Single cell transcriptomics of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [scRNA-seq cART+3HP]

We studied components of TB immunity that remain impaired after cART in the lung compartment, versus those that are restored by concurrent 3 months of once weekly isoniazid and rifapentine (3HP) and cART in the rhesus macaque (RM) model of LTBI and Simian Immunodeficiency Virus (SIV) co-infection. Concurrent administration of cART+3HP did improve clinical and microbiological attributes of Mtb/SIV co-infection compared to cART-naïve or -untreated RMs. While RMs in the cART+3HP group exhibited significantly lower granuloma volumes after treatment, they, however, continued to harbor caseous granulomas with increased FDG uptake. cART only partially restores the constitution of CD4+ T cells to the lung compartment in co-infected macaques. Concurrent therapy did not further enhance the frequency of reconstituted CD4+ T cells in BAL and lung of Mtb/SIV co-infected RMs compared to cART, and treated animals continued to display incomplete reconstitution to the lung. Furthermore, the reconstituted CD4+ T cells in BAL and lung of cART+3HP treated RMs exhibited an increased frequencies of activated, exhausted and inflamed phenotype compared to LTBI RMs. cART+3HP failed to restore the effector memory CD4+ T cell population that was significantly reduced in pulmonary compartment post SIV co-infection. Concurrent therapy was associated with the induction of Type I IFN transcriptional signatures and led to increased Mtb-specific TH1/TH17 responses correlated with protection, but decreased Mtb-specific TNF? responses, which could have a detrimental impact on long term protection. Overall design: These cells were isolated from bronchoalveolar lavage of rhesus macaques co-infected with Mtb/SIV and treated with cART+3HP

本研究以潜伏性结核感染（Latent Tuberculosis Infection，LTBI）与猴免疫缺陷病毒（Simian Immunodeficiency Virus，SIV）共感染的恒河猴（rhesus macaque，RM）模型为对象，对比分析了接受抗逆转录病毒联合治疗（combined antiretroviral therapy，cART）后肺脏微环境中仍存在受损的结核病免疫组分，以及同时辅以3个月每周1次异烟肼联合利福喷丁（3HP）治疗的免疫恢复组分。相较于未接受cART或未接受治疗的恒河猴，同时给予cART+3HP治疗可显著改善结核分枝杆菌（Mycobacterium tuberculosis，Mtb）/SIV共感染的临床与微生物学特征。尽管cART+3HP组恒河猴在治疗后肉芽肿体积显著降低，但仍存在干酪样肉芽肿，且氟代脱氧葡萄糖（Fluorodeoxyglucose，FDG）摄取量升高。单纯cART治疗仅能部分恢复共感染猕猴肺脏微环境中的CD4阳性T淋巴细胞组成；与单独cART治疗组相比，联合治疗并未进一步提升Mtb/SIV共感染恒河猴支气管肺泡灌洗液（Bronchoalveolar Lavage，BAL）与肺脏中重建CD4阳性T淋巴细胞的频率，且治疗组动物的肺脏CD4阳性T淋巴细胞重建仍不完全。此外，相较于单纯LTBI感染的恒河猴，接受cART+3HP治疗的恒河猴支气管肺泡灌洗液与肺脏中的重建CD4阳性T淋巴细胞，其活化、耗竭与炎症表型的频率显著升高。cART+3HP治疗未能恢复SIV共感染后肺脏微环境中显著减少的效应记忆CD4阳性T细胞群。联合治疗可诱导I型干扰素（Type I IFN）转录特征，并引发与保护作用相关的Mtb特异性Th1/Th17应答，但同时降低了Mtb特异性肿瘤坏死因子（Tumor Necrosis Factor，TNF）应答，这可能对长期免疫保护产生不利影响。总体实验设计：本研究的细胞样本分离自共感染Mtb/SIV且接受cART+3HP治疗的恒河猴的支气管肺泡灌洗液。