Linear regression for HSPB1 node.

Complex diseases such as Multiple Sclerosis (MS) cover a wide range of biological scales, from genes and proteins to cells and tissues, up to the full organism. In fact, any phenotype for an organism is dictated by the interplay among these scales. We conducted a multilayer network analysis and deep phenotyping with multi-omics data (genomics, phosphoproteomics and cytomics), brain and retinal imaging, and clinical data, obtained from a multicenter prospective cohort of 328 patients and 90 healthy controls. Multilayer networks were constructed using mutual information for topological analysis, and Boolean simulations were constructed using Pearson correlation to identified paths within and among all layers. The path more commonly found from the Boolean simulations connects protein MK03, with total T cells, the thickness of the retinal nerve fiber layer (RNFL), and the walking speed. This path contains nodes involved in protein phosphorylation, glial cell differentiation, and regulation of stress-activated MAPK cascade, among others. Specific paths identified were subsequently analyzed by flow cytometry at the single-cell level. Combinations of several proteins (GSK3AB, HSBP1 or RS6) and immune cells (Th17, Th1 non-classic, CD8, CD8 Treg, CD56 neg, and B memory) were part of the paths explaining the clinical phenotype. The advantage of the path identified from the Boolean simulations is that it connects information about these known biological pathways with the layers at higher scales (retina damage and disability). Overall, the identified paths provide a means to connect the molecular aspects of MS with the overall phenotype.

多发性硬化（Multiple Sclerosis, MS）等复杂疾病涵盖从基因、蛋白质到细胞、组织乃至完整生物体的多个生物学尺度层级。事实上，生物体的任何表型均由这些不同尺度间的相互作用所决定。本研究基于一项纳入328名患者与90名健康对照的多中心前瞻性队列，整合多组学数据（基因组学、磷酸化蛋白质组学与细胞组学）、脑与视网膜成像数据及临床数据，开展多层网络分析与深度表型分析。研究采用互信息构建多层网络以进行拓扑分析，并借助皮尔逊相关系数构建布尔模拟，以识别各网络层内部及层间的关联路径。布尔模拟中最常被检出的关联路径，连接了蛋白质MK03、总T细胞、视网膜神经纤维层（retinal nerve fiber layer, RNFL）厚度与步行速度。该路径包含参与蛋白质磷酸化、神经胶质细胞分化以及应激激活型丝裂原活化蛋白激酶（MAPK）级联调控等过程的节点。后续研究借助流式细胞术在单细胞水平对所识别的特异性路径展开验证分析。若干蛋白质（GSK3AB、HSBP1或RS6）与免疫细胞（Th17细胞、非经典Th1细胞、CD8+T细胞、CD8+调节性T细胞、CD56阴性细胞以及记忆B细胞）的组合，构成了解释临床表型的关联路径的组成部分。布尔模拟所识别的关联路径的优势在于，可将已知生物学通路的相关信息与更高层级的尺度（视网膜损伤与残疾状态）进行关联。总体而言，本研究所识别的关联路径为连接多发性硬化的分子层面特征与整体表型提供了可行途径。