A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples

Ryohei Narumi, Tatsuo Murakami, Takahisa Kuga, Jun Adachi, Takashi Shiromizu, Satoshi Muraoka, Hideaki Kume, Yoshio Kodera, Masaki Matsumoto, Keiichi Nakayama, Yasuhide Miyamoto, Makoto Ishitobi, Hideo Inaji, Kikuya Kato, Takeshi Tomonaga

研究成果: ジャーナルへの寄稿記事

67 引用 (Scopus)

抄録

Protein phosphorylation is a key mechanism of cellular signaling pathways and aberrant phosphorylation has been implicated in a number of human diseases. Thus, approaches in phosphoproteomics can contribute to the identification of key biomarkers to assess disease pathogenesis and drug targets. Moreover, careful validation of large-scale phosphoproteome analysis, which is lacking in the current protein-based biomarker discovery, significantly increases the value of identified biomarkers. Here, we performed large-scale differential phosphoproteome analysis using IMAC coupled with the isobaric tag for relative quantification (iTRAQ) technique and subsequent validation by selected/multiple reaction monitoring (SRM/MRM) of human breast cancer tissues in high- and low-risk recurrence groups. We identified 8309 phosphorylation sites on 3401 proteins, of which 3766 phosphopeptides (1927 phosphoproteins) were able to be quantified and 133 phosphopeptides (117 phosphoproteins) were differentially expressed between the two groups. Among them, 19 phosphopeptides were selected for further verification and 15 were successfully quantified by SRM using stable isotope peptides as a reference. The ratio of phosphopeptides between high- and low-risk groups quantified by SRM was well correlated with iTRAQ-based quantification with a few exceptions. These results suggest that large-scale phosphoproteome quantification coupled with SRM-based validation is a powerful tool for biomarker discovery using clinical samples.

元の言語英語
ページ(範囲)5311-5322
ページ数12
ジャーナルJournal of Proteome Research
11
発行部数11
DOI
出版物ステータス出版済み - 11 2 2012

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Phosphopeptides
Biomarkers
Phosphorylation
Tissue
Breast Neoplasms
Phosphoproteins
Cell signaling
Proteins
Isotopes
Recurrence
Peptides
Monitoring
Pharmaceutical Preparations

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

これを引用

Narumi, R., Murakami, T., Kuga, T., Adachi, J., Shiromizu, T., Muraoka, S., ... Tomonaga, T. (2012). A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples. Journal of Proteome Research, 11(11), 5311-5322. https://doi.org/10.1021/pr3005474

A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples. / Narumi, Ryohei; Murakami, Tatsuo; Kuga, Takahisa; Adachi, Jun; Shiromizu, Takashi; Muraoka, Satoshi; Kume, Hideaki; Kodera, Yoshio; Matsumoto, Masaki; Nakayama, Keiichi; Miyamoto, Yasuhide; Ishitobi, Makoto; Inaji, Hideo; Kato, Kikuya; Tomonaga, Takeshi.

:: Journal of Proteome Research, 巻 11, 番号 11, 02.11.2012, p. 5311-5322.

研究成果: ジャーナルへの寄稿記事

Narumi, R, Murakami, T, Kuga, T, Adachi, J, Shiromizu, T, Muraoka, S, Kume, H, Kodera, Y, Matsumoto, M, Nakayama, K, Miyamoto, Y, Ishitobi, M, Inaji, H, Kato, K & Tomonaga, T 2012, 'A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples', Journal of Proteome Research, 巻. 11, 番号 11, pp. 5311-5322. https://doi.org/10.1021/pr3005474
Narumi, Ryohei ; Murakami, Tatsuo ; Kuga, Takahisa ; Adachi, Jun ; Shiromizu, Takashi ; Muraoka, Satoshi ; Kume, Hideaki ; Kodera, Yoshio ; Matsumoto, Masaki ; Nakayama, Keiichi ; Miyamoto, Yasuhide ; Ishitobi, Makoto ; Inaji, Hideo ; Kato, Kikuya ; Tomonaga, Takeshi. / A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples. :: Journal of Proteome Research. 2012 ; 巻 11, 番号 11. pp. 5311-5322.
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abstract = "Protein phosphorylation is a key mechanism of cellular signaling pathways and aberrant phosphorylation has been implicated in a number of human diseases. Thus, approaches in phosphoproteomics can contribute to the identification of key biomarkers to assess disease pathogenesis and drug targets. Moreover, careful validation of large-scale phosphoproteome analysis, which is lacking in the current protein-based biomarker discovery, significantly increases the value of identified biomarkers. Here, we performed large-scale differential phosphoproteome analysis using IMAC coupled with the isobaric tag for relative quantification (iTRAQ) technique and subsequent validation by selected/multiple reaction monitoring (SRM/MRM) of human breast cancer tissues in high- and low-risk recurrence groups. We identified 8309 phosphorylation sites on 3401 proteins, of which 3766 phosphopeptides (1927 phosphoproteins) were able to be quantified and 133 phosphopeptides (117 phosphoproteins) were differentially expressed between the two groups. Among them, 19 phosphopeptides were selected for further verification and 15 were successfully quantified by SRM using stable isotope peptides as a reference. The ratio of phosphopeptides between high- and low-risk groups quantified by SRM was well correlated with iTRAQ-based quantification with a few exceptions. These results suggest that large-scale phosphoproteome quantification coupled with SRM-based validation is a powerful tool for biomarker discovery using clinical samples.",
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AU - Adachi, Jun

AU - Shiromizu, Takashi

AU - Muraoka, Satoshi

AU - Kume, Hideaki

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AU - Nakayama, Keiichi

AU - Miyamoto, Yasuhide

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