Journal: Molecular cell
Article Title: Increasing cell size remodels the proteome and promotes senescence.
doi: 10.1016/j.molcel.2022.07.017
Figure Lengend Snippet: Figure 7. Cell volume-to-ploidy ratio drives size-dependent proteome changes (A) hTERT RPE-1 cells expressing fluorescent cell- cycle reporters (Cdt1-mKO2, Geminin-mAG) were treated with an Aurora kinase inhibitor barasertib (75 nM, 48 h) to partially inhibit cytokinesis. Cells were then sorted based on ploidy and G1 cell-cycle phase. The attainment of differently sized G1 cells was confirmed using a Coulter counter. The histo- gram shows a representative example of size distri- butions for sorted cells, and the numbers next to it represent mean cell size ± standard error for n = 3 biological replicates. (B) Ploidy-sorted and size-sorted G1 cells were iso- lated by FACS and their proteomes measured using TMT. Ploidy-sorted protein slope values were calcu- lated by plotting the relative protein concentration against the mean cell size in the 2N, 4N, and 8N bins to obtain a slope value (Table S9). (C) Distributions of ploidy-sorted and size-sorted protein slope values. Despite large increases in cell size from 2N to 8N, concentration changes were minimal. (D) Slightly negative correlation between ploidy- sorted and size-sorted protein slope values are consistent with a small increase in DNA-to-cell vol- ume ratio in polyploid G1 cells. x-axis bins are shown in dark blue. Error bars represent the 95% confi- dence interval, and r denotes the Pearson’s correla- tion coefficient. (E) DNA-to-cell-volume-dependent concentration changes for a representative set of proteins. For each protein panel, dotted lines represent unique peptide measurements.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific Cat#23225 Sep-Pak 50mg C18 Cartridges Waters Cat##054955 High pH Revered-phased Peptide Fractionation Kit Thermo Scientific Cat#84868 Senescence b-Galactosidase Staining Kit Cell Signaling Technology Cat#9860 Direct-zol RNA Microprep Kit Zymo Research Cat#R2063 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit Thermo Fisher Scientific Cat#C10424 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Scientific Cat#C34554 Deposited data All Proteomics raw files and spectral searches This paper PRIDE: PXD033332 All RNAseq raw files This paper GEO: GSE208348 Experimental models: Cell lines hTERT RPE1 Stearns Lab (Stanford) RRID: CVCL_4388 Primary human fetal lung fibroblasts Cell Applications Cat#506-05f Software and algorithms FlowJo BD Biosciences, https://www.flowjo.com/solutions/flowjo RRID: SCR_008520 FIJI https://imagej.net/software/fiji/ RRID: SCR_002285 MaxQuant Mann Lab N/A Python - Jupyter Notebooks Anaconda N/A
Techniques: Expressing, Protein Concentration, Concentration Assay