Proteome-Wide Identification of RNA-Dependent Proteins in Lung Cancer Cells

SIMPLE SUMMARY: In this study, we identify RNA-dependent proteins in A549 lung cancer cells in a proteome-wide unbiased screen to elucidate the ribonucleoprotein complexes present in cancer cells. This dataset will help to understand and further dissect the role of RNA and RNA-dependent proteins in lung cancer. It is presented in the user-friendly R-DeeP 2.0 database which provides detailed information about RNA-dependent proteins and their properties in A549 along with data from HeLa cells to the scientific community. ABSTRACT: Following the concept of RNA dependence and exploiting its application in the R-DeeP screening approach, we have identified RNA-dependent proteins in A549 lung adenocarcinoma cells. RNA-dependent proteins are defined as proteins whose interactome depends on RNA and thus entails RNA-binding proteins (RBPs) as well as proteins in ribonucleoprotein complexes (RNPs) without direct RNA interaction. With this proteome-wide technique based on sucrose density gradient ultracentrifugation and fractionation followed by quantitative mass spectrometry and bioinformatic analysis, we have identified 1189 RNA-dependent proteins including 170 proteins which had never been linked to RNA before. R-DeeP provides quantitative information on the fraction of a protein being RNA-dependent as well as it allows the reconstruction of protein complexes based on co-segregation. The RNA dependence of three newly identified RNA-dependent proteins, DOCK5, ELMO2, also known as CED12A, and ABRAXAS1, also known as CCDC98, was validated using western blot analysis, and the direct RNA interaction was verified by iCLIP2 for the migration-related protein DOCK5 and the mitosis-related protein ABRAXAS1. The R-DeeP 2.0 database provides proteome-wide and cell line-specific information from A549 and HeLa S3 cells on proteins and their RNA dependence to contribute to understanding the functional role of RNA and RNA-binding proteins in cancer cells.