Discovery and characterization of a pancreatic β cell subpopulation expressing an unknown surface epitope through single cell proteomics

The pancreatic β cell surface proteome is essential for supporting cell communication, as it contributes to their secretory identity and maintains β cell responsiveness to any extra- and intracellular variations. Therefore, studies are actively looking to identify specific surface biomarkers that not only can differentiate dysfunctional cell populations, particularly in the context of diabetes, but also can be used to develop therapeutic targets. While β cell heterogeneity has been explored at the single-cell genomic and transcriptomic levels, in this study we aimed to demonstrate that even when a new plasma membrane epitope is identified, characterization of the proteome of cells expressing the same surface protein confirms that different subpopulations do exist. Using single-cell proteomic approach, we analyzed the proteome of MIN6 and αTc1 cells expressing Cd71, Cd99, and P538, which binds to a Fab-phage-538 identified in our previous study. Our findings suggest that the MIN6 (P538 ⁺ ) subpopulation may hold a more specialized functional identity compared to the other MIN6 (Cd71 ⁺ ), MIN6 (Cd99 ⁺ ), and control subpopulations. Moreover, we demonstrate that cell lines derived from the same tissue and expressing the same surface epitope can exhibit heterogeneity in their proteome. Indeed, while the specific expression of 17 protein groups confers to the MIN6 (P538 ⁺ ) subpopulation an insulin production and secretion-oriented identity, αTc1 (P538 ⁺ ), on the other hand, was characterized by only two proteins with no established involvement in glucagon production or secretion. Also, while the MIN6 (Cd99 ⁺ ) subpopulation may be predisposed to the development of insulin deficiency compared to MIN6 (Cd71 ⁺ ) and MIN6 (P538 ⁺ ), the proteomic profile of the αTc1 (Cd99 ⁺ ) subpopulation suggests that this subpopulation may hold an ability to adapt to stressful environmental conditions. Finally, when comparing MIN6 (Cd71 ⁺ ) to αTc1 (Cd71 ⁺ ), our findings suggest that the MIN6 subpopulation has probably a lesser role in Type 2 Diabetes Mellitus (T2DM) genesis in the context of iron homeostasis disruption than αTc1 (Cd71 ⁺ ).