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Comparative Analysis of Proteome and Transcriptome in Human Hepatocellular Carcinoma using 2D-DIGE and SAGE

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Abstract

Proteome analysis of human hepatocellular carcinoma was conducted using two-dimensional difference gel electrophoresis, and the protein expression profiles were compared to the mRNA expression profiles made from serial analysis of gene expression (SAGE) in identical samples from a single patient. Image-to-image analysis of protein abundances together with protein identification by peptide mass fingerprinting yielded the protein expression profiles. A total of 188 proteins were identified, and the expression profiles of 164 proteins which had the corresponding SAGE data were compared to the mRNA expression profiles. Among them, 40 proteins showed significant differences in the mRNA expression levels between non HCC and HCC. We compared expression changes of proteins with those of mRNAs. We found that the expression tendency of 24 proteins were similar to that of mRNA, whereas 16 proteins showed different or opposite tendency to the mRNA expression.

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Abbreviations

HCC:

Hepatocellular carcinoma

SAGE:

Serial analysis of gene expression

2-DE:

Two-dimensional gel electrophoresis

2D-DIGE:

Two-dimensional difference gel electrophoresis

IS:

Internal standard

PMSF:

Phenylmethyl sulfonyl fluoride

TFA:

Trifluoroacetic acid

ACN:

Acetonitrile

MALDI-TOF:

Matrix assisted laser desorption ionization time of flight

LC-ESI-IT MS/MS:

Liquid chromatography-electrospray ion trap tandem mass spectrometry

PMF:

Peptide mass fingerprinting

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Acknowledgments

We are grateful to Dr. K. Miyazaki and Dr. R. Teramoto for fruitful comments on this work, and N. Tetsura for technical assistance.

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Authors and Affiliations

  1. Fundamental and Environmental Research Laboratories, NEC Corporation, 34 Miyukigaoka, Tsukuba, Ibaraki, 305-8501, Japan

    Hirotaka Minagawa, Yo Tabuse & Kenichi Kamijo

  2. Department of Gastroenterology, School of Medicine, Kanazawa University, Kanazawa, Japan

    Taro Yamashita, Masao Honda & Shuichi Kaneko

  3. Proteomics Research Laboratory, Tokyo Rikakikai, Tsukuba, Japan

    Akira Tsugita

Authors
  1. Hirotaka Minagawa
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  2. Taro Yamashita
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  3. Masao Honda
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  4. Yo Tabuse
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  5. Kenichi Kamijo
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  6. Akira Tsugita
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  7. Shuichi Kaneko
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Correspondence to Hirotaka Minagawa.

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Minagawa, H., Yamashita, T., Honda, M. et al. Comparative Analysis of Proteome and Transcriptome in Human Hepatocellular Carcinoma using 2D-DIGE and SAGE. Protein J 27, 409–419 (2008). https://doi.org/10.1007/s10930-007-9123-y

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