Revealing the roles of HSV1 lytic and latent transcripts in AD pathogenesis and therapy

摘要 单纯疱疹病毒1型（HSV 1）可以以细胞类型特异性的方式建立裂解性和潜伏性感染， 已知的和新出现的神经病理学分支。挑衅性的数据现在链接重新激活 潜伏性HSV 1感染与阿尔茨海默病（AD）的关系，其病因学基础尚未完全确定。 在这里，我们建议采用强大的新基因组技术来识别和表征实际的细胞类型 潜伏和重新激活的HSV 1，扩展了最近的发现， 疱疹病毒的转录本在人类AD大脑的受影响区域。使用改良的单核测序 这种方法允许在同一个细胞核中评估DNA可及性和全局转录，我们 将询问人类对照和AD脑样品以及HSV 1感染的脑类器官和小鼠模型 急性和进行性HSV 1诱导的神经毒性。这些研究有望揭示细胞类型特异性 增强子景观和转录谱结果裂解，潜伏，或再激活HSV 1在大脑中 同时还提供了对其存在的细胞自主效应与非细胞自主效应的洞察。在 此外，我们还提出了一种新的先天免疫途径，通过这种途径HSV 1裂解性转录物触发了HSV 1的免疫反应。 前哨激酶PKR启动级联的核事件，包括次级激活的 转录调节因子PARP 1，并最终导致NF-κ B依赖性炎症基因表达程序， 可能提供了一种分子机制，通过这种机制，大脑中偶尔的HSV 1再激活可能有助于 炎症环境促进AD的发病。此外，这种分子途径可能 是大脑中多种微生物和可能的非微生物炎症触发因素的基础， 在AD中。我们还假设HSV 1潜伏相关转录本（LAT）与HSV 2和HSV 3之间存在不同的和相反的基因表达。 基因组功能以及宿主神经元和可能的非神经元脑细胞中的非基因组作用， 这种平衡保持了神经元细胞的完整性，但可能会促进慢性炎症， 潜伏感染的背景下，无论病毒再激活。基于诱人的初步证据，我们建议 为了研究有义（S）和反义（AS）LAT以部分二分的方式影响转录的想法， 通过与HSV 1和宿主基因组中的特定调控元件相关联， KRAB锌指蛋白（KZFP）辅助调节因子KAP 1。我们假设这些基因组事件影响了 AD过程通过KZFP介导的调节人类神经元功能而影响 内源性逆转录病毒（HERV）重复序列。我们进一步假设，LAT具有互补的非- 基因组的作用是减轻先天免疫反应并抑制细胞死亡程序，至少部分地， 通过抑制PKR。最后，我们建议利用HSV 1 LATs的这些保护特性作为一种独特的 AD的预防策略。

ABSTRACT Herpes Simplex Virus 1 (HSV1) can establish both lytic and latent infections in a cell type-specific fashion with known and emerging neuropathological ramifications, respectively. Provocative data now link reactivation of latent HSV1 infection to Alzheimer’s disease (AD), the etiological basis of which remains incompletely defined. Here we propose to employ powerful new genomic technologies to identify and characterize the actual cell types that harbor latent and reactivated HSV1, extending recent findings that have revealed an increased abundance of herpes virus transcripts in affected regions of human AD brains. Using a modified single-nucleus sequencing approach, which allows for DNA accessibility and global transcription to be assessed in the same nucleus, we will interrogate human control and AD brain samples as well a HSV1-infected brain organoids and mouse models of acute and progressive HSV1-induced neurotoxicity. These studies promise to reveal cell type-specific enhancer landscapes and transcriptional profiles consequent to lytic, latent, or reactivated HSV1 in the brain while also providing insights into the cell autonomous versus non-cell autonomous effects of its presence. In addition, we propose to elucidate a novel innate immune pathway by which HSV1 lytic transcripts trigger the sentinel kinase PKR to initiate a cascade of nuclear events that include the secondary activation of the transcriptional regulator PARP1 and culminate in a NF-kB-dependent inflammatory gene expression program, potentially providing a molecular mechanism by which occasional HSV1 reactivation in the brain could contribute to an inflammatory milieu that promotes the pathogenesis of AD. Furthermore, this molecular pathway may underlie diverse microbial and possibly non-microbial inflammatory triggers in the brain that have been implicated in AD. We also hypothesize that HSV1 latency-associated transcripts (LATs) have distinct and opposing genomic functions as well as non-genomic actions in host neurons and possibly non-neuronal brain cells, the balance of which preserves neuronal cell integrity but may facilitate low-grade, chronic inflammation in the context of latent infection irrespective of viral reactivation. Based on enticing preliminary evidence, we propose to investigate the idea that the sense (S) and antisense (AS) LATs impact transcription in a partially dichotomous fashion by associating with specific regulatory elements in the HSV1 and host genomes in collaboration with the KRAB zinc-finger protein (KZFP) co-regulator KAP1. We hypothesize that these genomic events influence the AD process by affecting neuronal function through modulation of KZFP-mediated regulation of human endogenous retrovirus (HERV) repeats. We further hypothesize that the LATs have a complementary non- genomic role that mitigates the innate immune response and suppresses cell death programs, at least in part, by inhibition of PKR. Finally, we propose to exploit these protective properties of the HSV1 LATs as a unique prophylactic strategy for AD.