Decoding epigenetic scars of smoldering neuroinflammation and CNS complications in people with HIV

项目摘要/摘要 这项提议的目标是解开驱动异常免疫激活和认知障碍的机制。 通过表观遗传编程的镜头对艾滋病毒携带者(PLWH)进行研究。尽管在以下方面取得了全面进展 对于接受抑制艺术的PLWH来说，他们的寿命和健康，一部分接受ART的人继续 显示神经免疫异常和相关的临床神经综合征，包括认知 并发症。脑脊液(CSF)研究是了解PLWH中枢神经系统的窗口，揭示了 中枢神经系统髓系细胞异常激活和持续病毒复制，尽管有明显的全身性病毒 用艺术来压制。我们自己对PLWH新鲜脑脊液细胞的单细胞基因组研究表明， 罕见的小胶质细胞样髓系细胞存在于PLWH患者的脑脊液中；这些细胞与HIV疾病有关 这些髓系细胞可以携带艾滋病毒DNA。此外，我们的研究表明，表观遗传学 在HIV感染中髓系细胞的特征迅速改变，这种异常的髓系表观遗传状态与 尽管在急性艾滋病毒感染期间立即启动了抗逆转录病毒疗法，但艾滋病毒感染的情况仍在继续。然而，尽管 髓系细胞被认为是表观遗传学中中枢神经系统异常的关键细胞介质 中枢神经系统髓系细胞和其他免疫细胞在PLWH中的情况仍然未知。我们的中心假设是 HIV在致炎基因网络的调节区留下了表观遗传的伤疤 尽管抗逆转录病毒治疗，但脑脊液髓系细胞亚群导致艾滋病毒相关的认知障碍。这一假设 将在我们在耶鲁大学建立的艾滋病毒相关水库和共病研究(HARC)队列中进行测试 包括来自HIV携带者和非HIV携带者的大容量腰椎穿刺术，并将进一步探索 利用国家神经艾滋病组织联盟(NNTC)的尸检脑标本。在PLWH，我们 是否会纵向评估新鲜的脑脊液髓系和T细胞单细胞表观遗传和转录细胞状态 ART疗程，询问脑脊液髓系和T细胞表观基因组是否受损 在艾滋病毒感染期间持续存在，随着时间的推移，成为表观遗传的“伤疤”。使用机器学习，我们将 评估PLWH的表观遗传扰动与中枢神经系统结果之间的关联，包括认知功能 炎症和神经元损伤的损害和脑脊液可溶性生物标志物的异常。我们还将探索 脉络丛脑组织中髓系和胶质细胞的单细胞表观遗传状态 在抑制性抗逆转录病毒疗法和配对对照中死亡的艾滋病毒感染者的脑室周围区。最后，我们 将应用一种创新的单细胞多因素染色质分析方法来分析组蛋白修饰。 这些建议对中枢神经系统和血液中不同的髓系细胞亚群进行了深入的多组单细胞分析， 结合认知评估，将揭示艾滋病毒感染对免疫细胞表观基因组的影响，以及 将揭示与PLWH认知并发症最密切相关的转录和表观遗传状态。这个 这一结果将促进基于免疫和病毒发病机制的PLWH中枢神经系统并发症的生物型研究。

PROJECT SUMMARY/ABSTRACT The goal of this proposal is to unravel mechanisms driving abnormal immune activation and cognitive impairment in people living with HIV (PLWH) through the lens of epigenetic programming. Despite overall advances in lifespan and health for PLWH who are on suppressive ART, a subset of individuals on ART continue to demonstrate neuroimmune abnormalities and associated clinical neurological syndromes including cognitive complications. Cerebrospinal fluid (CSF) studies are a window into the CNS of PLWH, revealing a role for abnormal myeloid cell activation and persistence viral replication in the CNS, despite apparent systemic viral suppression with ART. Our own single cell genomic studies of fresh CSF cells from PLWH have shown that a rare microglia-like myeloid cell population resides in the CSF in PLWH; that these cells are linked to HIV disease status; and that these myeloid cells can harbor HIV DNA. Additionally, our research has shown that epigenetic features of myeloid cells are rapidly altered in HIV infection and this aberrant myeloid epigenetic state associated with HIV infection persists despite the immediate initiation of ART during acute HIV infection. However, despite myeloid cells being recognized as crucial cellular mediators of CNS abnormalities in PLWH, the epigenetic landscapes of CNS myeloid and other immune cells in PLWH remain uncharted. Our central hypothesis is that HIV leaves epigenetic “scars” at regulatory regions of proinflammatory gene networks in distinct CSF myeloid cell subsets, contributing to HIV-related cognitive impairment despite ART. This hypothesis will be tested in our established HIV Associated Reservoirs and Comorbidities Study (HARC) cohort at Yale that includes large volume lumbar puncture from study participants with and without HIV and will be further explored utilizing postmortem brain specimens from the National NeuroAIDS Tissue Consortium (NNTC). In PLWH, we will longitudinally assess fresh CSF myeloid and T cell single cell epigenetic and transcriptional cell states over the course of ART treatment and ask whether there is damage to the epigenomes of CSF myeloid and T cells sustained during HIV infection that persists over time as epigenetic “scars”. Using machine learning, we will then assess for an association between epigenetic perturbations in PLWH and CNS outcomes, including cognitive impairment and abnormal CSF soluble biomarkers of inflammation and neuronal injury. We will also explore single cell epigenetic cell states of myeloid and glia in postmortem brain tissues from choroid plexus and periventricular zones of HIV-infected individuals who died on suppressive ART and matched controls. Lastly, we will apply an innovative new single cell assay for multifactorial chromatin profiling to assay histone modifications. These proposed, in-depth, multiomic single cell analyses of distinct myeloid cell subsets in the CNS and blood, combined with cognitive assessments, will reveal the effects of HIV infection on immune cell epigenomes, and will uncover transcriptional and epigenetic states most strongly related to cognitive complications in PLWH. The results will advance efforts to biotype CNS complications in PLWH based on immune and viral pathogenesis.