From proteomics and genomics to therapeutics in systemic sclerosis interstitial lung disease

肺受累于系统性硬化症(SSC)是常见的，在SSC中比其他结缔组织病更常见 组织疾病，是其主要死亡原因，表现为间质性肺疾病(ILD)或肺 动脉高血压(PAH)。只有两种食品和药物管理局(FDA)批准的化合物(九替达尼 和tocilizumab)已被证明可以减缓SSC-ILD患者肺功能的下降，但不能阻止或逆转 SSc-ILD的进展。这突显了一个尚未得到满足的医学需求，即改善对SSC的分子理解- ILD的发病机制为药物开发寻找新的靶点。SSC-ILD被认为是由 免疫介导的微血管损伤，诱导和维持炎症、自身免疫反应和 成纤维细胞到肌成纤维细胞的激活和随后的胶原沉积最终导致肺纤维化。我们 最近提供了人类和小鼠已知的最大的肺蛋白质组，涵盖了8000多个 蛋白质，发现推动肺纤维化的新的可药物介质和细胞类型。我们已经确定了几个 SSC皮损和IPF肺组织之间的共同纤维化介质(例如，SMAD3/转化生长因子-β途径)。 然而，对SSc肺蛋白质组的准确定量和表征仍有待进行。 利用新的技术进步，我们建议定义和量化纤维化的复杂成分 SSC肺，并发现肺蛋白质组中将作为外周生物标志物和/或药物的成分 分别为监测和治疗SSc-ILD的候选人。这个应用程序的主要目标是 1)最详细地确定SSC-ILD肺和外周血的分子组成，2) 识别用于改进药物的组织纤维化的新的疾病特异性网络模块和机制 发展，以及3)发现可以作为诊断、预测或预测的蛋白质 SSc-ILD的生物标志物。我们假设SSC肺蛋白质组识别SSC特定的可用药线索， 由常驻成纤维细胞产生，导致持续性肺纤维化。我们将定义并量化 SSc-ILD患者肺和血液蛋白质组组成与疾病的相关性 SSc-ILD患者横断面和纵向队列的严重程度。我们将为SSC-ILD肺提供 通过执行基因表达和开放，在单细胞分辨率下的表观遗传景观和转录组 铬单多组体ATAC+基因组核内表达分析检测染色质可及性 肺细胞悬液的制备。最后，我们将使用一个新的药物筛选平台转化生长因子-β-。 诱导SSC来源的原代成纤维细胞中的Smad易位及其抑制剂的特征 III磷脂酰肌醇-3-激酶(PI3K)空泡蛋白分类34(Vps34)作为新的靶点 抑制肺纤维化。我们将与其他CORT核心和项目密切合作，以生成新的数据 关于SSC-ILD用于识别潜在的新的可用药靶点的共同和特定驱动因素 SSc-ILD纤维化通路的病理生物学研究。

Lung involvement in systemic sclerosis (SSc) is common, occurs more frequently in SSc than in other connective tissue diseases and is its leading cause of death, manifesting as interstitial lung disease (ILD) or pulmonary arterial hypertension (PAH). Only two Food and Drug Administration (FDA)-approved compounds (nintedanib and tocilizumab) have been shown to slow the decline of lung function in SSc-ILD, but do not stop or reverse the progression of SSc-ILD. This highlights an unmet medical need for improved molecular understanding of SSc- ILD pathogenesis for identification of novel targets for drug development. SSc-ILD is thought to be triggered by immune-mediated microvascular injuries that induce and perpetuate inflammation, autoimmune responses, and fibroblast-to-myofibroblast activation with subsequent collagen deposition ultimately leading to lung fibrosis. We have recently provided the largest known lung proteome in human and mouse, encompassing more than 8000 proteins, uncovering novel druggable mediators and cell types driving lung fibrosis. We have identified several shared mediators of fibrosis (e.g., the SMAD3/TGF-beta pathway) between SSc skin lesions and IPF lung tissue. An accurate quantification and characterization of the SSc lung proteome, however, remains to be performed. Using novel technological advances, we propose to define and quantify the intricate composition of the fibrotic SSc lung and uncover components within the lung proteome that will serve as peripheral biomarkers and/or drug candidates for the monitoring and treatment of SSc-ILD, respectively. The overarching goal of this application is 1) to define, in greatest detail, the molecular composition of the SSc-ILD lung and peripheral blood, 2) to identify novel disease-specific network modules and mechanisms of tissue fibrosis for improved drug development, and 3) to uncover proteins that can serve as diagnostic, prognostic, or predictive biomarkers for SSC-ILD. We hypothesize that the SSc lung proteome identifies SSc-specific druggable cues, produced by resident fibroblasts, that drive persistent lung fibrosis. We will define and quantify changes in the composition of the proteomes of the lung and blood of SSc-ILD patients that correlate with disease severity in cross-sectional and longitudinal cohorts of SSc-ILD patients. We will provide the SSc-ILD lung’s epigenetic landscape and transcriptome at single cell resolution by performing gene expression and open chromatin accessibility assays using Chromium single multiome ATAC + Genome Expression analysis in nuclear preparations of lung cell suspensions. Finally, we will use a novel drug screening platform of TGF-beta- induced Smad translocation in SSc-derived primary fibroblasts, and characterize inhibitors of the class III phosphatidylinositol-3-kinase (PI3K) vacuolar protein sorting 34 (Vps34) as novel targets for the inhibition of lung fibrosis. We will work closely with the other CORT cores and projects to generate novel data on common and specific drivers of SSc-ILD for the identification of new druggable targets underlying the pathobiology of fibrotic pathways in SSc-ILD.