Targeted transcriptomic analysis of C57BL/6 and BALB/c mice during progressive chronic Toxoplasma gondii infection reveals changes in host and parasitic gene expression relating to neuropathology and resolution [Neuroinflammation]. Targeted transcriptomic analysis of C57BL/6 and BALB/c mice during progressive chronic Toxoplasma gondii infection reveals changes in host and parasitic gene expression relating to neuropathology and resolution [Neuroinflammation]

Toxoplasma gondii is a resilient parasite that infects a multitude of warm-blooded hosts and results in a lifelong chronic infection requiring continuous responses by the host. Chronic infection is characterized by a balanced immune response and neuropathology that are driven by changes in gene expression. Previous research pertaining to these processes has been conducted in various mouse models, and much knowledge of infection-induced gene expression changes has been acquired through the use of high throughput sequencing techniques in different mouse strains and post-mortem human studies. However, lack of infection time course data poses a prominent missing link in the understanding of chronic infection, and there is still much that is unknown regarding changes in genes specifically relating to neuropathology and resulting repair mechanisms as infection progresses throughout the different stages of chronicity. In this paper, we present a targeted approach to gene expression analysis during T. gondii infection through the use of NanoString nCounter gene expression assays. Wild type C57BL/6 and BALB/c background mice were infected, and transcriptional changes in the brain were evaluated at 14, 28, and 56 days post infection. Results demonstrate a dramatic shift in both previously demonstrated and novel gene expression relating to neuropathology and resolution in C57BL/6 mice. In addition, comparison between BALB/c and C57BL/6 mice demonstrate initial differences in gene expression that evolve over the course of infection and indicate decreased neuropathology and enhanced repair in BALB/c mice. In conclusion, these studies provide a targeted approach to gene expression analysis in the brain during infection and provide elaboration on previously identified transcriptional changes and also offer insights into further understanding the complexities of chronic T. gondii infection. Overall design: 24 samples were analyzed (12 from C57BL/6 mice and 12 from BALB/c mice), the 12 samples were comprised of 3 biological replicates for Naïve, 14day, 28day, and 56day post infection time points repecetively, Naïve time point was used as reference and control for analysis

刚地弓形虫（Toxoplasma gondii）是一种生命力顽强的寄生虫，可感染多种温血宿主，并引发终身慢性感染，需要宿主持续启动免疫应答。慢性感染以平衡的免疫应答与神经病理损伤为特征，上述特征由基因表达的改变所驱动。此前针对该过程的研究已在多种小鼠模型中开展，研究人员通过对不同小鼠品系实施高通量测序（high throughput sequencing）技术，并结合人体尸检研究，已积累了大量关于感染诱导基因表达变化的认知。然而，感染时间进程数据的缺失仍是理解慢性感染的关键短板，目前针对感染进入不同慢性阶段时，与神经病理损伤及后续修复机制直接相关的基因变化，仍有诸多未知之处。

本研究采用靶向策略，借助NanoString nCounter基因表达分析系统，对刚地弓形虫感染过程中的基因表达水平进行检测。研究选取野生型C57BL/6与BALB/c背景小鼠进行感染，并在感染后14、28、56天分别评估小鼠脑组织的转录组变化。结果显示，C57BL/6小鼠中，与神经病理损伤及损伤修复相关的已知及全新基因表达均发生了显著改变。此外，对比BALB/c与C57BL/6小鼠发现，二者的基因表达差异初始即存在，并随感染进程逐渐演化，且BALB/c小鼠表现出更轻微的神经病理损伤与更强的修复能力。

综上，本研究为感染过程中脑组织的基因表达分析提供了靶向研究方案，进一步阐明了此前已发现的转录组变化，并为深入理解刚地弓形虫慢性感染的复杂机制提供了新的见解。
整体实验设计：本研究共分析24份样本（12份来自C57BL/6小鼠，12份来自BALB/c小鼠），每组小鼠分别设置未感染组（Naïve）、感染后14天、28天及56天四个时间点，每个时间点设3个生物学重复（biological replicates）；以未感染组作为分析的参照对照。