Data_Sheet_1_Quantitative Proteomics Reveals the Dynamic Pathophysiology Across Different Stages in a Rat Model of Severe Traumatic Brain Injury.zip

BackgroundSevere traumatic brain injury (TBI) has become a global health problem and causes a vast worldwide societal burden. However, distinct mechanisms between acute and subacute stages have not been systemically revealed. The present study aimed to identify differentially expressed proteins in severe TBI from the acute to subacute phase.MethodsSixty Sprague Dawley (SD) rats were randomly divided into sham surgery and model groups. The severe TBI models were induced by the controlled cortical impact (CCI) method. We evaluated the neurological deficits through the modified neurological severity score (NSS). Meanwhile, H&E staining and immunofluorescence were performed to assess the injured brain tissues. The protein expressions of the hippocampus on the wounded side of CCI groups and the same side of Sham groups were analyzed by the tandem mass tag-based (TMT) quantitative proteomics on the third and fourteenth days. Then, using the gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and protein–protein interaction (PPI), the shared and stage-specific differentially expressed proteins (DEPs) were screened, analyzed, and visualized. Eventually, target proteins were further verified by Western blotting (WB).ResultsIn the severe TBI, the neurological deficits always exist from the acute stage to the subacute stage, and brain parenchyma was dramatically impaired in either period. Of the significant DEPs identified, 312 were unique to the acute phase, 76 were specific to the subacute phase, and 63 were shared in both. Of the 375 DEPs between Sham-a and CCI-a, 240 and 135 proteins were up-regulated and down-regulated, respectively. Of 139 DEPs, 84 proteins were upregulated, and 55 were downregulated in the Sham-s and CCI-s. Bioinformatics analysis revealed that the differential pathophysiology across both stages. One of the most critical shared pathways is the complement and coagulation cascades. Notably, three pathways associated with gastric acid secretion, insulin secretion, and thyroid hormone synthesis were only enriched in the acute phase. Amyotrophic lateral sclerosis (ALS) was significantly enriched in the subacute stage. WB experiments confirmed the reliability of the TMT quantitative proteomics results.ConclusionOur findings highlight the same and different pathological processes in the acute and subacute phases of severe TBI at the proteomic level. The results of potential protein biomarkers might facilitate the design of novel strategies to treat TBI.

背景：严重的脑外伤（TBI）已成为全球性的健康问题，并造成了巨大的全球社会负担。然而，急性期与亚急性期之间存在的不同机制尚未得到系统性揭示。本研究旨在从急性期到亚急性期识别严重TBI中差异表达的蛋白质。方法：将60只Sprague Dawley（SD）大鼠随机分为假手术组和模型组。通过可控皮质冲击（CCI）方法诱导严重TBI模型。我们通过改良神经严重程度评分（NSS）评估神经功能缺陷。同时，通过H&E染色和免疫荧光检测损伤的脑组织。采用串联质量标签（TMT）定量蛋白质组学在CCI组和假手术组损伤侧海马区以及相同侧的海马区，于第三天和第十四天分析蛋白质表达。然后，利用基因本体（GO）、京都基因与基因组百科全书（KEGG）和蛋白质-蛋白质相互作用（PPI）分析共有的和阶段特异性差异表达蛋白质（DEPs）。最终，通过蛋白质印迹（WB）进一步验证目标蛋白质。结果：在严重TBI中，从急性期到亚急性期，神经功能缺陷始终存在，且脑实质在这两个时期均受到严重损害。在鉴定的显著DEPs中，312个为急性期特有，76个为亚急性期特有，63个两者共有。在假手术-a和CCI-a之间的375个DEPs中，240个蛋白质上调，135个蛋白质下调。在139个DEPs中，84个蛋白质上调，55个蛋白质下调。生物信息学分析揭示了两个阶段间不同的病理生理学差异。其中，最重要的共有通路之一是补体和凝血级联反应。值得注意的是，与胃酸分泌、胰岛素分泌和甲状腺激素合成相关的三条通路仅在急性期富集。肌萎缩侧索硬化症（ALS）在亚急性期显著富集。WB实验证实了TMT定量蛋白质组学结果的可靠性。结论：我们的研究结果突出了严重TBI急性期和亚急性期在蛋白质组水平上的相同和不同病理过程。潜在蛋白质生物标志物的结果可能有助于设计新的治疗TBI的策略。