In vivo single-cell profiling of lncRNAs during Ebola virus infection (SABio)

Long non-coding RNAs (lncRNAs) are pivotal mediators of systemic immune response to viral infection yet most studies concerning their expression and functions upon immune stimulation are limited to in vitro bulk cell populations. This strongly constrains our understanding of how lncRNA expression varies at single-cell resolution, and whether differences with protein coding genes exist in their cell-type specific immune regulatory roles. Here, we perform the first in-depth characterization of lncRNA expression variation at single-cell resolution during Ebola virus (EBOV) infection in vivo. Using bulk RNA-sequencing from 119 samples and 12 tissue types, we significantly expand the current macaque lncRNA annotation. We then profile lncRNA expression variation in immune circulating single-cells during EBOV infection and find that lncRNAs' expression in fewer cells is a major differentiating factor to their protein coding gene counterparts. Upon EBOV infection, lncRNAs present dynamic and mostly cell-type specific changes in their expression profiles especially in monocytes, the main cell type targeted by EBOV. Such changes are associated with gene regulatory modules related to important innate immune responses such as interferon response and purine metabolism. Within infected cells, several lncRNAs have correlated and anti-correlated expression with viral load, suggesting that expression of some of these lncRNAs might be directly hijacked by EBOV to attack host cells. This study provides novel insights on the roles that lncRNAs play in the host response to acute viral infection and paves the way for future lncRNA studies at single-cell resolution. Overall design: Bulk RNA sequencing of tissues from infected macaques infected with EBOV. Some of the macaques were subministered an anti-Ebola virus IgG immunoglobulins cocktail.

长链非编码RNA（long non-coding RNAs，简称lncRNAs）是介导病毒感染后全身免疫应答的关键分子，但目前绝大多数关于免疫刺激下该类RNA表达与功能的研究，均局限于体外批量细胞群体。这极大限制了我们对长链非编码RNA表达在单细胞分辨率下的变化规律，以及其与蛋白编码基因在细胞类型特异性免疫调控功能上是否存在差异的认知。本研究首次对活体状态下埃博拉病毒（Ebola virus，简称EBOV）感染过程中，长链非编码RNA在单细胞分辨率下的表达变化进行了深入解析。我们通过对119份样本、12种组织的批量RNA测序数据，大幅扩充了现有的猕猴长链非编码RNA注释库。随后，我们对埃博拉病毒感染过程中循环免疫单细胞的长链非编码RNA表达变化进行了分析，并发现长链非编码RNA仅在少量细胞中表达是其与蛋白编码基因的核心差异特征。埃博拉病毒感染后，长链非编码RNA的表达谱呈现动态变化，且大多具有细胞类型特异性，其中以埃博拉病毒的主要靶细胞——单核细胞的变化最为显著。此类表达变化与调控重要天然免疫应答的基因调控模块密切相关，例如干扰素应答与嘌呤代谢过程。在受感染的细胞中，部分长链非编码RNA的表达与病毒载量呈正相关或负相关，这提示埃博拉病毒可能直接劫持其中部分长链非编码RNA的表达以攻击宿主细胞。本研究为解析长链非编码RNA在宿主应对急性病毒感染的应答过程中所发挥的作用提供了全新视角，并为未来开展单细胞分辨率下的长链非编码RNA研究铺平了道路。研究设计：本研究对感染埃博拉病毒的猕猴的组织进行了批量RNA测序，其中部分猕猴被给予了抗埃博拉病毒IgG免疫球蛋白混合制剂。