Research projects

The center develops single-cell proteomics technologies and uses them to test different conceptual frameworks and discriminate among different classes of models.



Developing technologies for analyzing proteins in single cells

Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made such analysis feasible for nucleic acids, but single-cell protein analysis remains limited. Mass-spectrometry is the most powerful method for protein analysis, but its application to single cells faces three major challenges: Efficiently delivering proteins/peptides to MS detectors, identifying their sequences, and scaling the analysis to many thousands of single cells. These challenges have motivated corresponding solutions, including SCoPE-design multiplexing and clean, automated, and miniaturized sample preparation. Synergistically applied, these solutions enable quantifying thousands of proteins across many single cells and establish a solid foundation for further advances. Building upon this foundation, the SCoPE concept will enable analyzing subcellular organelles and post-translational modifications while increases in multiplexing capabilities will increase the throughput and decrease cost.

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Mapping the Transcriptome and Proteome of Human Testis in 3D

This network will map the human testis in 3D using paired single-cell analysis by mass-spectrometry, clampFISH, and RNA-sequencing.

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Tracking proteome dynamics in single cells

One of the most significant recent developments in biomedical research and engineering is the explosion of technologies for quantifying thousands of genes in single cells. These technologies have transformed our ability to identify cell types and cell states in healthy and diseased human tissues. Our laboratory has contributed to these efforts by pioneering powerful methods for quantifying proteins in single cells at unprecedented scale. For the first time, we can examine single cells at systems level. Yet, these glimpses are static: we can only take one snapshot of a cell, showing us protein type and the amount of each protein, per cell. To overcome this limitation, we develop methods that will enable us to measure the abundance, the birth and and the death rates of proteins across time. By introducing isotopically-labeled amino acids at different time points over the life of a cell, we create a protein travelogue for each cell. Then, the travelogue of each cell is decoded by mass-spectrometry, thus revealing the protein dynamics underpinning the life and functions of each cell. This technology can move biomedical research from the era of still pictures to the era of dynamic movies, the era when we can finally see and understand the dynamics of protein interactions that animate each cell.

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