scholarly journals Glycoproteomic Analysis Reveals Aberrant Expression of Complement C9 and Fibronectin in the Plasma of Patients with Colorectal Cancer

Proteomes ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 26
Author(s):  
Juthamard Chantaraamporn ◽  
Voraratt Champattanachai ◽  
Amnart Khongmanee ◽  
Chris Verathamjamras ◽  
Naiyarat Prasongsook ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Interaction Analysis ◽  
Study Cohort ◽  
Healthy Controls ◽  
Label Free ◽  
Aberrant Expression ◽  
Protein Protein Interaction ◽  
Acetylneuraminic Acid ◽  
Novel Biomarkers ◽  
Complement C9

Colorectal cancer (CRC) is a major cause of cancer mortality. Currently used CRC biomarkers provide insufficient sensitivity and specificity; therefore, novel biomarkers are needed to improve the CRC detection. Label-free quantitative proteomics were used to identify and compare glycoproteins, enriched by wheat germ agglutinin, from plasma of CRC patients and age-matched healthy controls. Among 189 identified glycoproteins, the levels of 7 and 15 glycoproteins were significantly altered in the non-metastatic and metastatic CRC groups, respectively. Protein-protein interaction analysis revealed that they were predominantly involved in immune responses, complement pathways, wound healing and coagulation. Of these, the levels of complement C9 (C9) was increased and fibronectin (FN1) was decreased in both CRC states in comparison to those of the healthy controls. Moreover, their levels detected by immunoblotting were validated in another independent cohort and the results were consistent with in the study cohort. Combination of CEA, a commercial CRC biomarker, with C9 and FN1 showed better diagnostic performance. Interestingly, predominant glycoforms associated with acetylneuraminic acid were obviously detected in alpha-2 macroglobulin, haptoglobin, alpha-1-acid glycoprotein 1, and complement C4-A of CRC patient groups. This glycoproteomic approach provides invaluable information of plasma proteome profiles of CRC patients and identification of CRC biomarker candidates.

Quantitative proteomics analysis of FFPE tumor samples reveals the influences of novel targeting nanobubbles conjugated with NET-1 siRNA on tetraspanin protein involved in HCC

2020 ◽  
Author(s):  
Bolin Wu ◽  
Haitao Shang ◽  
Xitian Liang ◽  
Huajing Yang Huajing Yang ◽  
Hui Jing ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Interaction Analysis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Protein Protein Interaction ◽  
Study Results ◽  
Ffpe Tumor

Abstract Background: Hepatocellular carcinoma (HCC) poses a severe threat to human health. The NET-1 protein has been proved to be strongly associated with HCC proliferation and metastasis in our previous study. Methods: Here, we developed a label-free proteome mass spectrometry workflow to analyze formalin-fixed and paraffin-embedded HCC xenograft samples collected in our previous study. Results: The result showed that 78 proteins were differentially expressed after NET-1 protein inhibited. Among them, the expression of 61 proteins up-regulated and the expression of 17 proteins were significantly down-regulated. Of the differentially expressed proteins, the vast majority of Gene Ontology enrichment terms belong to the biological process. The KEGG pathway enrichment analysis showed that the 78 differentially expressed proteins significantly enriched in 45 pathways. We concluded that the function of the NET-1 gene is not only to regulate HCC but also to participate in a variety of biochemical metabolic pathways in the human body. Furthermore, the protein-protein interaction analysis indicated that the interactions of differentially expressed proteins are incredibly sophisticated. All the protein-protein interactions happened after the NET-1 gene has been silenced. Conclusions: Finally, our study also provides a useful proposal for targeted therapy based on tetraspanin proteins to treat HCC, and further mechanism investigations are needed to reveal a more detailed mechanism of action for NET-1 protein regulation of HCC.

scholarly journals Untargeted LC-HRMS-based metabolomics to identify novel biomarkers of metastatic colorectal cancer

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ariadna Martín-Blázquez ◽  
Caridad Díaz ◽  
Encarnación González-Flores ◽  
Daniel Franco-Rivas ◽  
Cristina Jiménez-Luna ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
High Resolution ◽  
Metastatic Colorectal Cancer ◽  
High Resolution Mass Spectrometry ◽  
Healthy Controls ◽  
High Resolution Mass ◽  
Novel Biomarkers ◽  
Resolution Mass

AbstractColorectal cancer is one of the main causes of cancer death worldwide, and novel biomarkers are urgently needed for its early diagnosis and treatment. The utilization of metabolomics to identify and quantify metabolites in body fluids may allow the detection of changes in their concentrations that could serve as diagnostic markers for colorectal cancer and may also represent new therapeutic targets. Metabolomics generates a pathophysiological ‘fingerprint’ that is unique to each individual. The purpose of our study was to identify a differential metabolomic signature for metastatic colorectal cancer. Serum samples from 60 healthy controls and 65 patients with metastatic colorectal cancer were studied by liquid chromatography coupled to high-resolution mass spectrometry in an untargeted metabolomic approach. Multivariate analysis revealed a separation between patients with metastatic colorectal cancer and healthy controls, who significantly differed in serum concentrations of one endocannabinoid, two glycerophospholipids, and two sphingolipids. These findings demonstrate that metabolomics using liquid-chromatography coupled to high-resolution mass spectrometry offers a potent diagnostic tool for metastatic colorectal cancer.

A New MicroRNA Expression Signature for Cervical Cancer

2017 ◽  
Vol 27 (2) ◽  
pp. 339-343 ◽  
Author(s):  
Ping Sun ◽  
Yong Shen ◽  
Jiao-Mei Gong ◽  
Li-Li Zhou ◽  
Jia-He Sheng ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Intraepithelial Neoplasia ◽  
Lymph Node Involvement ◽  
Healthy Controls ◽  
Aberrant Expression ◽  
Gynecology And Obstetrics ◽  
Significant Difference ◽  
Node Involvement ◽  
Novel Biomarkers ◽  
Cancer Tissues

BackgroundCervical cancer is the second most common cancer among women worldwide. The potential of microRNAs as novel biomarkers in cervical cancer is growing.ObjectivesIn this study, we investigated the functions and targets of miR-466 in cervical cancer tissues.MethodsFresh cervical tissues were obtained from 157 patients with cervical cancer, cervical intraepithelial neoplasia (CIN), and healthy controls, and the tissues were immediately frozen in liquid nitrogen until use. The RNA was extracted and quantitative real-time polymerase chain reaction (PCR) was performed.ResultsA total of 157 participants were summarized, including 56 patients with cervical cancer, 60 patients with CIN, and 49 healthy controls. The expression levels of miR-466 in cervical cancers (0.68) were higher than that in healthy controls (0.082) (P < 0.01). The average fold changes of miR-466 in the patients with CIN group and people group were 0.28 and 0.082, respectively (P < 0.01). It was a statistically significant difference in patients with lymph node involvement (P = 0.022). However, the expression of miR-466 was not correlated with International Federation of Gynecology and Obstetrics stages, tumor size, or vascular invasion (P = 0.506, P = 0.667, and P = 0.108, respectively).ConclusionsOur results indicate that the aberrant expression of miR-466 is closely associated with the occurrence and development of cervical cancer.

scholarly journals MiR-574-5P, miR-1827, And miR-4429 As Potential Biomarkers For Schizophrenia

2021 ◽  
Author(s):  
Omran Davarinejad ◽  
Sajad Najafi ◽  
Hossein Zhaleh ◽  
Farzaneh Golmohammadi ◽  
Farnaz Radmehr ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Meta Analysis ◽  
Interaction Network ◽  
Receiver Operating Curve ◽  
Healthy Controls ◽  
Protein Protein Interaction ◽  
Mirna Array ◽  
Expression Arrays ◽  
Limma Package ◽  
Novel Biomarkers

Abstract Schizophrenia is a severe chronic debilitating disorder with millions of affected individuals. Lack of a reliable mollecular diagnostic invokes the identification of novel biomarkers. To elucidate the molecular basis of the disease, two mRNA expression arrays including GSE93987 and GSE38485, and one miRNA array, GSE54914, were downloaded from GEO, and meta-analysis was performed for mRNA expression arrays by employment of metaDE package. By WGCNA package, we performed network analysis for both mRNA expression arrays separately. Then, we made protein-protein interaction network for significant modules. Limma package was employed to analyze the miRNA array and dysregulated miRNAs (DEMs) were identified. Using genes of significant modules and DEMs, a mRNA-miRNA network was constructed and hub genes and miRNAs were identified. To confirm the dysregulation of genes, expression values were evaluated by available datasets including GEO series GSE62333, GSE93987, and GSE38485. The ability of the detected hub miRNAs to discriminate Schizophrenia from healthy controls was evaluated by assessing the receiver-operating curve. Finally, by performing Real-Time PCR, the expression level of genes and miRNAs were evaluated in 40 Schizophrenia patients compared with healthy controls. The results confirmed dysregulation of hsa-miR-574-5P, hsa-miR-1827, hsa-miR-4429, CREBRF, ARPP19, TGFBR2, and YWHAZ in blood samples of schizophrenia patients.

scholarly journals Circulating proteomic patterns in AF related left atrial remodeling indicate involvement of coagulation and complement cascade

2018 ◽  
Author(s):  
Jelena Kornej ◽  
Petra Büttner ◽  
Elke Hammer ◽  
Beatrice Engelmann ◽  
Borislav Dinov ◽  
...  
Keyword(s):  
Disease Progression ◽  
Left Atrial ◽  
Low Voltage ◽  
Interaction Analysis ◽  
Proteome Analysis ◽  
Atrial Remodeling ◽  
Complement Cascade ◽  
Label Free ◽  
Therapeutic Success ◽  
Protein Protein Interaction

AbstractBackgroundLeft atrial (LA) electro-anatomical remodeling and diameter increase in atrial fibrillation (AF) indicates disease progression and is associated with poor therapeutic success. Furthermore, AF leads to a hypercoagulable state, which in turn promotes the development of a substrate for AF and disease progression in the experimental setting. The aim of this study was to identify pathways associated with LA remodeling in AF patients using untargeted proteomics approach.MethodsPeripheral blood samples of 48 patients (62±10 years, 63% males, 59% persistent AF) undergoing AF catheter ablation were collected before ablation. 24 patients with left atrial low voltage areas (LVA), defined as <0.5 mV, and 24 patients without LVA were matched for age, gender and CHA2DS2-VASc score. Untargeted proteome analysis was performed using LC-ESI-Tandem mass spectrometry in a label free intensity based workflow. Significantly different abundant proteins were identified and used for pathway analysis and protein-protein interaction analysis.ResultsAnalysis covered 280 non-redundant circulating plasma proteins. The presence of LVA correlated with 30 differentially abundant proteins of coagulation and complement cascade (q<0.05).ConclusionsThis pilot proteomic study identified plasma protein candidates associated with electro-anatomical remodeling in AF and pointed towards an imbalance in coagulation and complement pathway, tissue remodeling and inflammation

scholarly journals Identification of Hub Genes Associated With Sensitivity of 5-Fluorouracil Based Chemotherapy for Colorectal Cancer by Integrated Bioinformatics Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Ya Wang ◽  
Qunhui Wei ◽  
Yuqiao Chen ◽  
Shichao Long ◽  
Yuanbing Yao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Colorectal Adenocarcinoma ◽  
Malignant Tumors ◽  
Gene Expression Omnibus ◽  
Chemotherapy Response ◽  
Intrinsic Resistance ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Novel Biomarkers

Colorectal cancer (CRC) is one of the most common malignant tumors. 5-fluorouracil (5-FU) has been used for the standard first-line treatment for CRC patients for several decades. Although 5-FU based chemotherapy has increased overall survival (OS) of CRC patients, the resistance of CRC to 5-FU based chemotherapy is the principal cause for treatment failure. Thus, identifying novel biomarkers to predict response to 5-FU based chemotherapy is urgently needed. In the present study, the gene expression profile of GSE3964 from the Gene Expression Omnibus database was used to explore the potential genes related to intrinsic resistance to 5-FU. A gene module containing 81 genes was found to have the highest correlation with chemotherapy response using Weighted Gene Co-expression Network Analysis (WGCNA). Then a protein-protein interaction (PPI) network was constructed and ten hub genes (TGFBI, NID, LEPREL2, COL11A1, CYR61, PCOLCE, IGFBP7, COL4A2, CSPG2, and VTN) were identified using the CytoHubba plugin of Cytoscape. Seven of these hub genes showed significant differences in expression between chemotherapy-sensitive and chemotherapy-resistant samples. The prognostic value of these seven genes was evaluated using TCGA COAD (Colorectal Adenocarcinoma) data. The results showed that TGFBI was highly expressed in chemotherapy-sensitive patients, and patients with high TGFBI expression have better survival.

scholarly journals Correction to: Protein–protein interaction analysis reveals a novel cancer stem cell related target TMEM17 in colorectal cancer

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhao‑liang Yu ◽  
Yu‑feng Chen ◽  
Bin Zheng ◽  
Ze-rong Cai ◽  
Yi‑feng Zou ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Stem Cell ◽  
Cancer Stem Cell ◽  
Protein Interaction ◽  
Interaction Analysis ◽  
Related Target ◽  
Protein Protein Interaction

An amendment to this paper has been published and can be accessed via the original article.

scholarly journals Identification Novel Biomarker for Acute Aortic Dissection Using 4D-Label-Free Proteomics

2021 ◽  
Author(s):  
mengmeng wang ◽  
baozhu wang ◽  
Maitudi Maitusun ◽  
bangdang chen ◽  
Dilare Adi ◽  
...  
Keyword(s):  
Cell Activation ◽  
Functional Enrichment ◽  
Potential Candidate ◽  
Label Free ◽  
Target Proteins ◽  
Protein Protein Interaction ◽  
Parallel Reaction Monitoring ◽  
Novel Biomarkers ◽  
Cell Migration And Proliferation ◽  
Free Quantification

Abstract Purpose: we aimed to identify potential candidate biomarkers in aorta tissue from AAD patients. Methods: We used 4D label-free quantification (4D-LFQ) mass spectrometry to screen differentially expressed proteins in aorta tissues of AAD patients. Then we performed protein annotation, unsupervised hierarchical clustering, functional classification, functional enrichment and cluster, and protein-protein interaction analyses. Parallel Reaction Monitoring (PRM) technology was used to accurately and quantitatively confirm the selected target proteins. Results: A total of 3350 proteins were identified. Taking 1.5 times as the differential expression threshold, 139 were upregulated and 108 were downregulated as compared to the control groups. Bioinformatics analysis showed that the differential proteins were mainly distributed in extracellular matrix and cytoplasm. And their functions mainly involve cell migration and proliferation, inflammatory cell activation, cell contraction, muscle organ development and other processes. PRM technology accurately quantified the selected 20 target proteins, and found SAA1, LBP, MPO, and ENG were confirmed to be enriched in the aorta tissue of AAD patients. Conclusions: This is the first application of a 4D-LFQ-PRM workflow to identify and validate biomarkers in AAD patients. SAA1, LBP, MPO, and ENG represent novel biomarkers for the pathogenesis of AAD and might be a therapeutic target in the future.

scholarly journals Urinary MicroRNA Expression Analysis of miR-1, miR-215, miR-335, Let-7ain Childhood Nephrotic Syndrome

2021 ◽  
Author(s):  
C.D.Mohana Priya ◽  
Vettriselvi Venkatesan ◽  
P.Pricilla charmine ◽  
G.Sangeetha Geminiganesan ◽  
Sudha Ekambaram
Keyword(s):  
Expression Profiles ◽  
Urine Samples ◽  
Control Group ◽  
Healthy Controls ◽  
Aberrant Expression ◽  
Exosomal Mirnas ◽  
Healthy Control ◽  
Novel Biomarkers ◽  
Steroid Sensitive ◽  
Noninvasive Biomarkers

Abstract Background Recently, urinary exosomal miRNAs are gaining increasing attention as their expression profiles are often associated with specific diseases and they exhibit great potential as noninvasive biomarkers for the diagnosis of various diseases. The present study was aimed to evaluate the expression status of selected miRNAs (miR-1, miR-215-5p, miR-335-5p and let-7a-5p) in urine samples from children with NS [steroid sensitive (SSNS)] and [steroid resistant (SRNS)] along with healthy control group.Methods MicroRNA isolation was carried out in urine samples collected from SSNS (100 nos), SRNS (100 nos), and healthy controls (50 nos) using MiRNeasy Mini Kit, followed by cDNA conversion for all the four selected miRNAs using Taqman advanced miRNA cDNA synthesis kit and their expression was quantified by Taqman Advanced miRNA assay kits using Real Time PCR Machine and Rotogen-Q in SSNS and SRNS patients and healthy control subjects.ResultsQuantification of all the four miRNAs (miR-1, mir-215, miR-335, let 7a) were found to be upregulated in both SSNS and SRNS as compared to control group. Further, the comparison of microRNAs within the case groups revealed significant downregulation of three microRNAs - miR-1, miR-215, miR- 335 and upregulation of let-7a in SRNS group as compared to SSNS. The t-test performed for all the four miRNAs was found to be statistically significant. ConclusionsThe aberrant expression of all the four microRNAs in both SSNS and SRNS as compared to healthy subjects may serve as novel biomarkers to distinguish between NS and healthy controls. The differential expression of microRNA let-7a is useful to discriminate SSNS and SRNS.

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