弓形虫,原生动物寄生虫,经历了一个复杂且鲜为人知的发育过程,这对于在其中间宿主中建立慢性感染至关重要。这里,我们应用单细胞RNA测序(scRNA-seq)对>5,400弓形虫在速殖子和缓生阶段使用三个广泛研究的菌株构建细胞周期和无性发育的综合图谱,揭示与每个发育阶段相关的隐藏状态和转录因子。对SAG1相关序列(SRS)抗原性库的分析揭示了一种高度异质的,测量噪声无法解释的零星表达模式,细胞周期,或无性发育。此外,我们将AP2IX-1鉴定为一种转录因子,该转录因子可控制从泛在的SAG1向之前未在速殖子中观察到的罕见表面抗原的转换.此外,弓形虫和疟原虫scRNA-seq结果的比较分析揭示了基因集的协同表达,尽管细胞分裂存在根本差异。最后,我们构建了一个交互式数据浏览器,用于可视化我们的地图集资源。
弓形虫是一种单细胞寄生虫,可以感染大多数温血动物,但只能在家猫和野猫身上有性繁殖。与疟疾病原体有远缘,它目前感染了世界四分之一以上的人口。虽然它在大多数情况下是良性的,这种情况对于胎儿和免疫系统受损的人来说仍然是危险的。在人体中,弓形虫细胞渗透到肌肉和神经细胞中;在那里,它经历了复杂的转变,帮助寄生虫停止快速分裂,而是在休眠状态下隐藏在免疫系统中。目前还不清楚这种转变是如何展开的,特别是在任何给定时间打开和关闭哪些基因。为了理解这种转变,科学家经常测量哪些基因在一组寄生虫中是活跃的。然而,这种方法只给出了一个“平均”的画面,不允许对每个寄生虫进行分析,错过了个体之间可能存在的多样性。一个特别感兴趣的领域,例如,是一组称为SAG1相关序列的基因。它们编码了寄生虫的“分子外套”,位于弓形虫细胞表面的一系列蛋白质。每个弓形虫寄生虫的基因组中存在超过120个SAG1相关基因,创造了一整个蛋白质衣柜,这些蛋白质有可能隐藏免疫系统中的寄生虫。这里,薛等人。利用了一种叫做单细胞RNA测序的技术,这使得他们能够筛选出来自不同菌株的5400个弓形虫寄生虫中哪些基因是活跃的。分析包括寄生虫的快速分裂形式(存在于感染的初始阶段),以及在没有任何症状的携带弓形虫的人中发现的缓慢分裂的形式。由此产生的“地图集”包含有关寄生虫发育每个阶段使用的基因的先前隐藏的信息:其中包括弓形虫和疟疾病原体之间的意外相似性,以及两种弓形虫菌株之间的细微差别。该地图集还揭示了单个寄生虫如何打开与SAG1相关的序列。它揭示了弓形虫细胞在同一发育阶段运输的蛋白质外壳组成的惊人多样性,一种可能有助于挫败免疫系统的策略。特别是一种寄生虫,在快速和缓慢分裂的人类形式中发现了一种不寻常的外壳和其他蛋白质组合。这种寄生虫生长在人类细胞中,然而,更仔细的分析显示,它激活了几个基因(包括编码蛋白质外壳的基因),这些基因通常只在家猫和野猫的有性繁殖寄生虫中“开启”。这个新的数据图集有助于了解弓形虫如何传播和在人类体内生长,这可以帮助治疗的发展。最终,更好地了解这些寄生虫也可以带来有关导致疟疾的病原体的新信息。
Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
Toxoplasma gondii is a single-celled parasite that can infect most warm-blooded animals, but only reproduces sexually in domestic and wild cats. Distantly related to the malaria agent, it currently infects over a quarter of the world’s human population. Although it is benign in most cases, the condition can still be dangerous for foetuses and people whose immune system is compromised. In the human body, Toxoplasma cells infiltrate muscle and nerve cells; there it undergoes a complex transformation that helps the parasites to stop dividing quickly and instead hide from the immune system in a dormant state. It is still unclear how this transition unfolds, and in particular which genes are switched on and off at any given time. To understand this transformation, scientists often measure which genes are active across a group of parasites. However, this approach gives only an ‘average’ picture and does not allow each parasite to be profiled, missing out on the diversity that may exist between individuals. One area of particular interest, for example, is a set of genes called SAG1-related sequences. They code for the ‘molecular overcoat’ of the parasite, an array of proteins that sit on the surface of Toxoplasma cells. More than 120 SAG1-related genes exist in the genome of each Toxoplasma parasite, creating a whole wardrobe of proteins that potentially hide the parasites from the immune system. Here, Xue et al. harnessed a technique called single-cell RNA sequencing, which allowed them to screen which genes were active in 5,400 individual Toxoplasma parasites from different strains. The analysis included both the rapidly dividing form of the parasite (present in the initial stage of an infection), and the slowly dividing form found in people who carry Toxoplasma without any symptoms. The resulting ‘atlas’ contains previously hidden information about the genes used at each stage of parasite development: this included unexpected similarities between Toxoplasma and the malaria agent, as well as subtle differences between two of the Toxoplasma strains. The atlas also sheds light on how individual parasites turns on SAG1-related sequences. It reveals a surprising diversity in the composition of the protein coats sported by Toxoplasma cells at the same developmental stage, a strategy that may help to thwart the immune system. One individual parasite in particular had an unusual combination of coat and other proteins found in both the fast and slow-dividing human forms. This parasite had been grown in human cells, yet a closer analysis revealed that it had activated several genes (including ones encoding the protein coat) that are normally only ‘on’ in the parasites going through sexual reproduction in domestic and wild cats. This new data atlas helps to understand how Toxoplasma are transmitted to and grow within humans, which could aid the development of treatments. Ultimately, a better knowledge of these parasites could also bring new information about the agent that causes malaria.