Global Profiling of Remodeled Subcellular Structures Due to Drug Treatment and Disease

Abstract Cellular biochemistry arises from various interactions between macromolecules, including proteins, nucleic acids, and lipids. These make up membrane-bound organelles, membrane-less compartments, and molecular assemblies and scaffolds. Changes due to stimuli or disease can significantly impact cell fate and metabolism. We recently reported our protocol combining crosslinking and size exclusion chromatography with mass spectrometry (SEC-MS). In this study, we explore global changes to subcellular structure in Ewing sarcoma cell lines or in response to drug treatment. Crosslinking-dependent differential enrichment across four human cell lines is seen for proteins involved in splicing, mitochondria function, and cell division. We confirmed changes to nucleoli structure. We also examine structures affected by a transcription inhibitor, flavopiridol. Following flavopiridol treatment, we observed changes to the levels of transcription and mRNA processing machinery present in large subcellular structures. Unexpected effects were also found, including structural changes to a cytoplasmic organelle, the peroxisome. Along with a reduction in peroxisome function, dissociation of peroxisome pore proteins PEX13 and PEX14 was detected by STORM microscopy. We conclude that SEC-MS combined with crosslinking is a valuable method to detect and quantify drug or disease effects on subcellular structures and may shed light on new aspects to mechanisms underlying their biologic outcomes. Graphical Abstract Key Points Crosslinking plus SEC-MS shows global effects on subcellular structure in disease and treatment. Ewing sarcoma cell lines tested present distinct molecular composition in splicing, mitochondria, and nucleoli. A transcription inhibitor flavopiridol disrupts peroxisome function and protein import pores