Identification of Protein Expression Changes in Hepatocellular Carcinoma through iTRAQ

Background. Hepatocellular carcinoma (HCC) is a malignant tumor associated with a poor prognosis. Serum biomarkers of HCC have the potential to improve the diagnosis, provide a means to monitor the tumors, and predict their malignancy. Proteins that are expressed differentially between HCC patients and normal controls have the potential to be biomarkers. Method. Serum samples from 10 confirmed HCC patients and 10 controls were collected. The differentially expressed proteins in the serum were identified using an isobaric tags for relative and absolute quantitation- (iTRAQ-) based method. Potential serum biomarkers were validated by ELISA in another 20 HCC patients and 20 controls. Their expression data in HCC were extracted from The Cancer Genome Atlas (TCGA) dataset. Results. A total of 260 proteins were measured in the serum of HCC patients and compared to those in sex- and age-matched normal controls. Forty-one proteins displayed significant changes, with 26 being downregulated and 15 being upregulated. Upregulated proteins included alpha-1-antitrypsin (A1AT) and peroxiredoxin 2 (PRDX2), and downregulated proteins included paraoxonase 1 (PON1) and C-reactive protein (CRP). We then used ELISA to measure serum levels of A1AT, PRDX2, PON1, and CRP in another 20 patients with HCC and found that only PON1 levels were consistent with the iTRAQ result. In TCGA dataset, PON1 expression was downregulated in HCC tissues (P<0.001) and low expression of PON1 was associated with poor survival in HCC patients (P<0.001). Conclusions. PON1 could act as a biomarker for HCC to assist in the diagnosis of HCC.

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Quantitative Proteomics Analysis by Isobaric Tags for Relative and Absolute Quantitation Identified Lumican as a Potential Marker for Acute Aortic Dissection

Journal of Biomedicine and Biotechnology ◽

10.1155/2011/920763 ◽

2011 ◽

Vol 2011 ◽

pp. 1-10 ◽

Cited By ~ 12

Author(s):

Guorong Gu ◽

Weizhong Cheng ◽

Chenling Yao ◽

Jun Yin ◽

Chaoyang Tong ◽

...

Keyword(s):

Aortic Dissection ◽

Quantitative Proteomics ◽

Acute Aortic Dissection ◽

Serum Marker ◽

Serum Biomarkers ◽

Serum Samples ◽

Absolute Quantitation ◽

Itraq Analysis ◽

Potential Marker ◽

Isobaric Tags

Acute aortic dissection (AAD) is a serious vascular disease. Currently the diagnosis relies on clinical and radiological means whereas serum biomarkers are lacking. The purpose of this study was to identify potential serum biomarkers for AAD using isobaric tags for relative and absolute quantitation (iTRAQ) approach. A total of 120 serum samples were collected from three groups: AAD patients (n=60), patients with acute myocardial infarction (AMI,n=30), and healthy volunteers (n=30), whereas the first 10 samples from each group were used for iTRAQ analysis. Using iTRAQ approach, a total of 174 proteins were identified as significantly different between AAD patients and healthy subjects. Among them, forty-six proteins increased more than twofold, full-scale analysis using serum sample for the entire 120 subjects demonstrated that Lumican level was significantly increased relative to control and AMI samples. Further, Lumican level correlated with time from onset to admission in AAD but not AMI samples. Using iTRAQ approach, our study showed that Lumican may be a potential AAD-related serum marker that may assist the diagnosis of AAD.

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Quantitative proteomics identifies a plasma multi-protein model for detection of hepatocellular carcinoma

Scientific Reports ◽

10.1038/s41598-020-72510-9 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Zhenhua Du ◽

Xinyi Liu ◽

Xiaojun Wei ◽

Hongbo Luo ◽

Peiyao Li ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Membrane Proteins ◽

Early Detection ◽

Proteomic Analysis ◽

Quantitative Proteomics ◽

Serum Biomarkers ◽

Diagnostic Efficacy ◽

Protein Model ◽

Tumor Tissues ◽

Normal Controls

Abstract More efficient biomarkers are needed to facilitate the early detection of hepatocellular carcinoma (HCC). We aimed to identify candidate biomarkers for HCC detection by proteomic analysis. First, we performed a global proteomic analysis of 10 paired HCC and non-tumor tissues. Then, we validated the top-ranked proteins by targeted proteomic analyses in another tissue cohort. At last, we used enzyme-linked immunosorbent assays to validate the candidate biomarkers in multiple serum cohorts including HCC cases (HCCs), cirrhosis cases (LCs), and normal controls (NCs). We identified and validated 33 up-regulated proteins in HCC tissues. Among them, eight secretory or membrane proteins were further evaluated in serum, revealing that aldo–keto reductase family 1 member B10 (AKR1B10) and cathepsin A (CTSA) can distinguish HCCs from LCs and NCs. The area under the curves (AUCs) were 0.891 and 0.894 for AKR1B10 and CTSA, respectively, greater than that of alpha-fetoprotein (AFP; 0.831). Notably, combining the three proteins reached an AUC of 0.969, which outperformed AFP alone (P < 0.05). Furthermore, the serum AKR1B10 levels dramatically decreased after surgery. AKR1B10 and CTSA are potential serum biomarkers for HCC detection. The combination of AKR1B10, CTSA, and AFP may improve the HCC diagnostic efficacy.

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Acute Aortic Dissection Biomarkers Identified Using Isobaric Tags for Relative and Absolute Quantitation

BioMed Research International ◽

10.1155/2016/6421451 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Ziya Xiao ◽

Yuan Xue ◽

Chenling Yao ◽

Guorong Gu ◽

Yaping Zhang ◽

...

Keyword(s):

Aortic Dissection ◽

Sensitivity And Specificity ◽

Acute Aortic Dissection ◽

Roc Curves ◽

Diagnostic Value ◽

Serum Samples ◽

Absolute Quantitation ◽

Isobaric Tags ◽

Diagnostic Sensitivity And Specificity ◽

D Dimer

The purpose of this study was to evaluate the utility of potential serum biomarkers for acute aortic dissection (AAD) that were identified by isobaric Tags for Relative and Absolute Quantitation (iTRAQ) approaches. Serum samples from 20 AAD patients and 20 healthy volunteers were analyzed using iTRAQ technology. Protein validation was performed using samples from 120 patients with chest pain. A total of 355 proteins were identified with the iTRAQ approach; 164 proteins reached the strict quantitative standard, and 125 proteins were increased or decreased more than 1.2-fold (64 and 61 proteins were up- and downregulated, resp.). Lumican, C-reactive protein (CRP), thrombospondin-1 (TSP-1), and D-dimer were selected as candidate biomarkers for the validation tests. Receiver operating characteristic (ROC) curves show that Lumican and D-dimer have diagnostic value (area under the curves [AUCs] 0.895 and 0.891,P<0.05). For Lumican, the diagnostic sensitivity and specificity were 73.33% and 98.33%, while the corresponding values for D-dimer were 93.33% and 68.33%. For Lumican and D-dimer AAD combined diagnosis, the sensitivity and specificity were 88.33% and 95%, respectively. In conclusion, Lumican has good specificity and D-dimer has good sensitivity for the diagnosis of AAD, while the combined detection of D-dimer and Lumican has better diagnostic value.

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Predictive values of multiple serum biomarkers in women with suspected preeclampsia: a prospective study

10.21203/rs.3.rs-33584/v2 ◽

2020 ◽

Author(s):

Jing Wang ◽

Honghai Hu ◽

Xiaowei Liu ◽

Shenglong Zhao ◽

Yuanyuan Zheng ◽

...

Keyword(s):

Plasminogen Activator Inhibitor ◽

Serum Levels ◽

Serum Markers ◽

Serum Biomarkers ◽

Operating Characteristics ◽

Serum Samples ◽

Predictive Values ◽

A Prospective Study ◽

Activator Inhibitor

Abstract Background: Preeclampsia prediction improves maternal and fetal outcomes in pregnancy. We aimed to evaluate the preeclampsia prediction values of a series of serum biomarkers. Methods: Singleton pregnant women with preeclampsia-related clinical and/or laboratory presentations were recruited and had blood drawn at their first visits. The prospective cohort was further divided into preeclampsia-positive and preeclampsia-negative groups based on the follow-up results. The following markers were tested using the collected serum samples: soluble fms-like tyrosine kinase-1 ( sFlt-1); placental growth factor (PlGF); thrombomodulin (TM); tissue plasminogen activator inhibitor complex (tPAI-C); compliment factors C1q, B, and H; glycosylated fibronectin (GlyFn); pregnancy-associated plasma protein-A2 ( PAPP-A2); blood urea nitrogen (BUN); creatinine (Cre); uric acid (UA); and cystatin C (Cysc). Results: A total of 196 women with suspected preeclampsia were recruited with follow-up medical records. Twenty-five percent (n=49) of the recruited subjects developed preeclampsia before delivery, and 75% remained preeclampsia-negative (n=147). The serum levels of sFlt-1, BUN, Cre, UA, Cysc and PAPP-A2 were significantly elevated, and the PlGF level was significantly decreased in the preeclampsia-positive patients. In the receiver operating characteristics (ROC) analyses, the area under the curves were listed in the order of decreasing values: 0.73 (UA), 0.67 (sFlt-1/PlGF), 0.66 (Cysc), 0.65 (GlyFn/PlGF), 0.64 (PAPP-A2/PlGF), 0.63 (BUN), 0.63 (Cre), and 0.60 (PAPP-A2). With the cut-off values obtained from the ROC analyses, the positive predictive values of these serum markers were between 33.1% and 58.5%, and the negative predictive values were between 80.9% and 89.5%. Conclusions: Further studies are warranted to confirm the clinical utilities of the serum markers in preeclampsia prediction

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Serum Irisin Predicts Posthepatectomy Complications in Patients with Hepatocellular Carcinoma

Disease Markers ◽

10.1155/2019/9850191 ◽

2019 ◽

Vol 2019 ◽

pp. 1-7

Author(s):

Jia Zhang ◽

Mengyun Ke ◽

Yifan Ren ◽

Jianbin Bi ◽

Zhaoqing Du ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Ischemia Reperfusion Injury ◽

Ischemia Reperfusion ◽

Rank Correlation ◽

The Cancer Genome Atlas ◽

Comprehensive Complication Index ◽

Preoperative Serum ◽

Fibronectin Type Iii ◽

Tcga Dataset ◽

Fibronectin Type Iii Domain

Background. Hepatectomy remains one of the most effective treatments for patients with hepatocellular carcinoma (HCC); however, it can lead to serious complications. Irisin, a key regulator of energy metabolism, is secreted into the circulation by shedding of the extracellular portion of the fibronectin type III domain-containing 5 (FNDC5). We have shown that irisin administration alleviates liver ischemia-reperfusion injury in mice. However, the role of preoperative irisin levels in HCC patients who underwent hepatectomy remained unknown. The purpose of this study was to determine how irisin expression changes in HCC and to explore the relationship between preoperative serum irisin levels and complications after hepatectomy. Methods. FNDC5/irisin expression data in HCC were extracted from The Cancer Genome Atlas (TCGA) dataset. A total of 219 participants, including 102 healthy controls and 117 HCC patients, were recruited in this study. All HCC patients underwent hepatectomy at the First Affiliated Hospital of the Xi’an Jiaotong University. Preoperative serum irisin levels were measured by ELISA. Postoperative complications were assessed using the comprehensive complication index (CCI) score. The Pearson rank correlation coefficient was computed to assess the correlation between preoperative serum irisin levels and postoperative CCI scores. Results. In TCGA dataset, FNDC5/irisin expression was downregulated in HCC tissues (P<0.001). Similarly, serum irisin levels were decreased in HCC patients (P<0.001). Low preoperative serum irisin levels were significantly correlated with high CCI scores after hepatectomy. Conclusions. Irisin may be a novel serum biomarker in the diagnosis of HCC and a predictor of complications after hepatectomy.

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The Oncogenic Role of CENPA in Hepatocellular Carcinoma Development: Evidence from Bioinformatic Analysis

BioMed Research International ◽

10.1155/2020/3040839 ◽

2020 ◽

Vol 2020 ◽

pp. 1-8

Author(s):

Yuan Zhang ◽

Lei Yang ◽

Jia Shi ◽

Yunfei Lu ◽

Xiaorong Chen ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cox Regression ◽

Disease Free Survival ◽

Progression Free Survival ◽

Bioinformatic Analysis ◽

Gene Expression Omnibus ◽

The Cancer Genome Atlas ◽

Free Survival ◽

Tcga Dataset ◽

High Level

Objective. This study is aimed at investigating the predictive value of CENPA in hepatocellular carcinoma (HCC) development. Methods. Using integrated bioinformatic analysis, we evaluated the CENPA mRNA expression in tumor and adjacent tissues and correlated it with HCC survival and clinicopathological features. A Cox regression hazard model was also performed. Results. CENPA mRNA was significantly upregulated in tumor tissues compared with that in adjacent tissues, which were validated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) series (all P<0.01). In the Kaplan-Meier plotter platform, the high level of CENPA mRNA was significantly correlated with overall survival (OS), disease-free survival (DFS), recurrence-free survival (RFS), and progression-free survival (PFS) in HCC patients (all log rank P<0.01). For validation in GSE14520 and pan-TCGA dataset, HCC patients with CNEPA mRNA overexpression had poor OS compared with those with low CENPA mRNA (log rank P=0.025 and P<0.0001, respectively), and those with high CENPA had poor DFS in TCGA (log rank P=0.0001). Additionally, CENPA mRNA were upregulated in HCC patients with alpha-fetoprotein (AFP) elevation, advanced TNM stage, larger tumor size, advanced AJCC stage, advanced pathology grade, and vascular invasion (all P<0.05). A Cox regression model including CENPA, OIP5, and AURKB could predict OS in HCC patients effectively (AUC=0.683). Conclusion. Overexpressed in tumors, CENPA might be an oncogenic factor in the development of HCC patients.

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Lymphaticovenous Anastomosis Supermicrosurgery Decreases Oxidative Stress and Increases Antioxidant Capacity in the Serum of Lymphedema Patients

Journal of Clinical Medicine ◽

10.3390/jcm10071540 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1540

Author(s):

Johnson Chia-Shen Yang ◽

Lien-Hung Huang ◽

Shao-Chun Wu ◽

Pao-Jen Kuo ◽

Yi-Chan Wu ◽

...

Keyword(s):

Oxidative Stress ◽

Antioxidant Capacity ◽

Serum Proteins ◽

Serum Levels ◽

Volume Reduction ◽

Enzyme Linked Immunosorbent Assay ◽

Serum Samples ◽

Absolute Quantitation ◽

Good Outcome ◽

Mr Volumetry

Background: Excess lymphedematous tissue causes excessive oxidative stress in lymphedema. Lymphaticovenous anastomosis (LVA) supermicrosurgery is currently emerging as the first-line surgical intervention for lymphedema. No data are available regarding the changes in serum proteins correlating to oxidative stress and antioxidant capacity before and after LVA. Methods: A total of 26 patients with unilateral lower limb lymphedema confirmed by lymphoscintigraphy were recruited, and venous serum samples were collected before (pre-LVA) and after LVA (post-LVA). In 16 patients, the serum proteins were identified by isobaric tags for relative and absolute quantitation-based quantitative proteomic analysis with subsequent validation of protein expression by enzyme-linked immunosorbent assay. An Oxidative Stress Panel Kit was used on an additional 10 patients. Magnetic resonance (MR) volumetry was used to measure t limb volume six months after LVA. Results: This study identified that catalase (CAT) was significantly downregulated after LVA (pre-LVA vs. post-LVA, 2651 ± 2101 vs. 1448 ± 593 ng/mL, respectively, p = 0.033). There were significantly higher levels of post-LVA serum total antioxidant capacity (pre-LVA vs. post-LVA, 441 ± 81 vs. 488 ± 59 µmole/L, respectively, p = 0.031) and glutathione peroxidase (pre-LVA vs. post-LVA, 73 ± 20 vs. 92 ± 29 U/g, respectively, p = 0.018) than pre-LVA serum. In addition, after LVA, there were significantly more differences between post-LVA and pre-LVA serum levels of CAT (good outcome vs. fair outcome, −2593 ± 2363 vs. 178 ± 603 ng/mL, respectively, p = 0.021) and peroxiredoxin-2 (PRDX2) (good outcome vs. fair outcome, −7782 ± 7347 vs. −397 ± 1235 pg/mL, respectively, p = 0.037) in those patients with good outcomes (≥40% volume reduction in MR volumetry) than those with fair outcomes (<40% volume reduction in MR volumetry). Conclusions: The study revealed that following LVA, differences in some specific oxidative stress markers and antioxidant capacity can be found in the serum of patients with lymphedema.

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Quantitative Proteomics Analysis of Differentially Expressed Proteins in Serum of Former Uranium Miners by Isobaric Tags for the Relative and Absolute Quantitation

Dose-Response ◽

10.1177/15593258211056190 ◽

2021 ◽

Vol 19 (4) ◽

pp. 155932582110561

Author(s):

Xuhong Dang ◽

Haipeng Lin ◽

Yayi Yuan ◽

Biao Yang ◽

Juancong Dong ◽

...

Keyword(s):

Radiation Damage ◽

Process Analysis ◽

Density Lipoprotein ◽

Differentially Expressed ◽

Enzyme Linked Immunosorbent Assay ◽

Differentially Expressed Proteins ◽

Serum Samples ◽

Absolute Quantitation ◽

Uranium Miners ◽

Isobaric Tags

The carcinogenicity of radon has been convincingly documented through epidemiological studies of underground miners. However, there is a lack of early warning indicators for radon radiation damage. In this study, mixed serum samples of 3 groups were collected from 27 underground uranium miners and seven aboveground miners according to the radiation exposure dose. The differentially expressed proteins in the serum were identified using the isobaric tags for the relative and absolute quantitation (iTRAQ)-based method. Some differentially expressed proteins were validated by enzyme-linked immunosorbent assay (ELISA) in 84 underground and 32 aboveground miners. A total of 25 co-differentially expressed proteins in 2 underground miner groups were screened, of which 9 were downregulated and 13 were upregulated. Biological process analysis of these proteins using Metascape showed that 5 GO terms were enriched, such as negative regulation of very-low-density lipoprotein particle clearance, endocytosis, and regulated exocytosis. The results of the ELISA for the expression levels of GCN1, CIP2A, and IGHV1-24 in the serum of 116 miners’ serum showed that the levels of GCN1 and CIP2A were consistent with the iTRAQ results. In conclusion, APOC1, APOC2, APOC3, ORM1, ORM2, ANTXR1, GCN1, and CIP2A may be potential early markers of radon radiation damage.

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The use of AFP and DCP as serum biomarkers to differentiate between hepatocellular carcinoma and intrahepatic cholangiocarcinoma in non-cirrhotic livers.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.e15162 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. e15162-e15162

Author(s):

Ravindhi Lakmalee Nathavitharana ◽

Mabel Joey Teng ◽

Philip James Johnson ◽

Sarah Berhane ◽

Anna Skowronska ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Liver Cirrhosis ◽

Intrahepatic Cholangiocarcinoma ◽

Serum Biomarkers ◽

Queen Elizabeth Hospital ◽

Stepwise Logistic Regression ◽

Serum Samples ◽

Diagnostic Biomarkers ◽

Biopsy Methods ◽

Larger Sample

e15162 Background: Differential diagnosis of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) can be challenging in patients without evidence of liver cirrhosis. Definitive diagnosis is based on tissue biopsy. We investigated if the use of serum biomarkers could help differentiate between these two types of malignancies, thereby avoiding the risks associated with biopsy. Methods: Patients with cholangiocarcinoma and HCC were recruited from Queen Elizabeth Hospital, Birmingham, UK; blood samples were collected at time of diagnosis. Two biomarkers, alpha-fetoprotein (AFP) and des-gamma-carboxy prothrombin (DCP) were measured in the serum samples from 56 patients with cholangiocarcinoma and 35 patients with HCC without evidence of liver cirrhosis. Of the 56 patients with cholangiocarcinoma, 17 were intrahepatic and 39 were extrahepatic. Results: 17 ICC and 35 HCC were included in the analysis. The levels of AFP and DCP were much higher in HCC as compared to ICC. The median AFP was 64.6 (IQR 10.9, 3564.2) in HCC as compared to 3 (IQR 2.4, 3.9) in ICC. Similarly, the median DCP was 215.41 (IQR 22.46, 692.53) in HCC as compared to 0.33 (IQR 0.16, 1.08) in ICC. Stepwise logistic regression was performed using both biomarkers. Log- DCP remained significant at 95% level in predicting HCC from ICC, giving an AUC of 0.96. Conclusions: In patients with a non-cirrhotic liver and radiological evidence of cancer, measurement of serum AFP and DCP level may help differentiate between HCC and ICC. In this study, DCP is the most useful discriminator between HCC and ICC. Further prospective studies should be done with larger sample sizes to validate the use of AFP and DCP as diagnostic biomarkers in this clinical setting.

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

PeerJ ◽

10.7717/peerj.9971 ◽

2020 ◽

Vol 8 ◽

pp. e9971

Author(s):

Ming Li ◽

Mingzhu Wu ◽

Ying Qin ◽

Huaqing Liu ◽

Chengcheng Tu ◽

...

Keyword(s):

Childhood Asthma ◽

Serum Proteins ◽

Differentially Expressed ◽

Biological Information ◽

Noncommunicable Diseases ◽

Enzyme Linked Immunosorbent Assay ◽

Serum Samples ◽

Absolute Quantitation ◽

Children With Asthma ◽

Isobaric Tags

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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