To identify pathogenetic markers and potential drivers of different lesion types in the white matter (WM) of patients with progressive multiple sclerosis (PMS), we sequenced RNA from 73 different WM areas. Compared to 25 WM controls, 6713 out of 18,609 genes were significantly differentially expressed in MS tissues (FDR < 0.05). A computational systems medicine analysis was performed to describe the MS lesion endophenotypes. The cellular source of specific molecules was examined by RNAscope, immunohistochemistry, and immunofluorescence. To examine common lesion specific mechanisms, we performed de novo network enrichment based on shared differentially expressed genes (DEGs), and found TGFβ-R2 as a central hub. RNAscope revealed astrocytes as the cellular source of TGFβ-R2 in remyelinating lesions. Since lesion-specific unique DEGs were more common than shared signatures, we examined lesion-specific pathways and de novo networks enriched with unique DEGs. Such network analysis indicated classic inflammatory responses in active lesions; catabolic and heat shock protein responses in inactive lesions; neuronal/axonal specific processes in chronic active lesions. In remyelinating lesions, de novo analyses identified axonal transport responses and adaptive immune markers, which was also supported by the most heterogeneous immunoglobulin gene expression. The signature of the normal-appearing white matter (NAWM) was more similar to control WM than to lesions: only 465 DEGs differentiated NAWM from controls, and 16 were unique. The upregulated marker CD26/DPP4 was expressed by microglia in the NAWM but by mononuclear cells in active lesions, which may indicate a special subset of microglia before the lesion develops, but also emphasizes that omics related to MS lesions should be interpreted in the context of different lesions types. While chronic active lesions were the most distinct from control WM based on the highest number of unique DEGs (n = 2213), remyelinating lesions had the highest gene expression levels, and the most different molecular map from chronic active lesions. This may suggest that these two lesion types represent two ends of the spectrum of lesion evolution in PMS. The profound changes in chronic active lesions, the predominance of synaptic/neural/axonal signatures coupled with minor inflammation may indicate end-stage irreversible molecular events responsible for this less treatable phase.

中文翻译：

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进行性多发性硬化症患者脑白质中不同病变类型的分子标记。

为了在进行性多发性硬化症（PMS）患者的白质（WM）中鉴定致病标记物和不同病变类型的潜在驱动因素，我们对来自73个不同WM区域的RNA进行了测序。与25个WM对照相比，MS组织中18609个基因中有6713个基因显着差异表达（FDR <0.05）。进行了计算机系统医学分析，以描述MS病变的内表型。通过RNAscope，免疫组织化学和免疫荧光检查了特定分子的细胞来源。为了检查常见的病变特异性机制，我们基于共享的差异表达基因（DEG）进行了从头网络富集，并发现TGFβ-R2是中央枢纽。RNAscope揭示星形胶质细胞是髓鞘再生病灶中TGFβ-R2的细胞来源。由于特定于病变的独特DEG比共享签名更为常见，因此我们检查了特定于病变的途径和富含独特DEG的从头网络。这种网络分析表明活动性病变中有经典的炎症反应。非活动性病变中的分解代谢和热休克蛋白反应；慢性活动性病变中的神经元/轴突特定过程。在使髓鞘再生的病变中，从头分析确定了轴突转运反应和适应性免疫标记，这也得到了最不均匀的免疫球蛋白基因表达的支持。正常出现的白质（NAWM）的特征与对照WM相比与病灶更相似：只有465个DEG将NAWM与对照区分开，并且有16个是独特的。上调的标记CD26 / DPP4在NAWM中由小胶质细胞表达，但在活动性病变中由单核细胞表达，这可能表明在病变发展之前是小胶质细胞的特殊子集，但也强调与MS病变有关的组学应该在不同病变类型的背景下进行解释。基于最大数量的独特DEG（n = 2213），慢性活动性病变与对照WM的区别最大（n = 2213），髓鞘再生性病变的基因表达水平最高，分子图谱与慢性活动性病变最大。这可能表明这两种病变类型代表了PMS中病变演化谱的两端。慢性活动性病变的深刻变化，突触/神经/轴突信号的普遍存在以及轻微的炎症可能表明了这一不可治疗阶段的终末不可逆分子事件。但同时强调，与MS病变相关的组学应该在不同病变类型的背景下进行解释。基于最大数量的独特DEG（n = 2213），慢性活动性病变与对照WM最为不同，而髓鞘再生性病变的基因表达水平最高，分子图谱也不同于慢性活动性病变。这可能表明这两种病变类型代表了PMS中病变演化谱的两端。慢性活动性病变的深刻变化，突触/神经/轴突信号的普遍存在以及轻微的炎症可能表明了这一不可治疗阶段的终末不可逆分子事件。但同时强调，与MS病变相关的组学应该在不同病变类型的背景下进行解释。基于最大数量的独特DEG（n = 2213），慢性活动性病变与对照WM最为不同，而髓鞘再生性病变的基因表达水平最高，分子图谱也不同于慢性活动性病变。这可能表明这两种病变类型代表了PMS中病变演化谱的两端。慢性活动性病变的深刻变化，突触/神经/轴突信号的普遍存在以及轻微的炎症可能表明了这一不可治疗阶段的终末不可逆分子事件。基于最大数量的独特DEG（n = 2213），慢性活动性病变与对照WM最为不同，而髓鞘再生性病变的基因表达水平最高，分子图谱也不同于慢性活动性病变。这可能表明这两种病变类型代表了PMS中病变演化谱的两端。慢性活动性病变的深刻变化，突触/神经/轴突信号的普遍存在以及轻微的炎症可能表明了这一不可治疗阶段的终末不可逆分子事件。基于最大数量的独特DEG（n = 2213），慢性活动性病变与对照WM最为不同，而髓鞘再生性病变的基因表达水平最高，分子图谱也不同于慢性活动性病变。这可能表明这两种病变类型代表了PMS中病变演化谱的两端。慢性活动性病变的深刻变化，突触/神经/轴突信号的普遍存在以及轻微的炎症可能表明了这一不可治疗阶段的终末不可逆分子事件。这可能表明这两种病变类型代表了PMS中病变演化谱的两端。慢性活动性病变的深刻变化，突触/神经/轴突信号的普遍存在以及轻微的炎症可能表明了这一不可治疗阶段的终末不可逆分子事件。这可能表明这两种病变类型代表了PMS中病变演化谱的两端。慢性活动性病变的深刻变化，突触/神经/轴突信号的普遍存在以及轻微的炎症可能表明了这一不可治疗阶段的终末不可逆分子事件。