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Molecular & Cellular Proteomics

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Research

FusionPro, a versatile proteogenomic tool for identification of novel fusion transcripts and their potential translation products in cells

Chae-Yeon Kim, Keun Na, Saeram Park, Seul-Ki Jeong, Jin-Young Cho, Heon Shin, Min Jung Lee, Gyoonhee Han and View ORCID ProfileYoung-Ki Paik  Correspondence email
Molecular & Cellular Proteomics June 17, 2019, mcp.RA119.001456; https://doi.org/10.1074/mcp.RA119.001456
Chae-Yeon Kim
Yonsei University
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Keun Na
Yonsei University
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Saeram Park
Yonsei University
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Seul-Ki Jeong
Yonsei Proteome Research Center
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Jin-Young Cho
Yonsei University
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Heon Shin
Yonsei university
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Min Jung Lee
Yonsei Proteome Research Center, Yonsei University, Republic of Korea
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Gyoonhee Han
Yonsei University
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Young-Ki Paik
Yonsei Proteome Research Center, Yonsei University, Republic of Korea
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  • ORCID record for Young-Ki Paik
  • For correspondence: paikyk@gmail.com
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Abstract

Fusion proteoforms are translation products derived from gene fusion. Although very rare, the fusion proteoforms play important roles in biomedical science. For example, fusion proteoforms influence the development of tumors by serving as cancer markers or cell cycle regulators. Although numerous studies have reported bioinformatics tools that can predict fusion transcripts, few proteogenomic tools are available that can predict and identify proteoforms. In this study, we develop a versatile proteogenomic tool “FusionPro”, which facilitates the identification of fusion transcripts and their potential translatable peptides. FusionPro provides an independent gene fusion prediction module and can build sequence databases for annotated fusion proteoforms. FusionPro shows greater sensitivity than the available fusion finders when analyzing simulated or real RNA sequencing datasets. We use FusionPro to identify 18 fusion junction peptides and three potential fusion-derived peptides by MS/MS-based analysis of leukemia cell lines (Jurkat and K562) and ovarian cancer tissues from the Clinical Proteomic Tumor Analysis Consortium. Among the identified fusion proteins, we molecularly validate two fusion junction isoforms and a translation product of FAM133B:CDK6. Moreover, sequence analysis suggests that the fusion protein participates in the cell cycle progression. In addition, our prediction results indicate that fusion transcripts often have multiple fusion junctions and that these fusion junctions tend to be distributed in a non-random pattern at both the chromosome and gene levels. Thus, FusionPro allows users to detect various types of fusion translation products using a transcriptome-informed approach and to gain a comprehensive understanding of the formation and biological roles of fusion proteoforms.

  • Fusion transcript
  • Fusion proteoform
  • Customized database
  • Bioinformatics
  • Mass Spectrometry
  • Ovarian cancer
  • Proteogenomics
  • Translation*

Footnotes

  • Author contributions: C.-Y.K., K.N., S.P., and Y.-K.P. designed research; C.-Y.K., K.N., S.P., J.-Y.C., and H.S. performed research; C.-Y.K. and S.-K.J. contributed new reagents/analytic tools; C.-Y.K., K.N., S.P., J.-Y.C., M.J.L., and G.H. analyzed data; C.-Y.K. and Y.-K.P. wrote the paper.

  • Received March 19, 2019.
  • Revision received May 23, 2019.
  • Accepted June 17, 2019.
  • Published under license by The American Society for Biochemistry and Molecular Biology, Inc.
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FusionPro, a versatile proteogenomic tool for identification of novel fusion transcripts and their potential translation products in cells
Chae-Yeon Kim, Keun Na, Saeram Park, Seul-Ki Jeong, Jin-Young Cho, Heon Shin, Min Jung Lee, Gyoonhee Han, Young-Ki Paik
Molecular & Cellular Proteomics June 17, 2019, mcp.RA119.001456; DOI: 10.1074/mcp.RA119.001456

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FusionPro, a versatile proteogenomic tool for identification of novel fusion transcripts and their potential translation products in cells
Chae-Yeon Kim, Keun Na, Saeram Park, Seul-Ki Jeong, Jin-Young Cho, Heon Shin, Min Jung Lee, Gyoonhee Han, Young-Ki Paik
Molecular & Cellular Proteomics June 17, 2019, mcp.RA119.001456; DOI: 10.1074/mcp.RA119.001456
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