Our study aimed to reveal the underlying pathologic mechanisms of thyroid-associated ophthalmopathy (TAO) by integrative transcriptomics and proteomic analysis of extraocular muscles (EOM). The study involved 11 TAO patients (clinical activity score ≤ 2) and 11 control donors. Total RNA was extracted from EOM samples of 5 TAO patients and 5 control individuals for gene microarray analysis to reveal differentially expressed genes. Concurrently, EOM samples from 3 TAO patients and 3 control individuals were lysed for quantitative proteomic analysis. Differentially expressed genes and proteins were identified, followed by functional and pathway enrichment analysis and protein-protein interaction network construction. Concordance between proteins and transcripts was examined, and functional annotations were conducted. Expressions of versican (VCAN) and lipocalin 1 (LCN1) in EOM samples from another 3 TAO patients and 3 control individuals were measured by western blotting. In total, 952 genes and 137 proteins were identified as differentially expressed, as well as 96 differentially expressed proteins without significantly changed mRNA abundance. Proteins mainly related to the composition (such as MYH1, MYH2, and MYH13) and contraction force (MYH3, MYH8, ACTN3, and TNNT1) of the muscle fibers were significantly up-regulated in EOM samples of TAO, as well as those (such as VCAN, MPZ, and PTPRC) associated with cell adhesion. In addition, differentially expressed proteins related to the components and metabolism of extracellular matrix (ECM) (such as COL1A1, COL1A2, COL2A1, VCAN, OGN, and DCN) were identified. Similarly, expressions of genes involved in cell adhesion and ECM metabolism were significantly different between EOM samples of TAO patients and controls. Western blotting verified that VCAN involved in ECM proteoglycans and diseases associated with glycosaminoglycan metabolism was markedly higher in EOM samples of TAO, whereas LCN1 was obviously decreased. In conclusion, this study demonstrated the significantly altered cellular components of EOM, muscle contraction, cell adhesion and ECM metabolism, which might be involved in the pathologic mechanisms and/or consequences of TAO.

中文翻译：

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甲状腺相关性眼病患者眼外肌的整合转录组学和蛋白质组学分析。

我们的研究旨在通过整合转录组学和眼外肌蛋白质组学分析（EOM）揭示甲状腺相关性眼病（TAO）的潜在病理机制。该研究涉及11名TAO患者（临床活动评分≤2）和11名对照供体。从5位TAO患者和5位对照个体的EOM样品中提取总RNA，进行基因微阵列分析，以揭示差异表达的基因。同时，裂解来自3名TAO患者和3名对照个体的EOM样品以进行定量蛋白质组学分析。鉴定差异表达的基因和蛋白质，然后进行功能和途径富集分析以及蛋白质-蛋白质相互作用网络的构建。检查蛋白质和转录本之间的一致性，并进行功能注释。通过蛋白质印迹法检测另外3名TAO患者和3名对照个体的EOM样品中versican（VCAN）和lipocalin 1（LCN1）的表达。总共鉴定出952个基因和137个蛋白质是差异表达的，还有96个差异表达的蛋白质没有显着改变mRNA的丰度。在TAO的EOM样品以及这些样品中，肌肉组织的主要成分（例如MYH1，MYH2和MYH13）和肌肉纤维的收缩力（MYH3，MYH8，ACTN3和TNNT1）主要相关的蛋白质均显着上调。 （例如VCAN，MPZ和PTPRC）与细胞粘附相关。此外，还鉴定了与细胞外基质（ECM）的成分和代谢有关的差异表达蛋白（例如COL1A1，COL1A2，COL2A1，VCAN，OGN和DCN）。同样，在TAO患者和对照组的EOM样品之间，参与细胞粘附和ECM代谢的基因的表达差异显着。Western印迹证实，在TAO的EOM样品中，参与ECM蛋白聚糖和糖胺聚糖代谢相关疾病的VCAN明显升高，而LCN1则明显降低。总之，这项研究表明EOM，肌肉收缩，细胞粘附和ECM代谢的细胞成分发生了明显变化，这可能与TAO的病理机制和/或后果有关。而LCN1明显减少。总之，这项研究表明EOM，肌肉收缩，细胞粘附和ECM代谢的细胞成分发生了明显变化，这可能与TAO的病理机制和/或后果有关。而LCN1明显减少。总之，这项研究表明EOM，肌肉收缩，细胞粘附和ECM代谢的细胞成分发生了明显变化，这可能与TAO的病理机制和/或后果有关。