Identification of potential serum markers for nasopharyngeal carcinoma from a xenografted mouse model using Cy‐dye labeling combined with three‐dimensional fractionation

Wu, Chih‐Ching; Peng, Pei-Hua; Chang, Ya-Ting; Huang, Yunbo; Chang, Kai‐Ping; Hao, Sheng‐Po; Tsang, Ngan‐Ming; Yeh, Chau‐Ting; Chang, Yu‐Sun; Yu, Jau‐Song

doi:10.1002/pmic.200701034

Cited by 27 publications

(19 citation statements)

References 63 publications

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“…S2), and the SWATH results could pass the manual spectra inspection; 2) Wu et al . previously reported that CA2 was up-regulated in the serum of NPC xenograft mice29; and 3) the CA2’s diagnostic power had not been reported in the NPC field.…”

Section: Resultsmentioning

confidence: 97%

SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

Luo

Mok

Lin

et al. 2017

Sci Rep

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Nasopharyngeal carcinoma (NPC) is a serious threat to public health, and the biomarker discovery is of urgent needs. The data-independent mode (DIA) based sequential window acquisition of all theoretical fragment-ion spectra (SWATH) mass spectrometry (MS) has been proved to be precise in protein quantitation and efficient for cancer biomarker researches. In this study, we performed the first SWATH-MS analysis comparing the NPC and normal tissues. Spike-in stable isotope labeling by amino acids in cell culture (super-SILAC) MS was used as a shotgun reference. We identified and quantified 1414 proteins across all SWATH-MS analyses. We found that SWATH-MS had a unique feature to preferentially detect proteins with smaller molecular weights than either super-SILAC MS or human proteome background. With SWATH-MS, 29 significant differentially express proteins (DEPs) were identified. Among them, carbonic anhydrase 2 (CA2) was selected for further validation per novelty, MS quality and other supporting rationale. With the tissue microarray analysis, we found that CA2 had an AUC of 0.94 in differentiating NPC from normal tissue samples. In conclusion, SWATH-MS has unique features in proteome analysis, and it leads to the identification of CA2 as a potentially new diagnostic biomarker for NPC.

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Section: Resultsmentioning

confidence: 97%

SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

Luo

Mok

Lin

et al. 2017

Sci Rep

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“…Early indications were that parent ion intensities from MALDI analysis were in agreement with those of LC-ESI-MS (Griffin et al, 2001) and that parent and fragment ion intensities between separate runs of normal and diseased samples were consistent with Western blots or ELISA analysis of the same sample fractions (Marshall et al, 2003;Reynolds et al, 2003;Zhang et al, 2004;Malik et al, 2005;Yokoi et al, 2005;Yang et al, 2006;Haqqani et al, 2007;Morgan et al, 2007;Wilson et al, 2007;Barba de la Rosa et al, 2008;Gramolini et al, 2008;Hammerer-Lercher et al, 2008;Hao et al, 2008;Kolialexi et al, 2008;Kulasingam et al, 2008;Luque-Garcia et al, 2008;Marchi et al, 2008;Nicol et al, 2008;Plavina et al, 2008;Reichel, 2008;Xing et al, 2008;Wu et al, 2008a;Wang et al, 2008b;Zhao et al, 2008b;Domae et al, 2009;Fortin et al, 2009). Hence, where there is doubt regarding the best fit of the data, a second method such as accurate parent mass, targeted MS/MS, MRM, synthetic chromatography and spectrometry standards or immunological confirmation may be employed (Marshall et al, 2003;Zhang et al, 2004;Malik et al, 2005;Yokoi et al, 2005;Gao et al, 2005a;Haqqani et al, 2007;Plavina et al, 2007;Sardana,...…”

Section: Agreement Between Biochemical and Mass Spectral Methodsmentioning

confidence: 92%

“…Allelic variation may also be established with electrophoresis (Csaszar et al, 2001). The combination of column or other pre-fractionations prior to SDS-PAGE remains a popular approach (Wu et al, 2008a) that may yield thousands of proteins (Sennels et al, 2007). Electrophoresis of intact proteins after depletion and multi-dimensional separation permitted the detection of low abundance proteins from serum .…”

Section: E One-dimensional Poly Acrylamide Gel Electrophoresis (1d Pmentioning

confidence: 99%

“…A large number of protein isoforms in serum, or EDTA versus citrated plasma, were detected by fluorescent labeling prior to separation of the intact proteins by charge, hydrophobic character and molecular mass (Misek et al, 2005). A strategy of cyan dye labeling, chromatographic separation and 1D PAGE prior to LC-MS/MS identified potential serum markers for nasopharyngeal carcinoma (Wu et al, 2008a). A method for electric transfer of analytes from the one-dimensional gel electrophoresis (1-DE) gel to a MALDI target plate has been developed .…”

Section: E One-dimensional Poly Acrylamide Gel Electrophoresis (1d Pmentioning

confidence: 99%

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Mass spectrometry of peptides and proteins from human blood

Zhu

Bowden

Zhang

et al. 2010

Mass Spectrometry Reviews

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It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

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“…However, the progress of these studies has been hampered by the complex nature of serum/plasma samples and the large dynamic range between the concentrations of different proteins (14). As cancer biomarkers are likely to be present in low amounts in blood samples, the direct isolation of these markers from plasma and serum samples requires a labor-intensive process involving the depletion of abundant proteins and extensive protein fractionation prior to mass spectrometric analysis (15)(16)(17)(18). Alternatively, the secretome, or group of proteins secreted by cancer cells (19), can be analyzed to identify circulating molecules present at elevated levels in serum or plasma samples from cancer patients.…”

mentioning

confidence: 99%

Candidate Serological Biomarkers for Cancer Identified from the Secretomes of 23 Cancer Cell Lines and the Human Protein Atlas

Hsu

Chen

et al. 2010

Molecular & Cellular Proteomics

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183

204

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Although cancer cell secretome profiling is a promising strategy used to identify potential body fluid-accessible cancer biomarkers, questions remain regarding the depth to which the cancer cell secretome can be mined and the efficiency with which researchers can select useful candidates from the growing list of identified proteins. Therefore, we analyzed the secretomes of 23 human cancer cell lines derived from 11 cancer types using one-dimensional SDS-PAGE and nano-LC-MS/MS performed on an LTQ-Orbitrap mass spectrometer to generate a more comprehensive cancer cell secretome. A total of 31,180 proteins was detected, accounting for 4,584 non-redundant proteins, with an average of 1,300 proteins identified per cell line. Using protein secretionpredictive algorithms, 55.8% of the proteins appeared to be released or shed from cells. The identified proteins were selected as potential marker candidates according to three strategies: (i) proteins apparently secreted by one cancer type but not by others (cancer type-specific marker candidates), (ii) proteins released by most cancer cell lines (pan-cancer marker candidates), and (iii) proteins putatively linked to cancer-relevant pathways. We then examined protein expression profiles in the Human Protein Atlas to identify biomarker candidates that were simultaneously detected in the secretomes and highly expressed in cancer tissues. This analysis yielded 6 -137 marker candidates selective for each tumor type and 94 potential pan-cancer markers. Among these, we selectively validated monocyte differentiation antigen CD14 (for liver cancer), stromal cell-derived factor 1 (for lung cancer), and cathepsin L1 and interferon-induced 17-kDa protein (for nasopharyngeal carcinoma) as potential serological cancer markers. In summary, the proteins identified from the secretomes of 23 cancer cell lines and the Hu-

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Identification of potential serum markers for nasopharyngeal carcinoma from a xenografted mouse model using Cy‐dye labeling combined with three‐dimensional fractionation

Cited by 27 publications

References 63 publications

SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

Mass spectrometry of peptides and proteins from human blood

Candidate Serological Biomarkers for Cancer Identified from the Secretomes of 23 Cancer Cell Lines and the Human Protein Atlas

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