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The current state of proteomics in GI oncology.

Lin Y, Dynan WS, Lee JR, Zhu ZH, Schade RR - Dig. Dis. Sci. (2008)

Bottom Line: Proteomics refers to the study of the entire set of proteins in a given cell or tissue.In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years.We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA 30912, USA.

ABSTRACT
Proteomics refers to the study of the entire set of proteins in a given cell or tissue. With the extensive development of protein separation, mass spectrometry, and bioinformatics technologies, clinical proteomics has shown its potential as a powerful approach for biomarker discovery, particularly in the area of oncology. More than 130 exploratory studies have defined candidate markers in serum, gastrointestinal (GI) fluids, or cancer tissue. In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years. We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.

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Related in: MedlinePlus

Two-dimensional difference gel electrophoresis (2D-DIGE). a Representative gel images of proteins from analysis of a microdissected CRC specimen in our laboratory. Red represents Cy5-labeled sample proteins, and green represents Cy3-labeled pooled internal standard. In the multiplexed image, spots that are more abundant in the sample than in the standard appear red, spots that are less abundant in the sample appear green, and spots that are equal in the sample and the standard appear yellow. b Design of a clinical proteomics experiment. In this example, which is based on analysis of cancer-normal pairs, each patient contributes two samples: cancer and adjacent normal tissue. The number of gels equals the number of samples. For each spot in each gel, the ratio of emission at Cy5 and Cy3 wavelengths is measured. These “internal ratios” are used to compare the relative abundance of a given protein across the different specimens in the experiment
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Fig4: Two-dimensional difference gel electrophoresis (2D-DIGE). a Representative gel images of proteins from analysis of a microdissected CRC specimen in our laboratory. Red represents Cy5-labeled sample proteins, and green represents Cy3-labeled pooled internal standard. In the multiplexed image, spots that are more abundant in the sample than in the standard appear red, spots that are less abundant in the sample appear green, and spots that are equal in the sample and the standard appear yellow. b Design of a clinical proteomics experiment. In this example, which is based on analysis of cancer-normal pairs, each patient contributes two samples: cancer and adjacent normal tissue. The number of gels equals the number of samples. For each spot in each gel, the ratio of emission at Cy5 and Cy3 wavelengths is measured. These “internal ratios” are used to compare the relative abundance of a given protein across the different specimens in the experiment

Mentions: Two-dimensional difference gel electrophoresis (2D-DIGE) is the most common multiplex top-down approach [26, 27] (Fig. 4). Proteins are covalently labeled by reaction of cyanine dyes with cysteine or lysine residues. Spectrally distinct dyes are similar in molecular weight and do not change the protein charge. Thus, the same proteins in different samples, labeled in different colors, migrate to the same position in the gel. For each spot, the ratio of emission at different wavelengths provides a measure of relative abundance [28].Fig. 4


The current state of proteomics in GI oncology.

Lin Y, Dynan WS, Lee JR, Zhu ZH, Schade RR - Dig. Dis. Sci. (2008)

Two-dimensional difference gel electrophoresis (2D-DIGE). a Representative gel images of proteins from analysis of a microdissected CRC specimen in our laboratory. Red represents Cy5-labeled sample proteins, and green represents Cy3-labeled pooled internal standard. In the multiplexed image, spots that are more abundant in the sample than in the standard appear red, spots that are less abundant in the sample appear green, and spots that are equal in the sample and the standard appear yellow. b Design of a clinical proteomics experiment. In this example, which is based on analysis of cancer-normal pairs, each patient contributes two samples: cancer and adjacent normal tissue. The number of gels equals the number of samples. For each spot in each gel, the ratio of emission at Cy5 and Cy3 wavelengths is measured. These “internal ratios” are used to compare the relative abundance of a given protein across the different specimens in the experiment
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3045515&req=5

Fig4: Two-dimensional difference gel electrophoresis (2D-DIGE). a Representative gel images of proteins from analysis of a microdissected CRC specimen in our laboratory. Red represents Cy5-labeled sample proteins, and green represents Cy3-labeled pooled internal standard. In the multiplexed image, spots that are more abundant in the sample than in the standard appear red, spots that are less abundant in the sample appear green, and spots that are equal in the sample and the standard appear yellow. b Design of a clinical proteomics experiment. In this example, which is based on analysis of cancer-normal pairs, each patient contributes two samples: cancer and adjacent normal tissue. The number of gels equals the number of samples. For each spot in each gel, the ratio of emission at Cy5 and Cy3 wavelengths is measured. These “internal ratios” are used to compare the relative abundance of a given protein across the different specimens in the experiment
Mentions: Two-dimensional difference gel electrophoresis (2D-DIGE) is the most common multiplex top-down approach [26, 27] (Fig. 4). Proteins are covalently labeled by reaction of cyanine dyes with cysteine or lysine residues. Spectrally distinct dyes are similar in molecular weight and do not change the protein charge. Thus, the same proteins in different samples, labeled in different colors, migrate to the same position in the gel. For each spot, the ratio of emission at different wavelengths provides a measure of relative abundance [28].Fig. 4

Bottom Line: Proteomics refers to the study of the entire set of proteins in a given cell or tissue.In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years.We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA 30912, USA.

ABSTRACT
Proteomics refers to the study of the entire set of proteins in a given cell or tissue. With the extensive development of protein separation, mass spectrometry, and bioinformatics technologies, clinical proteomics has shown its potential as a powerful approach for biomarker discovery, particularly in the area of oncology. More than 130 exploratory studies have defined candidate markers in serum, gastrointestinal (GI) fluids, or cancer tissue. In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years. We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.

Show MeSH
Related in: MedlinePlus