Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90

Abstract

Most cancers are characterized by multiple molecular alterations, but identification of the key proteins involved in these signaling pathways is currently beyond reach. We show that the inhibitor PU-H71 preferentially targets tumor-enriched Hsp90 complexes and affinity captures Hsp90-dependent oncogenic client proteins. We have used PU-H71 affinity capture to design a proteomic approach that, when combined with bioinformatic pathway analysis, identifies dysregulated signaling networks and key oncoproteins in chronic myeloid leukemia. The identified interactome overlaps with the well-characterized altered proteome in this cancer, indicating that this method can provide global insights into the biology of individual tumors, including primary patient specimens. In addition, we show that this approach can be used to identify previously uncharacterized oncoproteins and mechanisms, potentially leading to new targeted therapies. We further show that the abundance of the PU-H71-enriched Hsp90 species, which is not dictated by Hsp90 expression alone, is predictive of the cell's sensitivity to Hsp90 inhibition.

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Figure 1: PU-H71 interacts with a restricted fraction of Hsp90 that is more abundant in cancer cells.
Figure 2: PU-H71 is selective for and isolates Hsp90 in complex with oncoproteins and cochaperones.
Figure 3: PU-H71 identifies the aberrant signalosome in CML cells.
Figure 4: PU-H71-identified proteins and networks are those important for the malignant phenotype.
Figure 5: Hsp90 facilitates an enhanced STAT5 activity in CML.

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Acknowledgements

This work was supported in part by the Geoffrey Beene Cancer Research Center of the Memorial Sloan-Kettering Cancer Center (G.C.), Leukemia and Lymphoma Society (G.C., M.L.G., S.D.N., X.Z. and R.L.), Breast Cancer Research Fund (G.C.), the SPORE Pilot Award and Research & Therapeutics Program in Prostate Cancer (G.C.), the Hirshberg Foundation for Pancreatic Cancer (G.C.), the Byrne Fund (G.C.), 1U01 AG032969-01A1 (G.C.), 1R01 CA155226-01 (G.C. and A.M.) and US National Cancer Institute (NCI) Cancer Center Support Grant P30 CA08748 (H.E.B.). K.B. and L.N. were supported by funds from the Intramural Program of the NCI. S.M.L. and P.M.S.-J. are supported by the Ludwig Center for Cancer Immunotherapy at MSKCC and by NCI Grant P50-CA86483. M.L.G. is funded by the US National Institutes of Health (NIH) through the NIH Director's New Innovator Award Program, 1 DP2 OD007399-01 and the V foundation. F.P. is funded by the American Italian Cancer Foundation. We thank D. Toft (Mayo Clinic) and M. Cox (University of Texas) for the gifts of H9010 Hsp90-specific antibodies, L.A. Fabrizio, A.M. Morrishow, H. Deng and J. Fernandez for help with MS analysis, A. Perl, C.T. Jordan, M. Becker and J. Nicoll for providing the primary CML samples or suggestions on their use, and B. Clarkson, J. Bromberg and P. Gregor for suggestions with the manuscript.

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K.M., J.H.A., H.Z., L.C., A.R., K.B., P.S.-J., F.P., K.H., L.P.V., X.Z., H.E.-B., N.P. and T.K. performed experiments and D.Z., T.T., A.R., R.L., S.M.L., M.L.G. and S.S.G. provided reagents. All authors participated in the design and analysis of various experiments and G.C., A.M., S.D.N., M.L.G. and L.N. wrote the paper.

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Correspondence to Stephen D Nimer or Ari Melnick or Len Neckers or Gabriela Chiosis.

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Competing interests

Memorial Sloan-Kettering Cancer Center holds the intellectual rights to PU-H71. Samus Therapeutics, of which G.C. has partial ownership, has licensed PU-H71.

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Moulick, K., Ahn, J., Zong, H. et al. Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90. Nat Chem Biol 7, 818–826 (2011). https://doi.org/10.1038/nchembio.670

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