Proteomic analysis of breast cancer tissues to identify biomarker candidates by gel-assisted digestion and label-free quantification methods using LC-MS/MS

Song, Mi Na; Moon, Pyong Gon; Lee, Jeong-Eun; Na, MinKyun; Kang, Wonku; Chae, Yee Soo; Park, Ji Young; Park, Ho-Yong; Baek, Moon Chang

doi:10.1007/s12272-012-1018-6

Cited by 38 publications

(32 citation statements)

References 29 publications

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“…Similar findings were reported by other research groups (Bini, et al 1997;Chahed, et al 2005;Kabbage, et al 2013;Song, et al 2012;Zamanian, et al 2016) that also observed high CALR expression in breast cancer samples compared to histologically normal tissues using proteomics analysis. CALR overexpression was also correlated with lymph node metastasis and with postoperative appearance of distant metastases in ERBB2 (Her2/neu) positive breast cancer (Eric, et al 2009).…”

Section: Breast Cancersupporting

confidence: 90%

CALR (calreticulin)

Machado-Neto¹,

Campos²,

Trainaen³

2018

Atlas of Genetics and Cytogenetics in Oncology and Haematology

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Calreticulin (CALR) is a multifunctional protein involved in molecular chaperoning and calcium homeostasis. CALR has also been associated with proliferation, cell cycle progression, migration, invasion and anoikis resistance in cancer cells. The prognostic impact of CALR expression is yet to be elucidated, however in some types of cancer, high CALR expression has been related to worse clinical outcomes. Notably, the discovery of recurrent mutations in the exon 9 of the CALR gene in myeloproliferative neoplasms has opened a new round of investigations. The present review contains data on CALR DNA/RNA, protein encoded and function.

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Section: Breast Cancersupporting

confidence: 90%

CALR (calreticulin)

Machado-Neto¹,

Campos²,

Trainaen³

2018

Atlas of Genetics and Cytogenetics in Oncology and Haematology

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“…The most widely accepted ECM extraction protocols involve differential tissue fractionation followed by solubilizing the remaining protein in a strong denaturing buffer; radioimmune precipitation assay buffer (Nonidet P-40, sodium deoxycholate and SDS) (10,29), SDS (23,24), guanidine-hydrochloride (11,25), or urea (21, 26 -28). Our pilot studies using these protocols resulted in relatively similar ECM protein profiles and uniformly yielded a protein-containing pellet after extraction.…”

Section: Resultsmentioning

confidence: 99%

“…Currently accepted and widely used digestion methods require proteins to be solubilized for bottom-up proteomic analysis (22). Recent papers have reported characterization of the ECM fraction from tissues through the use of strong chaotropes (11,21,(23)(24)(25)(26)(27) or cellular fractionation followed by strong detergent (10,28,29). However, in our experience, these protocols invariably yield various sizes of an insoluble protein-containing pellet when applied to a variety of tissue samples (heart, lung, and mammary gland).…”

mentioning

confidence: 99%

Quantification of Extracellular Matrix Proteins from a Rat Lung Scaffold to Provide a Molecular Readout for Tissue Engineering

Hill

Calle²,

Dzieciątkowska

et al. 2015

Molecular & Cellular Proteomics

140

156

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The use of extracellular matrix (ECM) 1 scaffolds, derived from decellularized tissues for engineered organ generation, holds enormous potential in the field of regenerative medicine. To support organ engineering efforts, we developed a targeted proteomics method to extract and quantify extracellular matrix components from tissues. Our method provides more complete and accurate protein characterization than traditional approaches. This is accomplished through the analysis of both the chaotropesoluble and -insoluble protein fractions and using recombinantly generated stable isotope labeled peptides for endogenous protein quantification. Using this approach, we have generated 74 peptides, representing 56 proteins to quantify protein in native (nondecellularized) and decellularized lung matrices. We have focused on proteins of the ECM and additional intracellular proteins that are challenging to remove during the decellularization procedure. Results indicate that the acellular lung scaffold is predominantly composed of structural collagens, with the majority of these proteins found in the insoluble ECM, a fraction that is often discarded using widely accepted proteomic methods. The decellularization procedure removes over 98% of intracellular proteins evaluated and retains, to varying degrees, proteoglycans and glycoproteins of the ECM. Accurate characterization of ECM proteins from tissue samples will help advance organ engineering efforts by generating a molecular readout that can be correlated with functional outcome to drive the next generation of engineered organs. Molecular & Cellular Proteomics

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“…Song and colleagues [30] published a proteomic comparison between normal and breast cancer tissues. Differentially expressed proteins in tumor tissues were related to glycolysis/gluconeogenesis among other pathways.…”

Section: Discussionmentioning

confidence: 99%

TP53 mutation hits energy metabolism and increases glycolysis in breast cancer

et al. 2016

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Promising new hallmarks of cancer is alteration of energy metabolism that involves molecular mechanisms shifting cancer cells to aerobe glycolysis. Our goal was to evaluate the correlation between mutation in the commonly mutated tumor suppressor gene TP53 and metabolism. We established a database comprising mutation and RNA-seq expression data of the TCGA repository and performed receiver operating characteristics (ROC) analysis to compare expression of each gene between TP53 mutated and wild type samples. All together 762 breast cancer samples were evaluated of which 215 had TP53 mutation. Top up-regulated metabolic genes include glycolytic enzymes (e.g. HK3, GPI, GAPDH, PGK1, ENO1), glycolysis regulator (PDK1) and pentose phosphate pathway enzymes (PGD, TKT, RPIA). Gluconeogenesis enzymes (G6PC3, FBP1) were down-regulated. Oxygen consumption and extracellular acidification rates were measured in TP53 wild type and mutant breast cell lines with a microfluorimetric analyzer. Applying metabolic inhibitors in the presence and absence of D-glucose and L-glutamine in cell culture experiments resulted in higher glycolytic and mitochondrial activity in TP53 mutant breast cancer cell lines. In summary, TP53 mutation influences energy metabolism at multiple levels. Our results provide evidence for the synergistic activation of multiple hallmarks linking to these the mutation status of a key driver gene.

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Proteomic analysis of breast cancer tissues to identify biomarker candidates by gel-assisted digestion and label-free quantification methods using LC-MS/MS

Cited by 38 publications

References 29 publications

CALR (calreticulin)

CALR (calreticulin)

Quantification of Extracellular Matrix Proteins from a Rat Lung Scaffold to Provide a Molecular Readout for Tissue Engineering

TP53 mutation hits energy metabolism and increases glycolysis in breast cancer

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