Proteins associated with the doubling time of the NCI-60 cancer cell lines

The varied nature of human cancers is recapitulated, at least to some extent, in the diverse NCI-60 panel of human cancer cell lines. Here, I used a basic, continuous variable of proliferating cells, their doubling time, to stratify the proteome across the NCI-60 cell lines. Among >7000 proteins quantified in the NCI-60 panel previously, the levels of 84 proteins increase in cells that proliferate slowly. This set overlapped with the hallmark molecular signature "epithelial-mesenchymal transition (EMT)" (p value = 1.1E-07). Conversely, the levels of 105 proteins increased in cells that proliferate faster and overlapped with the molecular signatures for "MYC targets V1" (p value = 3.8E-38) and "E2F targets" (p value = 2.4E-34). These data for the first time identify proteins whose levels are dynamically associated with doubling time, but not necessarily with cancer type origins, and argue for the incorporation of doubling time measurements in cell line-based profiling studies.