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Title: Clinical potential of mass spectrometry-based proteogenomics

Abstract

Cancer genomics research aims to advance personalized oncology by finding and targeting genetic alterations associated with cancers. In genome-driven oncology, treatments are selected for individual patients based on the genomic sequence of their tumor. This personalized oncology approach has prolonged survival for subsets of cancer patients. However, many patients do not respond to the predicted therapies based on genomic profiles of their tumors. Recent studies pairing genomic and proteomic analyses in the same tumors have shown that the proteome encodes novel information that is not discerned through genomic analysis alone. This has led to the concept of “proteogenomics,” in which both types of data are leveraged for a more complete view of tumor biology that may more effectively match cancer patients to efficacious treatments. Technological advances in methods for quantifying proteins, including targeted mass spectrometry, have opened a path for the clinical translation of proteogenomic findings into clinical research. We discuss the added value of a combined proteogenomics approach over the current genome-centric approach in characterizing human cancers, and summarize current efforts to incorporate targeted proteomic measurements based on multiple reaction monitoring mass spectrometry (MRM) into the clinical laboratory to facilitate clinical proteogenomics.

Authors:
 [1];  [2]; ;  [3]; ORCiD logo [4];  [2]
  1. Baylor College of Medicine
  2. Fred Hutchinson Cancer Research Center
  3. University of Washington
  4. BATTELLE (PACIFIC NW LAB)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1511197
Report Number(s):
PNNL-SA-134884
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Nature Reviews in Clinical Oncology
Additional Journal Information:
Journal Volume: 16; Journal Issue: 4
Country of Publication:
United States
Language:
English

Citation Formats

Zhang, Bing, Whiteaker, Jeffrey R., Hoofnagle, Andrew N., Baird, Geoffrey S., Rodland, Karin D., and Paulovich, Amanda G. Clinical potential of mass spectrometry-based proteogenomics. United States: N. p., 2019. Web. doi:10.1038/s41571-018-0135-7.
Zhang, Bing, Whiteaker, Jeffrey R., Hoofnagle, Andrew N., Baird, Geoffrey S., Rodland, Karin D., & Paulovich, Amanda G. Clinical potential of mass spectrometry-based proteogenomics. United States. doi:10.1038/s41571-018-0135-7.
Zhang, Bing, Whiteaker, Jeffrey R., Hoofnagle, Andrew N., Baird, Geoffrey S., Rodland, Karin D., and Paulovich, Amanda G. Mon . "Clinical potential of mass spectrometry-based proteogenomics". United States. doi:10.1038/s41571-018-0135-7.
@article{osti_1511197,
title = {Clinical potential of mass spectrometry-based proteogenomics},
author = {Zhang, Bing and Whiteaker, Jeffrey R. and Hoofnagle, Andrew N. and Baird, Geoffrey S. and Rodland, Karin D. and Paulovich, Amanda G.},
abstractNote = {Cancer genomics research aims to advance personalized oncology by finding and targeting genetic alterations associated with cancers. In genome-driven oncology, treatments are selected for individual patients based on the genomic sequence of their tumor. This personalized oncology approach has prolonged survival for subsets of cancer patients. However, many patients do not respond to the predicted therapies based on genomic profiles of their tumors. Recent studies pairing genomic and proteomic analyses in the same tumors have shown that the proteome encodes novel information that is not discerned through genomic analysis alone. This has led to the concept of “proteogenomics,” in which both types of data are leveraged for a more complete view of tumor biology that may more effectively match cancer patients to efficacious treatments. Technological advances in methods for quantifying proteins, including targeted mass spectrometry, have opened a path for the clinical translation of proteogenomic findings into clinical research. We discuss the added value of a combined proteogenomics approach over the current genome-centric approach in characterizing human cancers, and summarize current efforts to incorporate targeted proteomic measurements based on multiple reaction monitoring mass spectrometry (MRM) into the clinical laboratory to facilitate clinical proteogenomics.},
doi = {10.1038/s41571-018-0135-7},
journal = {Nature Reviews in Clinical Oncology},
number = 4,
volume = 16,
place = {United States},
year = {2019},
month = {4}
}

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Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
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Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach
journal, January 2014

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Functional precision cancer medicine—moving beyond pure genomics
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Proteogenomics for understanding oncology: recent advances and future prospects
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Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium
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Epigenetic plasticity and the hallmarks of cancer
journal, July 2017

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No Solid Evidence, Only Hollow Argument for Universal Tumor Sequencing: Show Me the Data
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Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction
journal, November 2016

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Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics
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Regulation of Alternative Splicing by Histone Modifications
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Proof of the quantitative potential of immunofluorescence by mass spectrometry
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Perspectives of targeted mass spectrometry for protein biomarker verification
journal, December 2009

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Proteogenomic-based discovery of minor histocompatibility antigens with suitable features for immunotherapy of hematologic cancers
journal, February 2016

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Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer
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Assessing the clinical utility of cancer genomic and proteomic data across tumor types
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Quantitative measurement of cancer tissue biomarkers in the lab and in the clinic
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Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment
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Alternative splicing in cancer: implications for biology and therapy
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High HER2 protein levels correlate with increased survival in breast cancer patients treated with anti-HER2 therapy
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The evolving role of mass spectrometry in cancer biomarker discovery
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Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes
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Quantification of Thyroglobulin, a Low-Abundance Serum Protein, by Immunoaffinity Peptide Enrichment and Tandem Mass Spectrometry
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Urine proteomics for discovery of improved diagnostic markers of Kawasaki disease
journal, December 2012

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