Pacific Northwest National Laboratories, Richland, Washington, USA.
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA.
Mol Cell Proteomics. 2023 Aug;22(8):100592. doi: 10.1016/j.mcpro.2023.100592. Epub 2023 Jun 15.
The need for a clinically accessible method with the ability to match protein activity within heterogeneous tissues is currently unmet by existing technologies. Our proteomics sample preparation platform, named microPOTS (Microdroplet Processing in One pot for Trace Samples), can be used to measure relative protein abundance in micron-scale samples alongside the spatial location of each measurement, thereby tying biologically interesting proteins and pathways to distinct regions. However, given the smaller pixel/voxel number and amount of tissue measured, standard mass spectrometric analysis pipelines have proven inadequate. Here we describe how existing computational approaches can be adapted to focus on the specific biological questions asked in spatial proteomics experiments. We apply this approach to present an unbiased characterization of the human islet microenvironment comprising the entire complex array of cell types involved while maintaining spatial information and the degree of the islet's sphere of influence. We identify specific functional activity unique to the pancreatic islet cells and demonstrate how far their signature can be detected in the adjacent tissue. Our results show that we can distinguish pancreatic islet cells from the neighboring exocrine tissue environment, recapitulate known biological functions of islet cells, and identify a spatial gradient in the expression of RNA processing proteins within the islet microenvironment.
目前，现有的技术无法满足对能够匹配异质组织中蛋白质活性的临床可及方法的需求。我们的蛋白质组学样品制备平台名为 microPOTS（微量样品一锅式微滴处理），可用于测量微米级样品中的相对蛋白质丰度，以及每个测量点的空间位置，从而将具有生物学意义的蛋白质和途径与不同的区域联系起来。然而，由于像素/体素数量较少，以及测量的组织量较少，标准的质谱分析流程已被证明不适用。在这里，我们描述了如何适应现有的计算方法，以专注于空间蛋白质组学实验中提出的具体生物学问题。我们应用这种方法来全面描述人类胰岛微环境，包括所涉及的所有复杂细胞类型，同时保持空间信息和胰岛影响范围的程度。我们确定了胰岛细胞特有的特定功能活性，并展示了它们的特征在相邻组织中可以检测到多远。我们的结果表明，我们可以区分胰岛细胞和邻近的外分泌组织环境，重现胰岛细胞的已知生物学功能，并确定胰岛微环境中 RNA 处理蛋白表达的空间梯度。
