Nusinow, D. P. et al. Cell 180, 387–402 (2020).
The Cancer Cell Line Encyclopedia (CCLE) is a catalog of nearly 1,000 human cancer cell lines that have been extensively profiled. Over the past decade data from gene expression, histone profiling, RNA-seq, DNA methylation, microRNA profiling, whole-genome sequencing, metabolite profiling and drug sensitivity screens have been added. In spite of extensive analyses, large-scale proteomics profiling data of human samples across such a diverse population are missing. Nusinow et al. have performed quantitative protein expression profiling of 375 cell lines distributed over 22 lineages in the CCLE, using mass spectrometry. This dataset allowed the researchers to analyze the proteome in microsatellite-instable colorectal cancers that display orders of magnitude more mutations than other tumors, revealing dysregulation of certain protein complexes associated with surveillance of mutation and translation. The resource will allow further exploration of other cancer types and non-cancer cellular processes.
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Singh, A. Quantitative proteomics of cancer cell lines. Nat Methods 17, 363 (2020). https://doi.org/10.1038/s41592-020-0814-z