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4058 Enhanced efficiency of large-scale clinical proteomic studies: when less is more

Published online by Cambridge University Press:  29 July 2020

Stefani Thomas
Affiliation:
University of Minnesota
Betty Friedrich
Affiliation:
Dept of Biology, Inst of Molec Systems Biology, ETH Zurich
Michael Schnaubelt
Affiliation:
Johns Hopkins University
Daniel W. Chan
Affiliation:
Johns Hopkins University
Hui Zhang
Affiliation:
Johns Hopkins University
Ruedi Aebersold
Affiliation:
ETH Zurich; University of Zurich
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Abstract

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OBJECTIVES/GOALS: Large-scale clinical proteomic studies of cancer tissues often entail complex workflows and are resource-intensive. In this study we analyzed ovarian tumors using an emerging, high-throughput proteomic technology termed SWATH. We compared SWATH with the more widely used iTRAQ workflow based on robustness, complexity, ability to detect differential protein expression, and the elucidated biological information. METHODS/STUDY POPULATION: Proteomic measurements of 103 clinically-annotated high-grade serous ovarian cancer (HGSOC) tumors previously genomically characterized by The Cancer Genome Atlas were conducted using two orthogonal mass spectrometry-based proteomic methods: iTRAQ and SWATH. The analytical differences between the two methods were compared with respect to relative protein abundances. To assess the ability to classify the tumors into subtypes based on proteomic signatures, an unbiased molecular taxonomy of HGSOC was established using protein abundance data. The 1,599 proteins quantified in both datasets were classified based on z-score-transformed protein abundances, and the emergent protein modules were characterized using weighted gene-correlation network analysis and Reactome pathway enrichment. RESULTS/ANTICIPATED RESULTS: Despite the greater than two-fold difference in the analytical depth of each proteomic method, common differentially expressed proteins in enriched pathways associated with the HGSOC Mesenchymal subtype were identified by both methods. The stability of tumor subtype classification was sensitive to the number of analyzed samples, and the statistically stable subgroups were identified by the data from both methods. Additionally, the homologous recombination deficiency-associated enriched DNA repair and chromosome organization pathways were conserved in both data sets. DISCUSSION/SIGNIFICANCE OF IMPACT: SWATH is a robust proteomic method that can be used to elucidate cancer biology. The lower number of proteins detected by SWATH compared to iTRAQ is mitigated by its streamlined workflow, increased sample throughput, and reduced sample requirement. SWATH therefore presents novel opportunities to enhance the efficiency of clinical proteomic studies.

Type
Precision Medicine
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
© The Association for Clinical and Translational Science 2020