Protein expression profile characteristic to hepatocellular carcinoma revealed by 2D-DIGE with supervised learning.
ABSTRACT Hepatocellular carcinoma (HCC) is one of the most common and aggressive human malignancies. Although several major risks related to HCC, e.g., hepatitis B and/or hepatitis C virus infection, aflatoxin B1 exposure, alcohol drinking and genetic defects have been revealed, the molecular mechanisms leading to the initiation and progression of HCC have not been clarified. To reduce the mortality and improve the effectiveness of therapy, it is important to detect the proteins which are associated with tumor progression and may be useful as potential therapeutic or diagnosis targets. However, previous studies have not yet revealed the associations among HCC cells, histological grade and AFP. Here, we performed two-dimensional difference gel electrophoresis (2D-DIGE) combined with MS for 18 HCC patients. To focus not on individual proteins but on multiple proteins associated with pathogenesis, we introduce the supervised feature selection based on stochastic gradient boosting (SGB) for identifying protein spots that discriminate HCC/non HCC, histological grade of moderate/well and high alpha-fetoprotein (AFP)/low AFP level without arbitrariness. We detected 18, 25 and 27 protein spots associated with HCC, histological grade and AFP level, respectively. We confirmed that SGB is able to identify the known HCC-related proteins, e.g., heat shock proteins, carbonic anhydrase 2. Moreover, we identified the differentially expressed proteins associated with histological grade of HCC and AFP level and found that aldo-keto reductase 1B10 (AKR1B10) is related to well differentiated HCC, keratin 8 (KRT8) is related to both histological grade and AFP level and protein disulfide isomerase-associated 3 (PDIA3) is associated with both HCC and AFP level. Our pilot study provides new insights on understanding the pathogenesis of HCC, histological grade and AFP level.
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ABSTRACT: Deregulated expression of the c-Myc transcription factor is found in a wide variety of human tumors. Because of this significant role in oncogenesis, considerable effort has been devoted to elucidating the molecular program initiated by deregulated c-myc expression. The primary transforming activity of Myc is thought to arise through transcriptional regulation of numerous target genes. Thus far, Myc target genes involved in mitochondrial function have not been characterized in depth. Here, we describe a nuclear c-Myc target gene, PRDX3, which encodes a mitochondrial protein of the peroxiredoxin gene family. Expression of PRDX3 is induced by the mycER system and is reduced in c-myc(-/-) cells. Chromatin immunoprecipitation analysis spanning the entire PRDX3 genomic sequence reveals that Myc binds preferentially to a 930-bp region surrounding exon 1. We show that PRDX3 is required for Myc-mediated proliferation, transformation, and apoptosis after glucose withdrawal. Results using mitochondria-specific fluorescent probes demonstrate that PRDX3 is essential for maintaining mitochondrial mass and membrane potential in transformed rat and human cells. These data provide evidence that PRDX3 is a c-Myc target gene that is required to maintain normal mitochondrial function.Proceedings of the National Academy of Sciences 06/2002; 99(10):6649-54. · 9.74 Impact Factor
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ABSTRACT: The comparison of two-dimensional (2-D) gel images from different samples is an established method used to study differences in protein expression. Conventional methods rely on comparing images from at least 2 different gels. Due to the high variation between gels, detection and quantification of protein differences can be problematic. Two-dimensional difference gel electrophoresis (Ettan trade mark DIGE) is an emerging technique for comparative proteomics, which improves the reproducibility and reliability of differential protein expression analysis between samples. In the application of DIGE different samples are labelled with mass and charge matched spectrally resolvable fluorescent dyes and are then separated on the same 2-D gel. Using an Escherichia coli lysate "spiked" with varying amounts of four different known proteins, we have tested a novel experimental design that exploits the sample multiplexing capabilities of DIGE, by including a standard sample in each gel. The standard sample comprises equal amounts of each sample to be compared and was found to improve the accuracy of protein quantification between samples from different gels allowing accurate detection of small differences in protein levels between samples.PROTEOMICS 02/2003; 3(1):36-44. · 4.13 Impact Factor
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ABSTRACT: To investigate a molecular basis for iron depletion in human hepatocellular carcinoma (HCC), 19 cases of HCC were analyzed by two-dimensional electrophoresis (2DE) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Results were compared with those of paired adjacent nontumorous liver tissues. Comparative analysis of the respective spot patterns in 2DE showed that tissue ferritin light chain (T-FLC), an iron-storage protein, was either severely suppressed or reduced to undetectable levels in HCC, which was further supported by Western blot and immunohistochemical analysis. In contrast, transferrin receptor (TfR) was shown to be overexpressed in the same HCC samples. Interestingly, the relative levels of messenger RNA (mRNA) expression of T-FLC in HCC, which were measured by a real-time quantitative reverse-transcription polymerase chain reaction (PCR), exhibited almost the same levels as those in normal tissues, suggesting that the translational or posttranslational modification of T-FLC may be the cause of T-FLC suppression in HCC. Furthermore, with PCR-based loss of heterozygosity analysis, only 1 of 19 HCCs showed chromosomal deletions at 19q13.3-q13.4 where T-FLC is located, indicating that the suppression of T-FLC is unlikely due to structural genomic changes with HCC. In conclusion, both proteomic and genomic evidence support not only a basis for the suppression of T-FLC in HCC but also provide a new clue to the unresolved question of iron depletion during hepatocarcinogenesis.Hepatology 07/2002; 35(6):1459-66. · 12.00 Impact Factor