Tony Ly

Lab members

Van Kelly

Cell state transitions during cell growth and division

Our lab is interested in cell state transitions during cell growth and division in human cells.

The major phases of the mitotic cell division cycle are G1, S, G2, and M. Cells can also enter a reversible quiescent state, called G0 (1). M-phase, or mitosis, can be further resolved into discrete subphases based on changes in cellular architecture that can be visualized by light microscopy, or by immunostaining for specific molecular signaling events, such as phosphorylation of histone H3 (e.g. at residues serine 10 and serine 28) and degradation of cyclin proteins (e.g. cyclin A and cyclin B). Some, but not all, signaling events that specifically mark mitotic subphases have also been shown to be regulatory drivers of cell state transitions. While the cell division cycle is largely linear (2), recent studies suggest that gap phases of the cell cycle are characterized by bifurcations in cell fate trajectories, leading to heterogeneous, temporally aligned cell states (3).

Comprehensive, molecular definitions of cell state and identity can be obtained using quantitative mass spectrometry-based proteomics. Recent developments in mass spectrometry (MS) enable the high throughput identification and quantitation of thousands of proteins in a single analysis. Static and dynamic parameters of proteins can be measured, including post translational modifications and protein half-life.

We developed a method combining fluorescence-activated cell sorting (FACS) and MS to measure protein changes during mitosis proteome-wide in an asynchronous culture of human leukemia cells (4 and 5).

Using this method, we aim to dissect cellular heterogeneity in gap phases of the mitotic cell division cycle using quantitative proteomics and phosphoproteomics as comprehensive readouts of cellular state.

Selected publications:

Ly, T., Whigham, A., Clarke, R., Brenes-Murillo, A. J., Estes, B., Wadsworth, P., & Lamond, A. I. (2017). Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS. BiorXiv,

Ly, T., Endo, A., & Lamond, A. I. (2015). Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells. eLife, 4.

Ly, T., Ahmad, Y., Shlien, A., Soroka, D., Mills, A., Emanuele, M. J., et al. (2014). A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. eLife, 3, e01630.