Identification of novel response and predictive biomarkers to Hsp90 inhibitors through proteomic profiling of patient-derived prostate tumor explants

Elizabeth V. Nguyen, Margaret M. Centenera, Max Moldovan, Rajdeep Das, Swati Irani, Andrew D. Vincent, Howard Chan, Lisa G. Horvath, David J. Lynn, Roger J. Daly, Lisa M. Butler

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Abstract

Inhibition of the heat shock protein 90 (Hsp90) chaperone is a promising therapeutic strategy to target expression of the androgen receptor (AR) and other oncogenic drivers in prostate cancer cells. However, identification of clinicallyrelevant responses and predictive biomarkers is essential to maximize efficacy and treatment personalization. Here, we combined mass spectrometry (MS)-based proteomic analyses with a unique patient-derived explant (PDE) model that retains the complex microenvironment of primary prostate tumors. Independent discovery and validation cohorts of PDEs (n = 16 and 30, respectively) were cultured in the absence or presence of Hsp90 inhibitors AUY922 or 17-AAG. PDEs were analyzed by LC-MS/MS with a hyper-reaction monitoring data independent acquisition (HRM-DIA) workflow, and differentially expressed proteins identified using repeated measure analysis of variance (ANOVA; raw p value <0.01). Using gene set enrichment, we found striking conservation of the most significantly AUY922-altered gene pathways between the discovery and validation cohorts, indicating that our experimental and analysis workflows were robust. Eight proteins were selectively altered across both cohorts by the most potent inhibitor, AUY922, including TIMP1, SERPINA3 and CYP51A (adjusted p < 0.01). The AUY922- mediated decrease in secretory TIMP1 was validated by ELISA of the PDE culture medium. We next exploited the heterogeneous response of PDEs to 17-AAG in order to detect predictive biomarkers of response and identified PCBP3 as a marker with increased expression in PDEs that had no response or increased in proliferation. Also, 17-AAG treatment led to increased expression of DNAJA1 in PDEs that exhibited a cytostatic response, revealing potential drug resistance mechanisms. This selective regulation of DNAJA1 was validated by Western blot analysis. Our study establishes "proof-of-principle" that proteomic profiling of drug-treated PDEs represents an effective and clinically-relevant strategy for identification of biomarkers that associate with certain tumorspecific responses.

Original languageEnglish
Pages (from-to)1470-1486
Number of pages17
JournalMolecular and Cellular Proteomics
Volume17
Issue number8
DOIs
Publication statusPublished - 1 Aug 2018

Keywords

  • prostate cancer biomarkers
  • patient cohorts
  • cancer therapeutics
  • tumor microenvironment
  • biomarker: diagnostic
  • biomarker: prognostic
  • ex vivo
  • Hsp90 inhibitors
  • patient-derived explants

Cite this

Nguyen, Elizabeth V. ; Centenera, Margaret M. ; Moldovan, Max ; Das, Rajdeep ; Irani, Swati ; Vincent, Andrew D. ; Chan, Howard ; Horvath, Lisa G. ; Lynn, David J. ; Daly, Roger J. ; Butler, Lisa M. / Identification of novel response and predictive biomarkers to Hsp90 inhibitors through proteomic profiling of patient-derived prostate tumor explants. In: Molecular and Cellular Proteomics. 2018 ; Vol. 17, No. 8. pp. 1470-1486.
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Identification of novel response and predictive biomarkers to Hsp90 inhibitors through proteomic profiling of patient-derived prostate tumor explants. / Nguyen, Elizabeth V.; Centenera, Margaret M.; Moldovan, Max; Das, Rajdeep; Irani, Swati; Vincent, Andrew D.; Chan, Howard; Horvath, Lisa G.; Lynn, David J.; Daly, Roger J.; Butler, Lisa M.

In: Molecular and Cellular Proteomics, Vol. 17, No. 8, 01.08.2018, p. 1470-1486.

Research output: Contribution to journalArticleResearchpeer-review

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T1 - Identification of novel response and predictive biomarkers to Hsp90 inhibitors through proteomic profiling of patient-derived prostate tumor explants

AU - Nguyen, Elizabeth V.

AU - Centenera, Margaret M.

AU - Moldovan, Max

AU - Das, Rajdeep

AU - Irani, Swati

AU - Vincent, Andrew D.

AU - Chan, Howard

AU - Horvath, Lisa G.

AU - Lynn, David J.

AU - Daly, Roger J.

AU - Butler, Lisa M.

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AB - Inhibition of the heat shock protein 90 (Hsp90) chaperone is a promising therapeutic strategy to target expression of the androgen receptor (AR) and other oncogenic drivers in prostate cancer cells. However, identification of clinicallyrelevant responses and predictive biomarkers is essential to maximize efficacy and treatment personalization. Here, we combined mass spectrometry (MS)-based proteomic analyses with a unique patient-derived explant (PDE) model that retains the complex microenvironment of primary prostate tumors. Independent discovery and validation cohorts of PDEs (n = 16 and 30, respectively) were cultured in the absence or presence of Hsp90 inhibitors AUY922 or 17-AAG. PDEs were analyzed by LC-MS/MS with a hyper-reaction monitoring data independent acquisition (HRM-DIA) workflow, and differentially expressed proteins identified using repeated measure analysis of variance (ANOVA; raw p value <0.01). Using gene set enrichment, we found striking conservation of the most significantly AUY922-altered gene pathways between the discovery and validation cohorts, indicating that our experimental and analysis workflows were robust. Eight proteins were selectively altered across both cohorts by the most potent inhibitor, AUY922, including TIMP1, SERPINA3 and CYP51A (adjusted p < 0.01). The AUY922- mediated decrease in secretory TIMP1 was validated by ELISA of the PDE culture medium. We next exploited the heterogeneous response of PDEs to 17-AAG in order to detect predictive biomarkers of response and identified PCBP3 as a marker with increased expression in PDEs that had no response or increased in proliferation. Also, 17-AAG treatment led to increased expression of DNAJA1 in PDEs that exhibited a cytostatic response, revealing potential drug resistance mechanisms. This selective regulation of DNAJA1 was validated by Western blot analysis. Our study establishes "proof-of-principle" that proteomic profiling of drug-treated PDEs represents an effective and clinically-relevant strategy for identification of biomarkers that associate with certain tumorspecific responses.

KW - prostate cancer biomarkers

KW - patient cohorts

KW - cancer therapeutics

KW - tumor microenvironment

KW - biomarker: diagnostic

KW - biomarker: prognostic

KW - ex vivo

KW - Hsp90 inhibitors

KW - patient-derived explants

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