High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways

High resolution spatial transcriptomics is a transformative technology that enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation of disease processes and therapeutically actionable pathways remain largely unexplored. Here we applied Slide-seqV2 to mouse and human kidneys, in healthy and in distinct disease paradigms. First, we established the feasibility of Slide-seqV2 in human kidney by analyzing tissue from 9 distinct donors, which revealed a cell neighborhood centered around a population of LYVE1+ macrophages. Second, in a mouse model of diabetic kidney disease, we detected changes in the cellular organization of the spatially-restricted kidney filter and blood flow regulating apparatus. Third, in a mouse model of a toxic proteinopathy, we identified previously unknown, disease-specific cell neighborhoods centered around macrophages. In a spatially-restricted subpopulation of epithelial cells, we also found perturbations in 77 genes associated with the unfolded protein response (UPR), including Tmed9. Treatment with a TMED9-targeting compound showed efficient removal of toxic mutant proteins and reversal of the UPR. Our studies illustrate and experimentally validate the utility of Slide-seqV2 for the discovery of disease-specific cell neighborhoods and actionable targets. For the BTBR experiments, the BTBR-wt/wt are controls and BTBR-ob/ob are diabetic samples. Seven arrays per mouse and 4 mice of each gentoptype were processed. For the UMOD experiments, UMOD-WT are controls and UMOD-KI are ADTKD samples. Five arrays per mouse and 3 WT mice and 5 KI mice were processed. There are 3 separate files types: BAMs, raw data which is unmapped spatial data, and processed data which contains QCed and mapped kidney cell types.高分辨率空间转录组学（high resolution spatial transcriptomics）是一项变革性技术，可直接在完整组织切片上绘制RNA表达图谱；然而，其在阐明疾病进程与可靶向治疗通路方面的应用价值仍未得到充分挖掘。本研究将Slide-seqV2应用于健康及不同疾病模型下的小鼠与人类肾脏组织：首先，通过分析9名不同供者的肾脏组织，验证了Slide-seqV2在人类肾脏样本中的应用可行性，研究发现了一类以LYVE1+巨噬细胞为核心的细胞邻域；其次，在糖尿病肾病小鼠模型中，检测到空间受限的肾脏滤过结构与血流调节装置的细胞组织发生改变；第三，在毒性蛋白病小鼠模型中，发现了此前未被报道的、以巨噬细胞为核心的疾病特异性细胞邻域。此外，在一类空间受限的上皮细胞亚群中，我们还发现包括Tmed9在内的77个与未折叠蛋白反应（unfolded protein response, UPR）相关的基因表达发生紊乱。使用靶向TMED9的化合物进行处理，可有效清除毒性突变蛋白并逆转未折叠蛋白反应。本研究阐明并通过实验验证了Slide-seqV2在发现疾病特异性细胞邻域与可靶向治疗靶点方面的应用价值。 针对BTBR相关实验：BTBR-wt/wt为对照组，BTBR-ob/ob为糖尿病模型样本；每只小鼠对应7张芯片，每种基因型使用4只小鼠完成实验。针对UMOD相关实验：UMOD-WT为对照组，UMOD-KI为ADTKD样本；每只小鼠对应5张芯片，共使用3只WT小鼠与5只KI小鼠完成实验。本数据集包含3类独立文件：BAM文件、未比对的空间转录组原始数据，以及经过质控并完成肾脏细胞类型注释的比对后处理数据。