Spatial transcriptome analysis of muscle sections from Icos-/- NOD mice with established myositis

Icos-/- NOD mice are a model of spontaneous myositis. By using Nanostring GeoMx technology (Mouse WTA), we aimed to investigate the differences in gene expression between myofibers of Icos+/+ NOD (WT) mice and myofibers from Icos-/- NOD mice either in direct contact or not with large infiltrate clusters. Using Nanostring technology, the transcriptomes of myofibers vs. immune cells were analysed separately by using desmin and CD45 markers. The present study includes the following AOIs: 4 AOIs from Icos+/+ NOD muscle (n=4 mice, 1 AOI/mouse, desmin+CD45-) , 6 AOIs from Icos-/- NOD muscle not directly adjacent to immune cell infiltrates (PROX, n=6 mice, 1 AOI/mouse, desmin+CD45-), 8 AOIs from Icos-/- NOD muscle directly adjacent to immune cell infiltrates (ADJ, n=6 mice, 1-2 AOI/mouse, desmin+CD45-), 8 AOIs from Icos-/- NOD muscle corresponding to immune cell infiltrates (INF, n=6 mice, 1-2 AOI/mouse, desmin-CD45+).Icos基因缺陷型（Icos-/-）非肥胖糖尿病（NOD）小鼠是自发性肌炎的研究模型。本研究采用Nanostring GeoMx技术（小鼠全转录组分析，Mouse WTA），旨在对比Icos+/+ NOD野生型（WT）小鼠肌纤维，与Icos-/- NOD小鼠中与免疫浸润大簇直接接触或未直接接触的肌纤维之间的基因表达差异。本研究通过结蛋白（desmin）与CD45白细胞共同抗原两种标记物，分别对肌纤维与免疫细胞的转录组进行独立分析。本次研究纳入以下感兴趣区域（AOIs，Areas of Interest）：4个AOIs取自Icos+/+ NOD小鼠肌肉组织（n=4只小鼠，每只小鼠1个AOI，结蛋白阳性、CD45阴性）；6个AOIs取自Icos-/- NOD小鼠未与免疫浸润灶直接毗邻的肌肉组织（PROX组，n=6只小鼠，每只小鼠1个AOI，结蛋白阳性、CD45阴性）；8个AOIs取自Icos-/- NOD小鼠与免疫浸润灶直接毗邻的肌肉组织（ADJ组，n=6只小鼠，每只小鼠1~2个AOI，结蛋白阳性、CD45阴性）；8个AOIs取自Icos-/- NOD小鼠对应免疫浸润灶的肌肉组织（INF组，n=6只小鼠，每只小鼠1~2个AOI，结蛋白阴性、CD45阳性）。