Single-Cell Proteomics Reveals Novel Cell Phenotypes in Marfan Mouse Aneurysm

This report describes single-cell proteomic analyses of cells dissociated from a complex mammalian tissue using direct label-free mass spectrometry (single-cell proteomics by mass spectrometry, SCP-MS). The nanoDTSC approach was applied to profile individual cells from aorta of male and female wild-type and Fbn1^C1041G/+ Marfan mice. Leiden clustering identified all major aortic cell types including seven distinct smooth muscle cell (SMC) subtypes, with informative differences in cell proportions and differentially expressed proteins within cell types observed for both genotype and sex. Comparisons between single-cell RNA and single-cell proteomic profiles showed similarities in detection of major subtypes but not differentiation between SMC subtypes. Integrated multiomics analysis further identified genotype-dependent enrichment of unique SMC subtypes, relative to either protein or RNA datasets. Multiplexed-fluorescence based spatial proteomics validated several of these key genotype markers. Overall, these studies demonstrate the power of SCP-MS to detect novel aneurysm biology and serve as a guide for future development of SCP-MS methodology as it is applied to complex tissue cell mixtures and its integration with other omic modalities.