A combined approach for single-cell mRNA and intracellular protein expression analysis

Abstract

Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation.

Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99

“…In contrast, the cell surface abundance of the CD99 protein displayed a more even distribution and a significant reduction in single cells with LOY. This result supports the view that proteins constitute more stable markers for cellular properties of single cells, compared with the generally more fluctuating mRNA levels 46 – 48 .…”

Ascorbic Acid/Retinol and/or Inflammatory Stimuli’s Effect on Proliferation/Differentiation Properties and Transcriptomics of Gingival Stem/Progenitor Cells

“…Although differences in NANOG, OCT4A, and SOX2 mRNA expressions were detectable between the groups at different time points, only NANOG was detectable on protein level, in line with earlier reports on dissimilar NANOG, OCT4A, and SOX2 protein and mRNA expression dynamics within mesenchymal stem/progenitor cells [54][55][56]. This AA/retinol-induced increase in the NANOG, especially in the presence of controlled inflammatory stimuli at 3 days, could be ascribed primarily to the capability of AA and retinol to activate the ten-eleven translocation (TET) DNA demethylases, initiating intracellular epigenetic reprogramming with pluripotency amplification [20,57].…”

Molecular mechanisms governing circulating immune cell heterogeneity across different species revealed by single cell sequencing

“…The connectome analysis might be influenced by potential species differences in ligand-receptor interaction relationships or homolog conversion. Last, the aim of this study was to focus on the single-cell altas of PBMCs from multiple species, even though mRNA and protein expression in immunce cells show discrepant by different methods 67-69 . In addition, the datasets of PBMCs for 12 species were obtained from different platforms, and differences caused by sample processing, scRNA-seq technical bias, and batch effects could impact the cells capture and cell type classifications, resulting in biological differences.…”