Native size exclusion chromatography-based mass spectrometry (SEC-MS) reveals new components of the early Heat Shock Protein 90 inhibition response among limited global changes

Rahul S. Samant (Lead / Corresponding author), Silvia Batista, Mark Larance, Bugra Ozer, Christopher I. Milton, Isabell Bludau, Estelle Wu, Laura Biggins, Simon Andrews, Alexia Hervieu, Harvey E. Johnston, Bissan Al-Lazikhani, Angus I. Lamond, Paul A. Clarke, Paul Workman (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review


The molecular chaperone heat shock protein 90 (HSP90) works in concert with co-chaperones to stabilize its client proteins, which include multiple drivers of oncogenesis and malignant progression. Pharmacologic inhibitors of HSP90 have been observed to exert a wide range of effects on the proteome, including depletion of client proteins, induction of heat shock proteins, dissociation of co-chaperones from HSP90, disruption of client protein signaling networks, and recruitment of the protein ubiquitylation and degradation machinery-suggesting widespread remodeling of cellular protein complexes. However, proteomics studies to date have focused on inhibitor-induced changes in total protein levels, often overlooking protein complex alterations. Here, we use size-exclusion chromatography in combination with mass spectrometry (SEC-MS) to characterize the early changes in native protein complexes following treatment with the HSP90 inhibitor tanespimycin (17-AAG) for 8 hours in the HT29 colon adenocarcinoma cell line. After confirming the signature cellular response to HSP90 inhibition (e.g., induction of heat shock proteins, decreased total levels of client proteins), we were surprised to find only modest perturbations to the global distribution of protein elution profiles in inhibitor-treated HT29 cells at this relatively early time-point. Similarly, co-chaperones that co-eluted with HSP90 displayed no clear difference between control and treated conditions. However, two distinct analysis strategies identified multiple inhibitor-induced changes, including known and unknown components of the HSP90-dependent proteome. We validate two of these-the actin-binding protein Anillin, and the mitochondrial isocitrate dehydrogenase 3 (IDH3) complex-as novel HSP90 inhibitor-modulated proteins. We present this dataset as a resource for the HSP90, proteostasis, and cancer communities (, laying the groundwork for future mechanistic and therapeutic studies related to HSP90 pharmacology. Data are available via ProteomeXchange with identifier PXD033459.

Original languageEnglish
Article number100485
JournalMolecular & Cellular Proteomics
Early online date19 Dec 2022
Publication statusE-pub ahead of print - 19 Dec 2022


  • molecular chaperone
  • heat shock protein
  • protein complexes
  • proteomics
  • HSP90 inhibitor
  • tanespimycin


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