Global organelle profiling reveals subcellular localization and remodeling at proteome scale

Defining the subcellular distribution of all human proteins and its remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immuno-capture coupled to mass spectrometry. We apply this workflow to a cell-wide collection of membranous and membrane-less compartments. A graph-based analysis reveals the subcellular localization of over 7,600 proteins, defines spatial networks, and uncovers interconnections between cellular compartments. Our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following hCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides unique insights for the elucidation of cellular responses, uncovering an essential role for ferroptosis in OC43 infection. Our dataset can be explored at organelles.czbiohub.org. Overall design: HEK293T cells were infected with hCoV-OC43 for 16, 24, and 48 hours at a multiplicity of infection (MOI) of 1.0, and subjected to single-cell transcriptomics processing on the 10x Genomics platform, along with uninfected control cells. MultiSeq was used to barcode the experimental condition before pooling all cells. We used the NextGEM Single-Cell V(D)J Reagents Kit v1.1, following a 5' workflow.