Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.
Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.
Int J Mol Sci. 2022 Apr 19;23(9):4515. doi: 10.3390/ijms23094515.
Circulating extracellular vesicles (cEV) are released by many kinds of cells and play an important role in cellular communication, signaling, inflammation modulation, coagulation, and tumor growth. cEV are of growing interest, not only as biomarkers, but also as potential treatment targets. However, very little is known about the effect of transporting biological samples from the clinical ward to the diagnostic laboratory, notably on the protein composition. Pneumatic tube systems (PTS) and human carriers (C) are both routinely used for transport, subjecting the samples to different ranges of mechanical forces. We therefore investigated qualitatively and quantitatively the effect of transport by C and PTS on the human cEV proteome and particle size distribution. We found that samples transported by PTS were subjected to intense, irregular, and multidirectional shocks, while those that were transported by C mostly underwent oscillations at a ground frequency of approximately 4 Hz. PTS resulted in the broadening of nanoparticle size distribution in platelet-free (PFP) but not in platelet-poor plasma (PPP). Cell-type specific cEV-associated protein abundances remained largely unaffected by the transport type. Since residual material of lymphocytes, monocytes, and platelets seemed to dominate cEV proteomes in PPP, it was concluded that PFP should be preferred for any further analyses. Differential expression showed that the impact of the transport method on cEV-associated protein composition was heterogeneous and likely donor-specific. Correlation analysis was nonetheless able to detect that vibration dose, shocks, and imparted energy were associated with different terms depending on the transport, namely in C with cytoskeleton-regulated cell organization activity, and in PTS with a release of extracellular vesicles, mainly from organelle origin, and specifically from mitochondrial structures. Feature selection algorithm identified proteins which, when considered together with the correlated protein-protein interaction network, could be viewed as surrogates of network clusters.
循环细胞外囊泡 (cEV) 由多种细胞释放，在细胞通讯、信号转导、炎症调节、凝血和肿瘤生长中发挥重要作用。cEV 不仅作为生物标志物受到越来越多的关注，而且还作为潜在的治疗靶点。然而，人们对从临床病房到诊断实验室运输生物样本对蛋白质组成的影响知之甚少。气动输送系统 (PTS) 和人员运输 (C) 都是常规的运输方式，这两种方式都会使样本受到不同范围的机械力作用。因此，我们定性和定量地研究了 C 和 PTS 对人 cEV 蛋白质组和颗粒大小分布的运输影响。我们发现，通过 PTS 运输的样本受到强烈、不规则和多方向的冲击，而通过 C 运输的样本主要经历大约 4 Hz 的地面频率的振荡。PTS 导致血小板游离 (PFP) 中的纳米颗粒大小分布变宽，但对血小板贫乏血浆 (PPP) 没有影响。细胞类型特异性 cEV 相关蛋白丰度受运输类型的影响基本不变。由于淋巴细胞、单核细胞和血小板的残留物质似乎在 PPP 中主导 cEV 蛋白质组，因此得出结论，PFP 应优先用于任何进一步的分析。差异表达表明，运输方法对 cEV 相关蛋白质组成的影响是异质的，并且可能是供体特异性的。然而，相关性分析能够检测到，振动剂量、冲击和传递的能量与不同的术语相关，具体取决于运输方式，即在 C 中与细胞骨架调节的细胞组织活性相关，而在 PTS 中与细胞外囊泡的释放相关，主要来自细胞器起源，特别是来自线粒体结构。特征选择算法确定了一些蛋白质，当与相关的蛋白质-蛋白质相互作用网络一起考虑时，可以被视为网络簇的替代物。
