Discovery and Verification of Gelsolin as a Potential Biomarker of Colorectal Adenocarcinoma in a Chinese Population: Examining Differential Protein Expression using an Itraq Labelling-Based Proteomics Approach

Despite the wide range of available colorectal cancer (CRC) screening tests, less than 50% of cases are detected at early stages. However, the identification of differentially expressed proteins or novel protein biomarkers in CRC may have some utility and, ultimately, improve patient care and survival. Proteomics combined with mass spectroscopy and liquid chromatography are emerging as powerful tools that have led to the discovery of potential markers in cancer biomarker discovery in several types of cancers. This article describes a novel technology that uses isotopic reagents to tag selected proteins that show a consistent pattern of differential expression in CRC.OBJECTIVE: To identify and validate potential biomarkers of colorectal adenocarcinoma using a proteomic approach.METHODS: Multidimensional liquid chromatography/mass spectrometry was used to analyze biological samples labelled with isobaric mass tags for relative and absolute quantitation to identify differentially expressed proteins in human colorectal adenocarcinoma and paired normal mucosa for the discovery of cancerous biomarkers. Cancerous and noncancerous samples were compared using online and offline separation. Protein identification was performed using mass spectrometry. The downregulation of gelsolin protein in colorectal adenocarcinoma samples was confirmed by Western blot analysis and validated using immunohistochemistry.RESULTS: A total of 802 nonredundant proteins were identified in colorectal adenocarcinoma samples, 82 of which fell outside the expression range of 0.8 to 1.2, and were considered to be potential cancer-specific proteins. Immunohistochemistry revealed a complete absence of gelsolin expression in 86.89% of samples and a reduction of expression in 13.11% of samples, yielding a sensitivity of 86.89% and a specificity of 100% for distinguishing colorectal adenocarcinoma from normal tissue.CONCLUSIONS: These findings suggest that decreased expression of gelsolin is a potential biomarker of colorectal adenocarcinoma.

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Differential Proteomics Based on TMT and PRM Reveal the Resistance Response of Bambusa pervariabilis × Dendrocalamopisis grandis Induced by AP-Toxin

Metabolites ◽

10.3390/metabo9080166 ◽

2019 ◽

Vol 9 (8) ◽

pp. 166 ◽

Cited By ~ 2

Author(s):

Qianqian He ◽

Xinmei Fang ◽

Tianhui Zhu ◽

Shan Han ◽

Hanmingyue Zhu ◽

...

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Metabolic Pathways ◽

Differentially Expressed ◽

Tandem Mass ◽

Differentially Expressed Proteins ◽

Liquid Chromatography Mass Spectrometry ◽

Chromatography Mass Spectrometry ◽

Tandem Mass Tag ◽

Mass Tag

Bambusa pervariabilis McClure × Dendrocalamopsis grandis (Q.H.Dai & X.l.Tao ex Keng f.) Ohrnb. blight is a widespread and dangerous forest fungus disease, and has been listed as a supplementary object of forest phytosanitary measures. In order to study the control of B. pervariabilis × D. grandis blight, this experiment was carried out. In this work, a toxin purified from the pathogen Arthrinium phaeospermum (Corda) Elli, which causes blight in B. pervariabilis × D. grandis, with homologous heterogeneity, was used as an inducer to increase resistance to B. pervariabilis × D. grandis. A functional analysis of the differentially expressed proteins after induction using a tandem mass tag labeling technique was combined with mass spectrometry and liquid chromatography mass spectrometry in order to effectively screen for the proteins related to the resistance of B. pervariabilis × D. grandis to blight. After peptide labeling, a total of 3320 unique peptides and 1791 quantitative proteins were obtained by liquid chromatography mass spectrometry analysis. Annotation and enrichment analysis of these peptides and proteins using the Gene ontology and Kyoto Encyclopedia of Genes and Genomes databases with bioinformatics software show that the differentially expressed protein functional annotation items are mainly concentrated on biological processes and cell components. Several pathways that are prominent in the Kyoto Encyclopedia of Genes and Genomes annotation and enrichment include metabolic pathways, the citrate cycle, and phenylpropanoid biosynthesis. In the Protein-protein interaction networks four differentially expressed proteins-sucrose synthase, adenosine triphosphate-citrate synthase beta chain protein 1, peroxidase, and phenylalanine ammonia-lyase significantly interact with multiple proteins and significantly enrich metabolic pathways. To verify the results of tandem mass tag, the candidate proteins were further verified by parallel reaction monitoring, and the results were consistent with the tandem mass tag data analysis results. It is confirmed that the data obtained by tandem mass tag technology are reliable. Therefore, the differentially expressed proteins and signaling pathways discovered here is the primary concern for subsequent disease resistance studies.

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The proteomics analysis of the effects of Zhishi Rhubarb soup on ischaemic stroke

Proteome Science ◽

10.1186/s12953-021-00181-z ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Jing-Hua Zhang ◽

Yue-Jia Shao ◽

Zhen Hui ◽

Su-Lei Wang ◽

Chi Huang ◽

...

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Tissue Injury ◽

Health Care Systems ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

National Health Care ◽

Care Systems ◽

Heavy Burden ◽

The Difference

Abstract Background Stroke has always been a major threat worldwide but is most severe in China, with 2.5 million new stroke cases each year and 7.5 million stroke survivors, placing a heavy burden on the social and national health care systems. Zhishi Rhubarb Soup (ZRS) is a traditional Chinese medicine (TCM) that has been used clinically for many years in China. To explore the potential mechanism of ZRS in the treatment of stroke, liquid chromatography with mass spectrometry (LC–MS) was performed. Methods In this study, a quantitative proteomic method with LC–MS was used to analyse the proteomic differences between MACO samples treated with ZRS and those without ZRS treatment. Results Liquid chromatography with mass spectrometry (LC–MS) analysis led to the identification of 35,006 peptides, with 5160.0 proteins identified and 4094.0 quantified. Significantly differentially expressed proteins were identified through data analysis, and the difference was found to be more than 1.2 times (P < 0.05). The Gene Ontology (GO) analysis provided a summary of the dysregulated protein expression in the biological process (BP), cell component (CC), and molecular function (MF) categories. Proteins related to brain repair, including BDNF, IL-10, IL-6, and TGF-β, were found to change significantly, partially demonstrating the effectiveness of ZRS to attenuate tissue injury. Conclusion In this study, LC–MS/MS was performed to assess the effects of ZRS on differentially expressed proteins in rats with cerebral infarction. These promising results could help to improve the understanding of the effects of drugs on stroke.

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Differential Proteome Analysis of Hybrid Bamboo (Bambusa pervariabilis × Dendrocalamopsis grandis) Under Fungal Stress (Arthrinium phaeospermum)

Scientific Reports ◽

10.1038/s41598-019-55229-0 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Shujiang Li ◽

Xinmei Fang ◽

Shan Han ◽

Tianhui Zhu ◽

Hanmingyue Zhu

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Quantitative Analysis ◽

Proteome Analysis ◽

Enrichment Analysis ◽

Pathogenic Fungi ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Differential Proteins ◽

Arthrinium Phaeospermum

AbstractIn this study, TMT (tandem mass tag)-labeled quantitative protein technology combined with LC–MS/MS (liquid chromatography-mass spectrometry/mass spectrometry) was used to isolate and identify the proteins of the hybrid bamboo (Bambusa pervariabilis × Dendrocalamopsis grandis) and the bamboo inoculated with the pathogenic fungi Arthrinium phaeospermum. A total of 3320 unique peptide fragments were identified after inoculation with either A. phaeospermum or sterile water, and 1791 proteins were quantified. A total of 102 differentially expressed proteins were obtained, of which 66 differential proteins were upregulated and 36 downregulated in the treatment group. Annotation and enrichment analysis of these peptides and proteins using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases with bioinformatics software showed that the differentially expressed protein functional annotation items were mainly concentrated on biological processes and cell components. The LC–PRM/MS (liquid chromatography-parallel reaction monitoring/mass spectrometry) quantitative analysis technique was used to quantitatively analyze 11 differential candidate proteins obtained by TMT combined with LC–MS/MS. The up–down trend of 10 differential proteins in the PRM results was consistent with that of the TMT quantitative analysis. The coincidence rate of the two results was 91%, which confirmed the reliability of the proteomic results. Therefore, the differentially expressed proteins and signaling pathways discovered here may be the further concern for the bamboo-pathogen interaction studies.

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LC-hrms metabolomics profiling in breast cancer: Searching for biomarkers in human plasma samples.

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.e23053 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. e23053-e23053

Author(s):

Pedro Sánchez Rovira ◽

Ana Laura Ortega Granados ◽

Mónica Fernández Navarro ◽

María Ruiz Sanjuan ◽

Capilla de la Torre Cabrera ◽

...

Keyword(s):

Breast Cancer ◽

Mass Spectrometry ◽

Liquid Chromatography ◽

New Technologies ◽

Biomarker Discovery ◽

Environmental Changes ◽

Plasma Samples ◽

Diagnostic Biomarkers ◽

Wide Range ◽

Significant Difference

e23053 Background: Breast cancer (BC) is most common cancer in women and development of new technologies for understanding molecular changes involved in BC progression is essential. Metabolic changes precede phenotypic changes, due to cellular regulation affects use of small-molecule substrates for cell division, growth or environmental changes, such as hypoxia. Metabolomics (profiling of metabolites in biofluid, cell and tissue) is routinely applied as a tool for biomarker discovery. Liquid chromatography−mass spectrometry(LC−MS)is the dominating platform. Methods: With the aim to find metabolomic profiles for diagnostic and prognostic of newly diagnosticated breast cancer (BC) we have investigated plasma samples in neoadjuvant setting (134 BC patients with median age of 51 years, stages T1-4,N1-2,M0 and 135 healthy controls) using high resolution mass spectrometry couple to liquid chromatography in reverse phase and HILIC modes which provided resolved chromatography of highly polar as well as hydrophobic analytes, enabling the analysis of a wide range of chemicals, necessary for untargeted metabolomics. Chromatograms were processed with software (Markerview) to generate a table listing retention times with associated ion masses and intensities. To identify potential biomarkers, we used in combination 2 independent variable selection techniques: principal component analysis and Student t-test. Results: We observed a significant difference in metabolic profile between the 2 groups. 15 molecular features [oleamide, KDNalpha2-3Galbeta1-4Glcbeta-Cer(d18:1/22:0)] were found significantly down/up regulated in BC patients compared with healthy subjects, and they were selected as diagnostic biomarkers. Additionally, ROC curve analysis was used to assess their clinical usefulness, obtaining an AUC of 0.963 (95% CI 0.919-0.989) when using a multivariate model of 3 features. As an outcome, we showed that selected biomarkers are useful as diagnostic biomarkers. Conclusions: The present study demonstrates potential of metabolomics in identifying novel biomarkers for BC. Further studies may reveal the potential of metabolites as diagnostics biomarkers for BC and their role in pathogenesis.

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Identification and Verification of Two Novel Differentially Expressed Proteins from Non-neoplastic Mucosa and Colorectal Carcinoma Via iTRAQ Combined with Liquid Chromatography-Mass Spectrometry

Pathology & Oncology Research ◽

10.1007/s12253-019-00651-y ◽

2019 ◽

Vol 26 (2) ◽

pp. 967-976 ◽

Cited By ~ 1

Author(s):

Yuru Bai ◽

Jiabao Wang ◽

Zhihua Gao ◽

Erqing Dai

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Colorectal Carcinoma ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Liquid Chromatography Mass Spectrometry ◽

Chromatography Mass Spectrometry

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Mass spectrometry imaging for identification of differentially expressed proteins between colorectal adenocarcinoma and colon adenoma

World Chinese Journal of Digestology ◽

10.11569/wcjd.v21.i34.3806 ◽

2013 ◽

Vol 21 (34) ◽

pp. 3806

Author(s):

Tao He ◽

Yun Guo ◽

Xuan He ◽

Xiao Hu ◽

Ting-Ting Yu ◽

...

Keyword(s):

Mass Spectrometry ◽

Mass Spectrometry Imaging ◽

Colorectal Adenocarcinoma ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Colon Adenoma

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VDAC1 and RhoA in Plasma Exosomes Influence the Severity of Adolescent Idiopathic Scoliosis

10.21203/rs.3.rs-65485/v1 ◽

2020 ◽

Author(s):

Huizhen Li ◽

Nan Shen ◽

Lin Mao ◽

Meijia Chen ◽

Xuan Zhou ◽

...

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Adolescent Idiopathic Scoliosis ◽

Tandem Mass Spectrometry ◽

Idiopathic Scoliosis ◽

Differentially Expressed ◽

Tandem Mass ◽

Healthy Controls ◽

Differentially Expressed Proteins ◽

Differentially Expressed Protein

Abstract Background: Adolescent idiopathic scoliosis (AIS) is the most common spine deformity, but biomarkers for its condition are lacking. Rhodopsin A (RhoA) and voltage-dependent anion-selective channel 1 (VDAC1) in plasma exosomes were defined as differentially expressed proteins between AIS patients and healthy controls. The purpose of this study was to assess exosomes as biomarkers for the occurrence and progression of AIS. Methods：We recruited 10 AIS patients and 8 healthy controls to detect expressed proteins from plasma by liquid chromatography coupled to tandem mass spectrometry. Plasma samples were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Pathway analysis identified that the VDAC1 and RhoA proteins were alterations expressed in the AIS patients, with the most different alteration was found in extracellular exosomes. Ultracentrifugation was carried out to isolate exosomes from plasma. Verification of the most differentially expressed protein was accessed by Western blot analysis and bioinformatics analysis was performed to predict the pathway of it.Results: 42 of significantly differentially expressed proteins were found in all subjects, and 17 proteins had significant difference. The differentially expressed proteins were enriched in plasma exosomes, and some proteins, such as FN1, were upregulated and others, such as VDAC1, RhoA and AHNAK, were downregulated in the AIS patients. Furthermore, ultracentrifugation was carried out to isolate exosomes from plasma, and RhoA and VDAC1 proteins in plasma exosomes were verified to downregulate by western blot. KEGG signaling pathways were used to predict potential pathways involved in the RhoA and VDAC1 proteins in the AIS patients. We found that the RhoA protein influences AIS probably through the chemokine signaling pathway, platelet activation and cAMP signaling pathway, and the VDAC1 protein is a key factor that participates in the necroptosis pathway, acting on the development of AIS.Conclusions: Consequently, this study mapped a profile of plasma protein, found the differentially expressed protein in AIS, which indicating that plasma exosomes, as a novel biomarker with high specificity, could be associated with the severity of AIS.

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Developments in mycotoxin analysis: an update for 2012-2013

World Mycotoxin Journal ◽

10.3920/wmj2013.1637 ◽

2014 ◽

Vol 7 (1) ◽

pp. 3-33 ◽

Cited By ~ 52

Author(s):

F. Berthiller ◽

P.A. Burdaspal ◽

C. Crews ◽

M.H. Iha ◽

R. Krska ◽

...

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Sample Preparation ◽

Ergot Alkaloids ◽

Tandem Mass ◽

Wide Range ◽

Rapid Spread ◽

Food And Feed ◽

Mycotoxin Analysis ◽

The Individual

This review highlights developments in mycotoxin analysis and sampling over a period between mid-2012 and mid-2013. It covers the major mycotoxins: aflatoxins, Alternaria toxins, ergot alkaloids, fumonisins, ochratoxins, patulin, trichothecenes and zearalenone. A wide range of analytical methods for mycotoxin determination in food and feed were developed last year, in particular immunochemical methods and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)-based methods. After a section on sampling and sample preparation, due to the rapid spread and developments in the field of LC-MS/MS multimycotoxin methods, a separate section has been devoted to this area of research. It is followed by a section on mycotoxins in botanicals and spices, before continuing with the format of previous reviews in this series with dedicated sections on method developments for the individual mycotoxins.

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