoptosis, and diminishes the expression of the mitochondrial proteins (COX-IV and mTFA). EMI reveals perturbations of mitochondria network similar to those found in INR following incubation of sorted memory CD4 T cells from HC with PCS or IS suggesting that PCS and IS may contribute to the diminished mitochondrial fitness of INR CD4 T cells. Using bacterial 16S rDNA assay INR stool were found enriched with proteolytic bacterial genera (Bifidobacterium, Ruminococcus, Lactobacillus) that metabolize tyrosine and phenylalanine amino acids to produce PCS. We propose that gut bacterial flora toxins may impair CD4 T cell recovery during ART and may contribute to CD4 T cell lymphopenia characteristic of INR. We propose, mechanistically, that PCS/IS induce toxicity to the mitochondrial network, mitochondrial DNA is then released in the cytosol and activates STING that triggers caspases of the mitochondrial death pathway, IRF3, and Interferon-Sensitive- Response Element (ISRE) genes implicated in apoptosis and pyroptosis induction (AIM1). We will address whether enrichment of plasma PCS/IS in a large cohort of INR is correlated to low CD4 T cell count, apoptosis/STING levels, and mitochondrial dysfunction in a set of ex-vivo experiments (AIM2). We will then explore, by performing metagenomics, metaproteomics, and metabolic analyses, whether commensal bacteria in the gut of INR subjects are in dysbiosis and enriched in bacterial strains overproducing PCS and IS (AIM3).

项目概要/摘要 HIV 感染者与免疫无反应者 (INR) 相比，其出现合并症和死亡的风险更大抗逆转录病毒治疗 (ART) 后恢复 CD4 T 细胞计数 (IR) 的免疫应答者 (IR)。印度卢比 CD4 T 细胞计数低 (<350 c/ul)、全身炎症加剧、CD4 T 细胞循环增加（KI67+）。我们之前通过转录组学和流式细胞术报道了 INR CD4 T 细胞中线粒体功能障碍细胞计数分析。在这里，我们报告了排序的记忆 CD3+CD4+CD45RO+T 细胞的代谢概况来自健康对照 (HC)、IR 和 INR 的结果，发现三羧酸循环 (TCA) 失调电子显微镜成像（EMI）证实提示线粒体功能障碍的中间体。高尔基体结构被破坏，线粒体数量减少，线粒体嵴不活跃，以及在 INR EMI 切片中检测到线粒体自噬。我们报告了记忆 CD4 T 细胞和来自多个队列的 INR 血浆样本富含肠道来源的细菌毒素 p- 硫酸甲酚 (PCS) 和硫酸吲哚酚 (IS) 均与 CD4 T 细胞计数呈负相关。孵化来自 HC 的外周血单核细胞 (PBMC) 与 PCS 或 IS 一起在体外阻断 CD4 T 细胞增殖，诱导细胞凋亡，并减少线粒体蛋白（COX-IV 和 mTFA）的表达。电磁干扰揭示了线粒体网络的扰动，类似于分选孵化后 INR 中发现的扰动来自 HC 的记忆 CD4 T 细胞与 PCS 或 IS 表明 PCS 和 IS 可能有助于减少 INR CD4 T 细胞的线粒体适应性。使用细菌16S rDNA检测发现粪便INR富集具有代谢酪氨酸的蛋白水解细菌属（双歧杆菌、瘤胃球菌、乳杆菌）和苯丙氨酸生产PCS。我们认为肠道细菌菌群毒素可能会损害 CD4 ART 期间 T 细胞恢复，可能导致 INR 特征性 CD4 T 细胞淋巴细胞减少。我们从机制上提出，PCS/IS 对线粒体网络产生毒性，然后线粒体 DNA 在细胞质中释放并激活 STING，从而触发线粒体死亡途径 IRF3 的半胱天冬酶，和干扰素敏感反应元件（ISRE）基因与细胞凋亡和细胞焦亡诱导有关（目标1）。我们将讨论大量 INR 中血浆 PCS/IS 的富集是否与低水平相关。一组离体实验中的 CD4 T 细胞计数、凋亡/STING 水平和线粒体功能障碍（目标2）。然后，我们将通过进行宏基因组学、宏蛋白质组学和代谢分析来探索， INR受试者肠道内的共生细菌是否处于生态失调且富含细菌菌株 PCS 和 IS (AIM3) 产量过剩。