Comparative serum proteome analysis reveals potential early pregnancy-specific protein biomarkers in pigs

2019 ◽  
Vol 31 (3) ◽  
pp. 613 ◽  
Author(s):  
Ankan De ◽  
Mohammad Ayub Ali ◽  
Tukheswar Chutia ◽  
Suneel Kumar Onteru ◽  
Parthasarathi Behera ◽  
...  
Keyword(s):  
Early Pregnancy ◽  
Inflammatory Responses ◽  
Proteome Analysis ◽  
Specific Protein ◽  
Protein Profiling ◽  
Differentially Expressed ◽  
Label Free ◽  
Protein Biomarkers ◽  
Serum Proteome ◽  
Pregnancy Zone Protein

In this study, the comparative serum proteome profile of Day 5, 12 and 16 of gestation, representing three early embryonic events, namely formation, elongation and implantation of blastocysts, and non-pregnant control were explored by a label-free quantitation-based mass spectrometric approach to identify early pregnancy biomarkers in pigs. A total of 131 proteins were identified with respect to different groups, out of which 105 were found to be differentially expressed proteins (DEPs). Among the DEPs, 54 and 66 proteins were found to be up and downregulated respectively in early pregnancy groups (fold change >2) and the maximum number of upregulated proteins was observed in the Day 12 pregnancy stage. Functional classification and pathway analysis of the DEPs revealed involvement of most of the proteins in complement and coagulation cascades, metabolic processes and immune and inflammatory responses. Proteins such as glutathione peroxidise (GPX), pregnancy zone protein (PZP), thrombospondin-1 (THBS1), α-1-antitrypsin (AAT) and mannose-binding lectin C (MBLC) were differentially expressed during early pregnancy and actively involved in different pregnancy-related activities. To the best of our knowledge, this is the first report on comparative serum protein profiling of different early pregnancy stages in pigs and our results provide a set of proteins that can be used as potential biomarkers for early pregnancy diagnosis in pigs.

Label-Free Mass Spectrometry-Based Plasma Proteomics Identified LY6D, DSC3, CDSN, SERPINB12, and SLURP1,as Novel Protein Biomarkers For Pulmonary Tuberculosis

2019 ◽  
Vol 17 ◽  
Author(s):  
Xiaoli Yu ◽  
Lu Zhang ◽  
Na Li ◽  
Peng Hu ◽  
Zhaoqin Zhu ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Search Algorithm ◽  
Differentially Expressed ◽  
P Value ◽  
Plasma Samples ◽  
Label Free ◽  
Protein Biomarkers ◽  
Protein Database ◽  
Leave One Out ◽  
Potential Biomarkers

Aim: We aimed to identify new plasma biomarkers for the diagnosis of Pulmonary tuberculosis. Background: Tuberculosis is an ancient infectious disease that remains one of the major global health problems. Until now, effective, convenient, and affordable methods for diagnosis of Pulmonary tuberculosis were still lacked. Objective: This study focused on construct a label-free LC-MS/MS based comparative proteomics between six tuberculosis patients and six healthy controls to identify differentially expressed proteins (DEPs) in plasma. Method: To reduce the influences of high-abundant proteins, albumin and globulin were removed from plasma samples using affinity gels. Then DEPs from the plasma samples were identified using a label-free Quadrupole-Orbitrap LC-MS/MS system. The results were analyzed by the protein database search algorithm SEQUEST-HT to identify mass spectra to peptides. The predictive abilities of combinations of host markers were investigated by general discriminant analysis (GDA), with leave-one-out cross-validation. Results: A total of 572 proteins were identified and 549 proteins were quantified. The threshold for differentially expressed protein was set as adjusted p-value < 0.05 and fold change ≥1.5 or ≤0.6667, 32 DEPs were found. ClusterVis, TBtools, and STRING were used to find new potential biomarkers of PTB. Six proteins, LY6D, DSC3, CDSN, FABP5, SERPINB12, and SLURP1, which performed well in the LOOCV method validation, were termed as potential biomarkers. The percentage of cross-validated grouped cases correctly classified and original grouped cases correctly classified is greater than or equal to 91.7%. Conclusion: We successfully identified five candidate biomarkers for immunodiagnosis of PTB in plasma, LY6D, DSC3, CDSN, SERPINB12, and SLURP1. Our work supported this group of proteins as potential biomarkers for pulmonary tuberculosis, and be worthy of further validation.

scholarly journals Label-Free Proteome Analysis of Plasma from Patients with Breast Cancer: Stage-Specific Protein Expression

2017 ◽  
Vol 7 ◽  
Author(s):  
Marina Duarte Pinto Lobo ◽  
Frederico Bruno Mendes Batista Moreno ◽  
Gustavo Henrique Martins Ferreira Souza ◽  
Sara Maria Moreira Lima Verde ◽  
Renato de Azevedo Moreira ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Protein Expression ◽  
Proteome Analysis ◽  
Specific Protein ◽  
Cancer Stage ◽  
Label Free

scholarly journals Label-Free Quantitative Mass Spectrometry Reveals a Panel of Differentially Expressed Proteins in Colorectal Cancer

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Nai-Jun Fan ◽  
Jiang-Ling Gao ◽  
Yan Liu ◽  
Wei Song ◽  
Zhan-Yang Zhang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Performance ◽  
Cell Structure ◽  
Protein Profiling ◽  
Differentially Expressed ◽  
Antimicrobial Protein ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Mucosal Tissues ◽  
And Function

To identify potential biomarkers involved in CRC, a shotgun proteomic method was applied to identify soluble proteins in three CRCs and matched normal mucosal tissues using high-performance liquid chromatography and mass spectrometry. Label-free protein profiling of three CRCs and matched normal mucosal tissues were then conducted to quantify and compare proteins. Results showed that 67 of the 784 identified proteins were linked to CRC (28 upregulated and 39 downregulated). Gene Ontology and DAVID databases were searched to identify the location and function of differential proteins that were related to the biological processes of binding, cell structure, signal transduction, cell adhesion, and so on. Among the differentially expressed proteins, tropomyosin-3 (TPM3), endoplasmic reticulum resident protein 29 (ERp29), 18 kDa cationic antimicrobial protein (CAMP), and heat shock 70 kDa protein 8 (HSPA8) were verified to be upregulated in CRC tissue and seven cell lines through western blot analysis. Furthermore, the upregulation of TPM3, ERp29, CAMP, and HSPA8 was validated in 69 CRCs byimmunohistochemistry (IHC) analysis. Combination of TPM3, ERp29, CAMP, and HSPA8 can identify CRC from matched normal mucosal achieving an accuracy of 73.2% using IHC score. These results suggest that TPM3, ERp29, CAMP, and HSPA8 are great potential IHC diagnostic biomarkers for CRC.

Mass Spectrometry-Based Proteomics: From Cancer Biology to Protein Biomarkers, Drug Targets, and Clinical Applications

2014 ◽  
pp. e504-e510 ◽  
Author(s):  
Connie R. Jimenez ◽  
Henk M. W. Verheul
Keyword(s):  
Mass Spectrometry ◽  
Cancer Biology ◽  
Drug Targets ◽  
Large Scale ◽  
Specific Protein ◽  
Protein Profiling ◽  
Clinical Samples ◽  
Post Translational Modification ◽  
Protein Biomarkers ◽  
Mass Spectrometry Technology

Proteomics is optimally suited to bridge the gap between genomic information on the one hand and biologic functions and disease phenotypes at the other, since it studies the expression and/or post-translational modification (especially phosphorylation) of proteins—the major cellular players bringing about cellular functions—at a global level in biologic specimens. Mass spectrometry technology and (bio)informatic tools have matured to the extent that they can provide high-throughput, comprehensive, and quantitative protein inventories of cells, tissues, and biofluids in clinical samples at low level. In this article, we focus on next-generation proteomics employing nanoliquid chromatography coupled to high-resolution tandem mass spectrometry for in-depth (phospho)protein profiling of tumor tissues and (proximal) biofluids, with a focus on studies employing clinical material. In addition, we highlight emerging proteogenomic approaches for the identification of tumor-specific protein variants, and targeted multiplex mass spectrometry strategies for large-scale biomarker validation. Below we provide a discussion of recent progress, some research highlights, and challenges that remain for clinical translation of proteomic discoveries.

scholarly journals Comparative Proteomic Analysis of Walnut (Juglans regia L.) Pellicle Tissues Reveals the Regulation of Nut Quality Attributes

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 314
Author(s):  
Paulo A. Zaini ◽  
Noah G. Feinberg ◽  
Filipa S. Grilo ◽  
Houston J. Saxe ◽  
Michelle R. Salemi ◽  
...  
Keyword(s):  
Juglans Regia ◽  
Proteome Analysis ◽  
Specific Protein ◽  
Proteomics Data ◽  
Protein Biomarkers ◽  
Early Maturity ◽  
Major Producer ◽  
Light Color ◽  
Developmental Responses ◽  
Related Proteins

Walnuts (Juglans regia L.) are a valuable dietary source of polyphenols and lipids, with increasing worldwide consumption. California is a major producer, with ’Chandler’ and ’Tulare’ among the cultivars more widely grown. ’Chandler’ produces kernels with extra light color at a higher frequency than other cultivars, gaining preference by growers and consumers. Here we performed a deep comparative proteome analysis of kernel pellicle tissue from these two valued genotypes at three harvest maturities, detecting a total of 4937 J. regia proteins. Late and early maturity stages were compared for each cultivar, revealing many developmental responses common or specific for each cultivar. Top protein biomarkers for each developmental stage were also selected based on larger fold-change differences and lower variance among replicates, including proteins for biosynthesis of lipids and phenols, defense-related proteins and desiccation stress-related proteins. Comparison between the genotypes also revealed the common and specific protein repertoires, totaling 321 pellicle proteins with differential abundance at harvest stage. The proteomics data provides clues on antioxidant, secondary, and hormonal metabolism that could be involved in the loss of quality in the pellicles during processing for commercialization.

scholarly journals Mass-Spectrometry Based Proteome Comparison of Extracellular Vesicle Isolation Methods: Comparison of ME-kit, Size-Exclusion Chromatography, and High-Speed Centrifugation

Biomedicines ◽  
2020 ◽  
Vol 8 (8) ◽  
pp. 246 ◽  
Author(s):  
Anders Askeland ◽  
Anne Borup ◽  
Ole Østergaard ◽  
Jesper V. Olsen ◽  
Sigrid M. Lund ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Size Exclusion Chromatography ◽  
High Speed ◽  
Proteome Analysis ◽  
Extracellular Vesicle ◽  
Size Exclusion ◽  
Label Free ◽  
Protein Biomarkers ◽  
Transmission Electron ◽  
Exclusion Chromatography

Extracellular vesicles (EVs) are small membrane-enclosed particles released by cells under various conditions specific to cells’ biological states. Hence, mass-spectrometry (MS) based proteome analysis of EVs in plasma has gained much attention as a method to discover novel protein biomarkers. MS analysis of EVs in plasma is challenging and EV isolation is usually necessary. Therefore, we compared differences in abundance, subtypes, and contamination for EVs isolated by high-speed centrifugation, size exclusion chromatography (SEC), and peptide-affinity precipitation (PAP/ME kit) for subsequent MS-based proteome analysis. Successful EV isolation was evaluated by nanoparticle-tracking analysis, immunoblotting, and transmission electron microscopy, while EV abundance, EV subtypes, and contamination was evaluated by label-free tandem MS. High-speed centrifugation and SEC isolates showed high EV abundance at the expense of contamination by non-EV proteins and lipoproteins, respectively. These two methods also resulted in EVs of a similar type, however, with smaller EVs in SEC isolates. PAP isolates had a relatively low EV abundance and high contamination. We consider high-speed centrifugation and SEC suitable as EV isolation for MS biomarker studies, where the choice between the two should depend on the scientific questions and whether the focus is on larger or smaller EVs or a combination of both.

Nanomonitors: Nanomaterial Based Devices Towards Clinical Immunoassays

2008 ◽  
Vol 1095 ◽  
Author(s):  
Shalini Prasad ◽  
Manish Bothara ◽  
Ravikiran Reddy ◽  
John Carruthers ◽  
Thomas Barrett
Keyword(s):  
Specific Protein ◽  
Solid Substrate ◽  
Optical Methods ◽  
Signal Acquisition ◽  
Label Free ◽  
Electrical Detection ◽  
Protein Biomarkers ◽  
Accurate Identification ◽  
Non Invasive ◽  
Diagnostic Applications

AbstractThe immobilization of biomolecules on a solid substrate and their localization in “small” regions are major requirements for a variety of biomedical diagnostic applications, where rapid and accurate identification of multiple biomolecules is essential. In this specific application we have fabricated nanomitors for identifying specific protein biomarkers based on the electrical detection of antibody-antigen binding events.The nanomonitor, lab-on-a-chip device technology is based on electrical detection of protein biomarkers. It is based on developing high density, low volume multi-well plate devices. The scientific core of this technology lies in integrating nanomaterial with micro fabricated chip platforms and exploiting the improve surface area to volume to improve the detection.The devices that have been developed utilize electrical detection mechanisms where capacitance and conductance changes due to protein binding are used as “signatures” for biomarker profiling. In comparison to optical methods, the electrical detection technique is non-invasive as well as a label free. The signal acquisition is simple and it uses the existing data acquisition and signal analysis methods

scholarly journals Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hongcheng Fang ◽  
Xia Liu ◽  
Yuhui Dong ◽  
Shan Feng ◽  
Rui Zhou ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Gene Networks ◽  
Colletotrichum Gloeosporioides ◽  
Early Stage ◽  
Juglans Regia ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Molecular Response ◽  
Label Free ◽  
Underlying Mechanisms

Abstract Background Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease affecting walnut production. The resistance of walnut fruit to C. gloeosporioides is a highly complicated and genetically programmed process. However, the underlying mechanisms have not yet been elucidated. Results To understand the molecular mechanism underlying the defense of walnut to C. gloeosporioides, we used RNA sequencing and label-free quantitation technologies to generate transcriptomic and proteomic profiles of tissues at various lifestyle transitions of C. gloeosporioides, including 0 hpi, pathological tissues at 24 hpi, 48 hpi, and 72 hpi, and distal uninoculated tissues at 120 hpi, in anthracnose-resistant F26 fruit bracts and anthracnose-susceptible F423 fruit bracts, which were defined through scanning electron microscopy. A total of 21,798 differentially expressed genes (DEGs) and 1929 differentially expressed proteins (DEPs) were identified in F26 vs. F423 at five time points, and the numbers of DEGs and DEPs were significantly higher in the early infection stage. Using pairwise comparisons and weighted gene co-expression network analysis of the transcriptome, we identified two modules significantly related to disease resistance and nine hub genes in the transcription expression gene networks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of the DEGs and DEPs revealed that many genes were mainly related to immune response, plant hormone signal transduction, and secondary metabolites, and many DEPs were involved in carbon metabolism and photosynthesis. Correlation analysis between the transcriptome data and proteome data also showed that the consistency of the differential expression of the mRNA and corresponding proteins was relatively higher in the early stage of infection. Conclusions Collectively, these results help elucidate the molecular response of walnut fruit to C. gloeosporioides and provide a basis for the genetic improvement of walnut disease resistance.

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