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 (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 7 distinct smooth muscle cell 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 smooth muscle cell subtypes. Integrated multi-omics 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.