Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics

Wang, Hui; Barbieri, Christopher E.; He, Jintang; Gao, Yuqian; Shi, Tujin; Wu, Chaochao; Schepmoes, Athena A.; Fillmore, Thomas L.; Chae, Sung-Suk; Huang, Dennis; Mosquera, Juan Miguel; Qian, Wei-Jun; Smith, Richard D.; Srivastava, Sudhir; Kagan, Jacob; Camp, David G.; Rodland, Karin D.; Rubin, Mark A.; Liu, Tao

doi:10.1186/s12967-017-1276-7

Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics

Journal Article · Tue Aug 15 00:00:00 EDT 2017 · Journal of Translational Medicine

DOI:https://doi.org/10.1186/s12967-017-1276-7· OSTI ID:1406773

Wang, Hui ^[1]; Barbieri, Christopher E. ^[2]; He, Jintang ^[1]; Gao, Yuqian ^[1]; Shi, Tujin ^[1]; Wu, Chaochao ^[1]; Schepmoes, Athena A. ^[1]; Fillmore, Thomas L. ^[1]; Chae, Sung-Suk ^[2]; Huang, Dennis ^[2]; Mosquera, Juan Miguel ^[2]; Qian, Wei-Jun ^[1]; ^[1]; Srivastava, Sudhir ^[3]; Kagan, Jacob ^[3]; Camp, David G. ^[1]; ^[1]; Rubin, Mark A. ^[2]; ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Weill Cornell Medical College, New York, NY (United States). Inst. of Precision Medicine
National Cancer Institute, Bethesda, MD (United States). Division of Cancer Prevention, Cancer Biomarkers Research Group

Speckle-type POZ protein (SPOP) is an E3 ubiquitin ligase adaptor protein that functions as a potential tumor suppressor, and SPOP mutations have been identified in ~10% of human prostate cancers. However, it remains unclear if mutant SPOP proteins can be utilized as biomarkers for early detection, diagnosis, prognosis or targeted therapy of prostate cancer. Moreover, the SPOP mutation sites are distributed in a relatively short region where multiple lysine residues, posing significant challenges for bottom-up proteomics analysis of the SPOP mutations. To address this issue, PRISM (high-pressure, high-resolution separations coupled with intelligent selection and multiplexing)-SRM (selected reaction monitoring) mass spectrometry assays have been developed for quantifying wild-type SPOP protein and 11 prostate cancer-derived SPOP mutations. Despite inherent limitations due to amino acid sequence constraints, all the PRISM-SRM assays developed using Arg-C digestion showed a linear dynamic range of at least two orders of magnitude, with limits of quantification range from 0.1 to 1 fmol/μg of total protein in the cell lysate. Applying these SRM assays to analyze HEK293T cells with and without expression of the three most frequent SPOP mutations in prostate cancer (Y87N, F102C or F133V) led to confident detection of all three SPOP mutations in corresponding positive cell lines but not in the negative cell lines. Expression of the F133V mutation and wild-type SPOP was at much lower levels compared to that of F102C and Y87N mutations; however, at present it is unknown if this also affects the activity of the SPOP protein. In summary, PRISM-SRM enables multiplexed, isoform-specific detection of mutant SPOP proteins in cell lysates, which holds great potential in biomarker development for prostate cancer.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1406773

Alternate ID(s):: OSTI ID: 1757986

Report Number(s):: PNNL-SA--125993; 49639; 453040220

Journal Information:: Journal of Translational Medicine, Journal Name: Journal of Translational Medicine Journal Issue: 1 Vol. 15; ISSN 1479-5876

Publisher:: BioMed Central Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

References (38)

Current trends in quantitative proteomics Elliott, Monica H.; Smith, Derek S.; Parker, Carol E. Journal of Mass Spectrometry https://doi.org/10.1002/jms.1692	journal	January 2009
An improved quantitative mass spectrometry analysis of tumor specific mutant proteins at high sensitivity Ruppen-Cañás, Isabel; López-Casas, Pedro P.; García, Fernando PROTEOMICS, Vol. 12, Issue 9 https://doi.org/10.1002/pmic.201100611	journal	May 2012
Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present Bantscheff, Marcus; Lemeer, Simone; Savitski, Mikhail M. Analytical and Bioanalytical Chemistry, Vol. 404, Issue 4 https://doi.org/10.1007/s00216-012-6203-4	journal	July 2012
Spheroid culture of LuCaP 147 as an authentic preclinical model of prostate cancer subtype with SPOP mutation and hypermutator phenotype Saar, Matthias; Zhao, Hongjuan; Nolley, Rosalie Cancer Letters, Vol. 351, Issue 2 https://doi.org/10.1016/j.canlet.2014.06.014	journal	September 2014
The emerging role of speckle-type POZ protein (SPOP) in cancer development Mani, Ram-Shankar Drug Discovery Today, Vol. 19, Issue 9 https://doi.org/10.1016/j.drudis.2014.07.009	journal	September 2014
Clinico-pathological significance of the molecular alterations of the SPOP gene in prostate cancer García-Flores, María; Casanova-Salas, Irene; Rubio-Briones, José European Journal of Cancer, Vol. 50, Issue 17 https://doi.org/10.1016/j.ejca.2014.08.009	journal	November 2014
Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment Shi, Tujin; Gao, Yuqian; Gaffrey, Matthew J. Analytical Chemistry, Vol. 87, Issue 2 https://doi.org/10.1021/ac503797x	journal	December 2014
Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) Anderson, N. Leigh; Anderson, Norman G.; Haines, Lee R. Journal of Proteome Research, Vol. 3, Issue 2 https://doi.org/10.1021/pr034086h	journal	April 2004
Targeted Quantification of Low ng/mL Level Proteins in Human Serum without Immunoaffinity Depletion Shi, Tujin; Sun, Xuefei; Gao, Yuqian Journal of Proteome Research, Vol. 12, Issue 7 https://doi.org/10.1021/pr400178v	journal	June 2013
A Highly Sensitive Targeted Mass Spectrometric Assay for Quantification of AGR2 Protein in Human Urine and Serum Shi, Tujin; Gao, Yuqian; Quek, Sue Ing Journal of Proteome Research, Vol. 13, Issue 2 https://doi.org/10.1021/pr400912c	journal	December 2013
Mutant proteins as cancer-specific biomarkers Wang, Q.; Chaerkady, R.; Wu, J. Proceedings of the National Academy of Sciences, Vol. 108, Issue 6 https://doi.org/10.1073/pnas.1019203108	journal	January 2011
Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum Shi, T.; Fillmore, T. L.; Sun, X. Proceedings of the National Academy of Sciences, Vol. 109, Issue 38 https://doi.org/10.1073/pnas.1204366109	journal	September 2012
Correction for Geng et al., Prostate cancer-associated mutations in speckle-type POZ protein (SPOP) regulate steroid receptor coactivator 3 protein turnover No authors listed Proceedings of the National Academy of Sciences, Vol. 116, Issue 28, p. 14386-14387 https://doi.org/10.1073/pnas.1908767116	journal	June 2019
Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods He, Jintang; Schepmoes, Athena A.; Shi, Tujin Journal of Translational Medicine, Vol. 13, Issue 1 https://doi.org/10.1186/s12967-015-0418-z	journal	January 2015
SPOP the mutation Rider, Leah; Cramer, Scott D. eLife, Vol. 4 https://doi.org/10.7554/elife.11760	journal	October 2015
Less label, more free: Approaches in label-free quantitative mass spectrometry Neilson, Karlie A.; Ali, Naveid A.; Muralidharan, Sridevi PROTEOMICS, Vol. 11, Issue 4 https://doi.org/10.1002/pmic.201000553	journal	January 2011
The Molecular Taxonomy of Primary Prostate Cancer Abeshouse, Adam; Ahn, Jaeil; Akbani, Rehan Cell, Vol. 163, Issue 4 https://doi.org/10.1016/j.cell.2015.10.025	journal	November 2015
Destruction of Full-Length Androgen Receptor by Wild-Type SPOP, but Not Prostate-Cancer-Associated Mutants An, Jian; Wang, Chenji; Deng, Yibin Cell Reports, Vol. 6, Issue 4 https://doi.org/10.1016/j.celrep.2014.01.013	journal	February 2014
Exome Sequencing of Prostate Cancer Supports the Hypothesis of Independent Tumour Origins Lindberg, Johan; Klevebring, Daniel; Liu, Wennuan European Urology, Vol. 63, Issue 2 https://doi.org/10.1016/j.eururo.2012.03.050	journal	February 2013
Re: The Molecular Taxonomy of Primary Prostate Cancer Schlomm, Thorsten European Urology, Vol. 69, Issue 6 https://doi.org/10.1016/j.eururo.2016.02.024	journal	June 2016
Targeted proteomic strategy for clinical biomarker discovery Schiess, Ralph; Wollscheid, Bernd; Aebersold, Ruedi Molecular Oncology, Vol. 3, Issue 1, p. 33-44 https://doi.org/10.1016/j.molonc.2008.12.001	journal	December 2008
GeLC-MRM Quantitation of Mutant KRAS Oncoprotein in Complex Biological Samples Halvey, Patrick J.; Ferrone, Cristina R.; Liebler, Daniel C. Journal of Proteome Research, Vol. 11, Issue 7 https://doi.org/10.1021/pr300161j	journal	June 2012
Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases Kim, Sangtae; Gupta, Nitin; Pevzner, Pavel A. Journal of Proteome Research, Vol. 7, Issue 8 https://doi.org/10.1021/pr8001244	journal	August 2008
The cancer genome Stratton, Michael R.; Campbell, Peter J.; Futreal, P. Andrew Nature, Vol. 458, Issue 7239 https://doi.org/10.1038/nature07943	journal	April 2009
MS-GF+ makes progress towards a universal database search tool for proteomics Kim, Sangtae; Pevzner, Pavel A. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6277	journal	October 2014
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer Barbieri, Christopher E.; Baca, Sylvan C.; Lawrence, Michael S. Nature Genetics, Vol. 44, Issue 6 https://doi.org/10.1038/ng.2279	journal	May 2012
SCISSOR: a framework for identifying structural changes in RNA transcripts Choi, Hyo Young; Jo, Heejoon; Zhao, Xiaobei Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-020-20593-3	journal	January 2021
Prostate cancer-associated mutations in speckle-type POZ protein (SPOP) regulate steroid receptor coactivator 3 protein turnover Geng, C.; He, B.; Xu, L. Proceedings of the National Academy of Sciences, Vol. 110, Issue 17 https://doi.org/10.1073/pnas.1304502110	journal	April 2013
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments MacLean, Brendan; Tomazela, Daniela M.; Shulman, Nicholas Bioinformatics, Vol. 26, Issue 7 https://doi.org/10.1093/bioinformatics/btq054	journal	February 2010
The path to routine use of genomic biomarkers in the cancer clinic Boutros, Paul C. Genome Research, Vol. 25, Issue 10 https://doi.org/10.1101/gr.191114.115	journal	October 2015
Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer Theurillat, Jean-Philippe P.; Udeshi, Namrata D.; Errington, Wesley J. Science, Vol. 346, Issue 6205 https://doi.org/10.1126/science.1250255	journal	October 2014
Androgen Receptor Is the Key Transcriptional Mediator of the Tumor Suppressor SPOP in Prostate Cancer Geng, Chuandong; Rajapakshe, Kimal; Shah, Shrijal S. Cancer Research, Vol. 74, Issue 19 https://doi.org/10.1158/0008-5472.CAN-14-0476	journal	September 2014
The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification Wang, Hui; Shi, Tujin; Qian, Wei-Jun Expert Review of Proteomics, Vol. 13, Issue 1 https://doi.org/10.1586/14789450.2016.1122529	journal	December 2015
SPOP Mutations in Prostate Cancer across Demographically Diverse Patient Cohorts Blattner, Mirjam; Lee, Daniel J.; O'Reilly, Catherine Neoplasia, Vol. 16, Issue 1 https://doi.org/10.1593/neo.131704	journal	January 2014
The Molecular Taxonomy of Primary Prostate Cancer Charles, Perou, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/weaq-yt78	text	January 2015
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer Barbieri, Christopher E.; Al, Et Nature Publishing Group https://doi.org/10.5167/uzh-62954	text	January 2012
SPOP mutations in prostate cancer across demographically diverse patient cohorts Mirjam, Blattner,; J., Lee, Daniel; Catherine, O'Reilly, Neoplasia Press https://doi.org/10.5167/uzh-95695	text	January 2014
SPOP mutation leads to genomic instability in prostate cancer Boysen, Gunther; Barbieri, Christopher E.; Prandi, Davide eLife, Vol. 4 https://doi.org/10.7554/eLife.09207	journal	September 2015

Cited By (1)

Quantitative Mass Spectrometry-Based Proteomic Profiling for Precision Medicine in Prostate Cancer Flores-Morales, Amilcar; Iglesias-Gato, Diego Frontiers in Oncology, Vol. 7 https://doi.org/10.3389/fonc.2017.00267	journal	November 2017

Similar Records

Higher-order SPOP assembly reveals a basis for cancer mutant dysregulation

Journal Article · Sun Jan 22 19:00:00 EST 2023 · Molecular Cell · OSTI ID:2425479

Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods

Journal Article · Wed Dec 31 19:00:00 EST 2014 · Journal of Translational Medicine · OSTI ID:1184918

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
PRISM-SRM
SPOP M
biomarker
mass spectometry
prostate cancer
targeted proteomics

Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/M9.FIGSHARE.C.3854275 The current record is supplemented by this collection	collection	January 2017
MOESM2 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/M9.FIGSHARE.C.3854275_D2 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM3 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/M9.FIGSHARE.C.3854275_D3 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM5 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/M9.FIGSHARE.C.3854275_D5 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM6 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/M9.FIGSHARE.C.3854275_D6 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM8 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/M9.FIGSHARE.C.3854275_D8 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM9 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/M9.FIGSHARE.C.3854275_D9 The current record is supplemented by this audiovisual	audiovisual	January 2017
Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275.v1 The current record is supplemented by this collection	collection	January 2017
MOESM1 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d1 The current record is supplemented by this dataset	dataset	January 2017
MOESM1 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d1.v1 The current record is supplemented by this dataset	dataset	January 2017
MOESM2 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d2.v1 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM3 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d3.v1 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM4 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d4 The current record is supplemented by this dataset	dataset	January 2017
MOESM4 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d4.v1 The current record is supplemented by this dataset	dataset	January 2017
MOESM5 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d5.v1 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM6 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d6.v1 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM7 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d7 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM7 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d7.v1 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM8 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d8.v1 The current record is supplemented by this audiovisual	audiovisual	January 2017
MOESM9 of Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics Wang, Hui; Barbieri, Christopher; He, Jintang https://doi.org/10.6084/m9.figshare.c.3854275_d9.v1 The current record is supplemented by this audiovisual	audiovisual	January 2017

Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics

Citation Formats

References (38)

Cited By (1)

Linked Research (20)

Similar Records

Related Subjects