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Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma.

Wiśniewski JR, Ostasiewicz P, Duś K, Zielińska DF, Gnad F, Mann M - Mol. Syst. Biol. (2012)

Bottom Line: Functionally similar changes in the proteome were observed comparing rapidly growing and differentiated CaCo-2 cells.In contrast, there was minimal proteomic remodeling between primary cancer and metastases, suggesting that no drastic proteome changes are necessary for the tumor to propagate in a different tissue context.Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer.

View Article: PubMed Central - PubMed

Affiliation: Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany. jwisniew@biochem.mpg.de

ABSTRACT
We report a proteomic analysis of microdissected material from formalin-fixed and paraffin-embedded colorectal cancer, quantifying > 7500 proteins between patient matched normal mucosa, primary carcinoma, and nodal metastases. Expression levels of 1808 proteins changed significantly between normal and cancer tissues, a much larger fraction than that reported in transcript-based studies. Tumor cells exhibit extensive alterations in the cell-surface and nuclear proteomes. Functionally similar changes in the proteome were observed comparing rapidly growing and differentiated CaCo-2 cells. In contrast, there was minimal proteomic remodeling between primary cancer and metastases, suggesting that no drastic proteome changes are necessary for the tumor to propagate in a different tissue context. Additionally, we introduce a new way to determine protein copy numbers per cell without protein standards. Copy numbers estimated in enterocytes and cancer cells are in good agreement with CaCo-2 and HeLa cells and with the literature data. Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer.

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Related in: MedlinePlus

Abundance of proteins matching selected subcellular locations (A–G) and functions (H–N). The numbers of proteins belonging to each class are given in the parentheses. The protein abundances were calculated on the basis of total spectral intensities of all quantified proteins. Red boxes indicate that the changes between cancer and normal were significant with P<0.01. Note that serum albumin levels (gray boxes) are similar between the three types of samples, indicating absence of differential contamination with plasma proteins. In (L), summed abundance of core and linker histones are shown by separate boxes. The purple boxes are for linker histones whereas the core histones by red boxes.
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f2: Abundance of proteins matching selected subcellular locations (A–G) and functions (H–N). The numbers of proteins belonging to each class are given in the parentheses. The protein abundances were calculated on the basis of total spectral intensities of all quantified proteins. Red boxes indicate that the changes between cancer and normal were significant with P<0.01. Note that serum albumin levels (gray boxes) are similar between the three types of samples, indicating absence of differential contamination with plasma proteins. In (L), summed abundance of core and linker histones are shown by separate boxes. The purple boxes are for linker histones whereas the core histones by red boxes.

Mentions: To describe the protein content constituting defined cellular compartments or molecular functions and to provide insight into differences between cellular states, we used the total signal intensities of the peptides identifying each protein as determined in the MaxQuant software (normalized values for LFQ intensities). These peptide intensities are a good proxy for the absolute abundance of the proteins, especially when a set of proteins is considered because inaccuracies for specific proteins are averaged out. Panels A–G in Figure 2 show representative examples of the protein content of selected subcellular compartments. Clear alterations were apparent between N and C, but not between C and M. In particular, the abundance of extracellular and integral to plasma membrane proteins in the N proteome was 20–30% higher than in the C proteome whereas the abundance of nuclear proteins was about 30% less (Figure 2A, B). We did not find clear differences between N and C in the overall abundance of proteins belonging to cytoplasm (Figure 2C) and its major components such as the Golgi body, mitochondrion, and endoplasmic reticulum (Figure 2D–F). We next investigated selected functional categories related to the altered subcellular compartments (Figure 2H–N). Partial loss of integral plasma membrane proteins in cancer was accompanied by a 50 and 30% decrease in the abundance of channel and transporter proteins, respectively (Figure 2H and I). Several individual examples of this global decrease are shown in Tables I and II. They included a >10-fold decrease of chloride and sodium channels and three- to five-fold reduction of FXYD ion transport regulators 1 and 3 (Table I). The latter proteins are also known as Phospholemnan and Mat-8 and are known modulators of Na,K-ATP-ases that affect their kinetic properties (Garty and Karlish, 2006). The increase of the total content of nuclear proteins correlates well with changes in the content of histones, subunits of the RNA polymerases, and transcription factors (Figure 2J, K). We found that general transcription factors and chromatin activators such as histone deacetylases and the high mobility group proteins were 2- to 10-fold upregulated in the cancer samples (Table I). A similar increase of protein abundance was found for a number of nuclear transporters (Table II).


Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma.

Wiśniewski JR, Ostasiewicz P, Duś K, Zielińska DF, Gnad F, Mann M - Mol. Syst. Biol. (2012)

Abundance of proteins matching selected subcellular locations (A–G) and functions (H–N). The numbers of proteins belonging to each class are given in the parentheses. The protein abundances were calculated on the basis of total spectral intensities of all quantified proteins. Red boxes indicate that the changes between cancer and normal were significant with P<0.01. Note that serum albumin levels (gray boxes) are similar between the three types of samples, indicating absence of differential contamination with plasma proteins. In (L), summed abundance of core and linker histones are shown by separate boxes. The purple boxes are for linker histones whereas the core histones by red boxes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472694&req=5

f2: Abundance of proteins matching selected subcellular locations (A–G) and functions (H–N). The numbers of proteins belonging to each class are given in the parentheses. The protein abundances were calculated on the basis of total spectral intensities of all quantified proteins. Red boxes indicate that the changes between cancer and normal were significant with P<0.01. Note that serum albumin levels (gray boxes) are similar between the three types of samples, indicating absence of differential contamination with plasma proteins. In (L), summed abundance of core and linker histones are shown by separate boxes. The purple boxes are for linker histones whereas the core histones by red boxes.
Mentions: To describe the protein content constituting defined cellular compartments or molecular functions and to provide insight into differences between cellular states, we used the total signal intensities of the peptides identifying each protein as determined in the MaxQuant software (normalized values for LFQ intensities). These peptide intensities are a good proxy for the absolute abundance of the proteins, especially when a set of proteins is considered because inaccuracies for specific proteins are averaged out. Panels A–G in Figure 2 show representative examples of the protein content of selected subcellular compartments. Clear alterations were apparent between N and C, but not between C and M. In particular, the abundance of extracellular and integral to plasma membrane proteins in the N proteome was 20–30% higher than in the C proteome whereas the abundance of nuclear proteins was about 30% less (Figure 2A, B). We did not find clear differences between N and C in the overall abundance of proteins belonging to cytoplasm (Figure 2C) and its major components such as the Golgi body, mitochondrion, and endoplasmic reticulum (Figure 2D–F). We next investigated selected functional categories related to the altered subcellular compartments (Figure 2H–N). Partial loss of integral plasma membrane proteins in cancer was accompanied by a 50 and 30% decrease in the abundance of channel and transporter proteins, respectively (Figure 2H and I). Several individual examples of this global decrease are shown in Tables I and II. They included a >10-fold decrease of chloride and sodium channels and three- to five-fold reduction of FXYD ion transport regulators 1 and 3 (Table I). The latter proteins are also known as Phospholemnan and Mat-8 and are known modulators of Na,K-ATP-ases that affect their kinetic properties (Garty and Karlish, 2006). The increase of the total content of nuclear proteins correlates well with changes in the content of histones, subunits of the RNA polymerases, and transcription factors (Figure 2J, K). We found that general transcription factors and chromatin activators such as histone deacetylases and the high mobility group proteins were 2- to 10-fold upregulated in the cancer samples (Table I). A similar increase of protein abundance was found for a number of nuclear transporters (Table II).

Bottom Line: Functionally similar changes in the proteome were observed comparing rapidly growing and differentiated CaCo-2 cells.In contrast, there was minimal proteomic remodeling between primary cancer and metastases, suggesting that no drastic proteome changes are necessary for the tumor to propagate in a different tissue context.Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer.

View Article: PubMed Central - PubMed

Affiliation: Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany. jwisniew@biochem.mpg.de

ABSTRACT
We report a proteomic analysis of microdissected material from formalin-fixed and paraffin-embedded colorectal cancer, quantifying > 7500 proteins between patient matched normal mucosa, primary carcinoma, and nodal metastases. Expression levels of 1808 proteins changed significantly between normal and cancer tissues, a much larger fraction than that reported in transcript-based studies. Tumor cells exhibit extensive alterations in the cell-surface and nuclear proteomes. Functionally similar changes in the proteome were observed comparing rapidly growing and differentiated CaCo-2 cells. In contrast, there was minimal proteomic remodeling between primary cancer and metastases, suggesting that no drastic proteome changes are necessary for the tumor to propagate in a different tissue context. Additionally, we introduce a new way to determine protein copy numbers per cell without protein standards. Copy numbers estimated in enterocytes and cancer cells are in good agreement with CaCo-2 and HeLa cells and with the literature data. Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer.

Show MeSH
Related in: MedlinePlus