Label-free peptide quantification coupled with in silico mapping of proteases for identification of potential serum biomarkers in gastric adenocarcinoma patients

Oliveira, Antonio Thomaz de; Lacerda, José Thalles Jocelino Gomes de; Leite, Giuseppe Gianini Figueirêdo; Dias, Mirella; Mendes, Maria Anita; Kassab, P; Silva, Clisleyd Glaucielly Sales e; Juliano, María A.; Forones, Nora Manoukian

doi:10.1016/j.clinbiochem.2020.02.010

Cited by 7 publications

(8 citation statements)

References 66 publications

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“…Protein fold changes (FC) of at least 1.5 were obtained, and P < 0.05 was considered a statistically significant difference. A FC < 1.5 represented upregulated proteins and a FC < 0.667 represented downregulated proteins; a FC between 0.667 and 1.5 indicated no obvious change in protein expression between the two groups ( Morrissey et al, 2013 ; Oliveira et al, 2020 ; Rawat et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics

Qin

et al. 2020

PeerJ

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Background Although asthma is one of the most common chronic, noncommunicable diseases worldwide, the pathogenesis of childhood asthma is not yet clear. Genetic factors and environmental factors may lead to airway immune-inflammation responses and an imbalance of airway nerve regulation. The aim of the present study was to determine which serum proteins are differentially expressed between children with or without asthma and to ascertain the potential roles that these differentially expressed proteins (DEPs) may play in the pathogenesis of childhood asthma. Methods Serum samples derived from four children with asthma and four children without asthma were collected. The DEPs were identified by using isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses. Using biological information technology, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Cluster of Orthologous Groups of Proteins (COG) databases and analyses, we determined the biological processes associated with these DEPs. Key protein glucose-6-phosphate dehydrogenase (G6PD) was verified by enzyme linked immunosorbent assay (ELISA). Results We found 46 DEPs in serum samples of children with asthma vs. children without asthma. Among these DEPs, 12 proteins were significantly (>1.5 fold change) upregulated and 34 proteins were downregulated. The results of GO analyses showed that the DEPs were mainly involved in binding, the immune system, or responding to stimuli or were part of a cellular anatomical entity. In the KEGG signaling pathway analysis, most of the downregulated DEPs were associated with cardiomyopathy, phagosomes, viral infections, and regulation of the actin cytoskeleton. The results of a COG analysis showed that the DEPs were primarily involved in signal transduction mechanisms and posttranslational modifications. These DEPs were associated with and may play important roles in the immune response, the inflammatory response, extracellular matrix degradation, and the nervous system. The downregulated of G6PD in the asthma group was confirmed using ELISA experiment. Conclusion After bioinformatics analyses, we found numerous DEPs that may play important roles in the pathogenesis of childhood asthma. Those proteins may be novel biomarkers of childhood asthma and may provide new clues for the early clinical diagnosis and treatment of childhood asthma.

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Section: Methodsmentioning

confidence: 99%

Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics

Qin

et al. 2020

PeerJ

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“…A number of serum peptidome studies have described distinctive FpA patterns associated to clinically-relevant outcomes; however, their biological significance in the blood of cancer patients is still debated. Although FpA-derived fragments were mainly found overexpressed in cancer patients [ 18 , 50 , 51 , 52 , 53 ], a downmodulation has also been associated with several cancer conditions [ 52 , 54 ]. In 2006 Villanueva et al published a study in which lower levels of FpA-derived fragments were found in serum from patients affected by prostate, bladder and breast cancer [ 12 ].…”

Section: Discussionmentioning

confidence: 99%

A Circulating Risk Score, Based on Combined Expression of Exo-miR-130a-3p and Fibrinopeptide A, as Predictive Biomarker of Relapse in Resectable Non-Small Cell Lung Cancer Patients

Marconi

Croce

Chiorino

et al. 2022

Cancers

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To date, the 5-year overall survival rate of 60% for early-stage non-small cell lung cancer (NSCLC) is still unsatisfactory. Therefore, reliable prognostic factors are needed. Growing evidence shows that cancer progression may depend on an interconnection between cancer cells and the surrounding tumor microenvironment; hence, circulating molecules may represent promising markers of cancer recurrence. In order to identify a prognostic score, we performed in-depth high-throughput analyses of plasma circulating markers, including exosomal microRNAs (Exo-miR) and peptides, in 67 radically resected NSCLCs. The miRnome profile selected the Exo-miR-130a-3p as the most overexpressed in relapsed patients. Peptidome analysis identified four progressively more degraded forms of fibrinopeptide A (FpA), which were depleted in progressing patients. Notably, stepwise Cox regression analysis selected Exo-miR-130a-3p and the greatest FpA (2-16) to build a score predictive of recurrence, where high-risk patients had 18 months of median disease-free survival. Moreover, in vitro transfections showed that higher levels of miR-130a-3p lead to a deregulation of pathways involved in metastasis and angiogenesis, including the coagulation process and metalloprotease increase which might be linked to FpA reduction. In conclusion, by integrating circulating markers, the identified risk score may help clinicians predict early-stage NSCLC patients who are more likely to relapse after primary surgery.

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“…The relative quantification levels of proteins in both replicates of experimental samples significantly different from control samples ( p values <0.05) and with fold changes (FCs) ≥1.5 were considered upregulated proteins, whereas those with FC ≤0.667 were considered downregulated proteins. A FC between 0.667 and 1.5 or with p > 0.05 indicated no change in protein expression between the two groups 16–18 …”

Section: Methodsmentioning

confidence: 99%

“…A FC between 0.667 and 1.5 or with p > 0.05 indicated no change in protein expression between the two groups. 16 , 17 , 18 …”

Section: Methodsmentioning

confidence: 99%

Biomarkers of connective tissue disease‐associated interstitial lung disease in bronchoalveolar lavage fluid: A label‐free mass spectrometry‐based relative quantification study

Liu

et al. 2022

Clinical Laboratory Analysis

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Background:The pathogenesis of connective tissue disease-associated interstitial lung disease (CTD-ILD) is unclear. This study aims to identify differentially expressed proteins (DEPs) in CTD-ILD to determine the potential role of these DEPs that may play in the pathogenesis of CTD-ILD and to offer potential therapeutic targets.Methods: Bronchoalveolar lavage fluid (BALF) samples were collected from four patients with CTD-ILD and four patients without CTD-ILD. Label-free mass spectrometrybased relative quantification was used to identify the DEPs. Bioinformatics were used to determine the potential biological processes and signaling pathways associated with these DEPs.

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Label-free peptide quantification coupled with in silico mapping of proteases for identification of potential serum biomarkers in gastric adenocarcinoma patients

Cited by 7 publications

References 66 publications

Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics

Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics

A Circulating Risk Score, Based on Combined Expression of Exo-miR-130a-3p and Fibrinopeptide A, as Predictive Biomarker of Relapse in Resectable Non-Small Cell Lung Cancer Patients

Biomarkers of connective tissue disease‐associated interstitial lung disease in bronchoalveolar lavage fluid: A label‐free mass spectrometry‐based relative quantification study

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