Single-cell spatial transcriptomics of an inducible destabilized-domain Cre mouse line to target disease associated microglia

This dataset contains the results from a single-cell spatial transcriptomics experiment performed using Bruker Nanostring CosMx technology on 10µm thick fresh-frozen coronal brain sections from the following groups: 5xFAD hemizygous, Cst7 DD-Cre, Ai14tdTomato double heterozygous (AD, n = 3), and Cst7 DD-Cre/Ai14tdTomato double heterozygous (WT, n = 1) mice treated with TMP, and Cst7 DD-Cre/Ai14tdTomato double heterozygous mice treated with cuprizone (CPZ) and TMP (CPZ, n = 2). The dataset is provided as an .RDS file, which includes raw and corrected counts, along with comprehensive metadata. Metadata includes experimental group, sample ID, cell type annotations, and X-Y coordinates of each cell.

The function of microglia during progression of Alzheimer's disease (AD) can be investigated using mouse models that enable genetic manipulation of microglial subpopulations in a temporal manner. We developed mouse lines that express either Cre recombinase (Cre) for constitutive targeting, or destabilized-domain Cre recombinase (DD-Cre) for inducible targeting from the Cst7 locus (Cst7 DD-Cre) to specifically manipulate disease associated microglia (DAM) and crossed with Ai14 tdTomato cre-reporter line mice. Cst7Cre was found to target all brain resident myeloid cells, due to transient developmental expression of Cst7, but no expression was found in the inducible Cst7 DD-Cre mice. Further crossing of this line with 5xFAD mice combined with dietary administration of trimethoprim to induce DD-Cre activity produces long-term labeling in DAM without evidence of leakiness, with tdTomato-expression restricted to cells surrounding plaques. Using this model, we found that DAMs are a subset of plaque-associated microglia (PAMs) and their transition to DAM increases with age and disease stage. Spatial transcriptomic analysis revealed that tdTomato+ cells show higher expression of disease and inflammatory genes compared to other microglial populations, including non-labeled PAMs. These models allow either complete cre-loxP targeting of all brain myeloid cells (Cst7Cre), or inducible targeting of DAMs, without leakiness (Cst7 DD-Cre).

本数据集收录了采用布鲁克纳米串（Bruker Nanostring）CosMx技术开展的单细胞空间转录组学实验所得结果，实验样本取自以下组别小鼠的厚度为10μm的新鲜冷冻冠状脑切片：5xFAD半合子小鼠、Cst7 DD-Cre与Ai14tdTomato双杂合阿尔茨海默病模型组（AD，n=3）小鼠，经甲氧苄啶（TMP）处理的Cst7 DD-Cre/Ai14tdTomato双杂合野生型（WT，n=1）小鼠，以及经铜嗪（CPZ）与甲氧苄啶（TMP）处理的Cst7 DD-Cre/Ai14tdTomato双杂合小鼠（CPZ组，n=2）。本数据集以.RDS文件格式提供，内含原始计数与校正后计数，以及完备的元数据。元数据涵盖实验组别、样本ID、细胞类型注释，以及每个细胞的X-Y坐标。

阿尔茨海默病（AD）进程中小胶质细胞的功能可通过可时序性遗传操控小胶质细胞亚群的小鼠模型开展研究。我们构建了两类小鼠品系：一类表达Cre重组酶（Cre recombinase，Cre）以实现组成型靶向，另一类表达不稳定结构域Cre重组酶（destabilized-domain Cre recombinase，DD-Cre）以从Cst7基因座实现诱导型靶向（Cst7 DD-Cre），从而特异性操控疾病相关小胶质细胞（disease associated microglia，DAM），并将该品系与Ai14 tdTomato Cre报告基因小鼠进行杂交。由于Cst7存在暂时性发育表达，Cst7Cre可靶向所有脑内驻留髓系细胞，但诱导型Cst7 DD-Cre小鼠未检测到该表达。进一步将该品系与5xFAD小鼠杂交，并通过日粮给予甲氧苄啶以诱导DD-Cre活性，可在疾病相关小胶质细胞中实现长期标记且无渗漏现象，tdTomato表达仅局限于斑块周围细胞。利用该模型，我们发现疾病相关小胶质细胞是斑块相关小胶质细胞（plaque-associated microglia，PAM）的一个亚群，且其向疾病相关小胶质细胞的转化随年龄与疾病进程推进而增强。空间转录组学分析显示，相较于其他小胶质细胞群（包括未标记的斑块相关小胶质细胞），tdTomato阳性细胞的疾病相关基因与炎症基因表达水平更高。上述模型既可实现所有脑内髓系细胞的完整Cre-loxP靶向（Cst7Cre），也可实现无渗漏的疾病相关小胶质细胞诱导型靶向（Cst7 DD-Cre）。