Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence

ABSTRACT: 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. Graphical Abstract Highlights • microPOTS enables deep proteome imaging of pancreatic islets and their microenvironment.• We identified and quantified over 6000 proteins from ∼50,000 μm2 tissue area samples.• Differential expression and network analyses identified pathways uniquely active in islets.• Rank-based statistics enable the characterization of gradients across individual tissue images. In Brief We applied our Microdroplet Processing in One pot for Trace Samples (microPOTS) TMT platform to study the pancreatic islet microenvironment in the human pancreas. We were able to quantify over 6000 proteins from seven different regions within the same patient. Here we describe enhancements to existing computational approaches to extract functional hypotheses from this first-of-its-kind dataset. In addition to recapitulating known functions of the islet, we can identify specific immune and RNA processing activities with spatial heterogeneity in expression.

SUBMITTER: Gosline S 

PROVIDER: S-EPMC10460696 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature