Proteins differentially interact with each other across cellular states and conditions, but an efficient proteome-wide strategy to monitor them is lacking. We report the application of thermal proximity coaggregation (TPCA) for high-throughput intracellular monitoring of protein complex dynamics. Significant TPCA signatures observed among well-validated protein-protein interactions correlate positively with interaction stoichiometry and are statistically observable in more than 350 annotated human protein complexes. Using TPCA, we identified many complexes without detectable differential protein expression, including chromatin-associated complexes, modulated in S phase of the cell cycle. Comparison of six cell lines by TPCA revealed cell-specific interactions even in fundamental cellular processes. TPCA constitutes an approach for system-wide studies of protein complexes in nonengineered cells and tissues and might be used to identify protein complexes that are modulated in diseases.

Global profiling of protein expression through the cell cycle has revealed subsets of periodically expressed proteins. However, expression levels alone only give a partial view of the biochemical processes determining cellular events. Using a proteome-wide implementation of the cellular thermal shift assay (CETSA) to study specific cell-cycle phases, we uncover changes of interaction states for more than 750 proteins during the cell cycle. Notably, many protein complexes are modulated in specific cell-cycle phases, reflecting their roles in processes such as DNA replication, chromatin remodeling, transcription, translation, and disintegration of the nuclear envelope. Surprisingly, only small differences in the interaction states were seen between the G1 and the G2 phase, suggesting similar hardwiring of biochemical processes in these two phases. The present work reveals novel molecular details of the cell cycle and establishes proteome-wide CETSA as a new strategy to study modulation of protein-interaction states in intact cells.

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IntroductionFragment crystallizable receptors (FcRs) are receptors on immune cells that bind to the Fc region of immunoglobulins. Fc␥Rs that bind to the most common type of immunoglobulin (IgG), are expressed on the surface of many different immune cell types including monocytes, macrophages, dendritic cells, and neutrophils. [1][2][3] In humans, 3 different classes of activatory IgG receptors have been defined: Fc␥RI (CD64), Fc␥RIIa (CD32a), and Fc␥RIII (CD16), each of which has a variety of isoforms with differing affinities for IgG, tissue distribution, and level of expression. [1][2][3][4][5][6] The high affinity IgG receptor, Fc␥RI, is a 72-kD type-I membrane glycoprotein constitutively expressed on monocyte and macrophage lineage cells. 4 Fc␥RI is a member of the multichain immune recognition receptor family, comprising hetero-oligomeric complexes of a ligand-binding ␣-chain and a signaling ␥-chain usually found in association with other immune receptors. [1][2][3][4][5][6] The ␥-chain contains a signaling motif termed the "immunoreceptor tyrosinebased activation motif" (ITAM): it is through the ITAM-bearing chain that most FcRs trigger intracellular signal transduction cascades. The low-affinity receptor, Fc␥RIIa, is the most broadly distributed human Fc␥R and is expressed on many cell types, such as monocytes, neutrophils, and platelets. 1,7 This low-affinity receptor preferentially binds complexes of IgG and is the only Fc receptor that contains an ITAM of its own. Thus, it is the only Fc receptor that does not need to oligomerize with a ␥-chain in order to signal. 4,8,9 There is no identified murine equivalent of Fc␥RIIa. 1 On myeloid cells, aggregation of Fc␥Rs during the early stages of infection leads to several cellular responses, including the internalization of immune complexes by endocytosis or opsonized particles through phagocytosis, degranulation with the release of proteases, activation of respiratory burst, and secretion of cytokines. 5,[10][11][12] The presentation of antigens derived from internalized complexes forms an important component of our adaptive immune response, and dysregulation of this pathway is reported to be linked to increased susceptibility to bacterial sepsis. 13 The safe clearance of immune complexes toward the latter stages of infection is also dependent on FcR expressing mononuclear phagocytes. Dysfunction in the clearance of immune complexes is reported to be associated with immunopathology, autoimmunity, and allergic disease. 9,14 This represents one of the critical but poorly understood functions of Fc receptors, ie, the determination of the antigenic fate of immune complexes; specifically, whether to internalize and digest them in a way that is noninflammatory or to reinforce antigen presentation combined with immune activation and associated proinflammatory signaling.Studies on differential functions mediated by individual Fc receptors in immune activation/homeostasis are complicated by the coexistence of several FcRs on phagocytic cells-it is difficult to identi...