Potential glioblastoma biomarkers identified by mass spectroscopy and iTRAQ labeling.
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ABSTRACT:
SUBMITTER: Feng R
PROVIDER: S-EPMC10363635 | biostudies-literature | 2023 Sep
REPOSITORIES: biostudies-literature
Publications
Potential glioblastoma biomarkers identified by mass spectroscopy and iTRAQ labeling.
Feng Ruili R Chen Mingyu M Luo Guanghong G Chen Yanlu Y Wang Jiao J Xu Jian J Xu Ming M Zhong Ping P Wen Tieqiao T
Genes & diseases 20221223 5
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Project description:BackgroundEpithelial-derived ovarian adenocarcinoma (EOC) is the most deadly gynecologic tumor, and the principle cause of the poor survival rate is diagnosis at a late stage. Screening and diagnostic biomarkers with acceptable specificity and sensitivity are lacking. Ovarian cyst fluid should harbor early ovarian cancer biomarkers because of its closeness to the tumor. We investigated ovarian cyst fluid as a source for discovering biomarkers for use in the diagnosis of EOC.ResultsUsing quantitative mass spectrometry, iTRAQ MS, we identified 837 proteins in cyst fluid from benign, EOC stage I, and EOC stage III. Only patients of serous histology were included in the study. Comparing the benign (n = 5) with the malignant (n = 10) group, 87 of the proteins were significantly (p < 0.05) differentially expressed. Two proteins, serum amyloid A-4 (SAA4) and astacin-like metalloendopeptidase (ASTL), were selected for verification of the iTRAQ method and external validation with immunoblot in a larger cohort with mixed histology, in plasma (n = 68), and cyst fluid (n = 68). The protein selections were based on either high significance and high fold change or abundant appearance and several peptide recognitions in the sample sets (p = 0.04, FC = 1.95) and (p < 0.001, FC = 8.48) for SAA4 and ASTL respectively. Both were found to be significantly expressed (p < 0.05), but the methods did not correlate concerning ASTL.ConclusionsFluid from ovarian cysts connected directly to the primary tumor harbor many possible new tumor-specific biomarkers. We have identified 87 differentially expressed proteins and validated two candidates to verify the iTRAQ method. However several of the proteins are of interest for validation in a larger setting.
| S-EPMC3637236 | biostudies-literature
Project description:Multidimensional LC-MS/MS has been used for the analysis of biological samples labeled with isobaric mass tags for relative and absolute quantitation (iTRAQ) to identify proteins that are differentially expressed in human head-and-neck squamous cell carcinomas (HNSCCs) in relation to non-cancerous head-and-neck tissues (controls) for cancer biomarker discovery. Fifteen individual samples (cancer and non-cancerous tissues) were compared against a pooled non-cancerous control (prepared by pooling equal amounts of proteins from six non-cancerous tissues) in five sets by on-line and off-line separation. We identified 811 non-redundant proteins in HNSCCs, including structural proteins, signaling components, enzymes, receptors, transcription factors, and chaperones. A panel of proteins showing consistent differential expression in HNSCC relative to the non-cancerous controls was discovered. Some of the proteins include stratifin (14-3-3sigma); YWHAZ (14-3-3zeta); three calcium-binding proteins of the S100 family, S100-A2, S100-A7 (psoriasin), and S100-A11 (calgizarrin); prothymosin alpha (PTHA); L-lactate dehydrogenase A chain; glutathione S-transferase Pi; APC-binding protein EB1; and fascin. Peroxiredoxin2, carbonic anhydrase I, flavin reductase, histone H3, and polybromo-1D (BAF180) were underexpressed in HNSCCs. A panel of the three best performing biomarkers, YWHAZ, stratifin, and S100-A7, achieved a sensitivity of 0.92 and a specificity of 0.91 in discriminating cancerous from non-cancerous head-and-neck tissues. Verification of differential expression of YWHAZ, stratifin, and S100-A7 proteins in clinical samples of HNSCCs and paired and non-paired non-cancerous tissues by immunohistochemistry, immunoblotting, and RT-PCR confirmed their overexpression in head-and-neck cancer. Verification of YWHAZ, stratifin, and S100-A7 in an independent set of HNSCCs achieved a sensitivity of 0.92 and a specificity of 0.87 in discriminating cancerous from non-cancerous head-and-neck tissues, thereby confirming their overexpressions and utility as credible cancer biomarkers.
| S-EPMC2424195 | biostudies-literature
Project description:Lung adenocarcinoma, the most common type of lung cancer, has increased in recent years. Prognosis is still poor, and pathogenesis remains unclear. This study aimed to investigate the membrane protein profile differences between lung adenocarcinoma and normal tissue. Manual microdissection was used to isolate the target cells from tumor tissue and normal tissue. iTRAQ labeling combined with 2D-LC-MS/MS yielded a differential expression profile of membrane proteins. Bioinformatic analysis was performed using Gene Ontology, WEGO, PID, and KEGG. S100A14 protein was selectively verified by Western blotting. The relationship of S100A14 expression with clinicopathological features in lung cancer patients was evaluated using immunohistochemistry. As a result, 568 differential proteins were identified; 257 proteins were upregulated and 311 were downregulated. Of these proteins, 48% were found to be membrane bound or membrane associated. These proteins enable the physiological functions of binding, catalysis, molecular transduction, transport, and molecular structure. For these differential proteins, 35 pathways were significantly enriched through the Pathway Interaction Database, whereas 19 pathways were enriched via KEGG. The overexpression and cellular distribution of S100A14 in lung cancer were confirmed. We found that upregulation of S100A14 was associated with well or moderate differentiation. The iTRAQ-coupled 2D-LC-MS/MS technique is a potential method for comparing membrane protein profiles between tumor and normal tissue. Such analysis may also help in identifying novel biomarkers and the mechanisms underlying carcinogenesis.
| S-EPMC4058308 | biostudies-literature
Project description:BackgroundAsthma is a chronic respiratory disease that affects billions of people. Due to its diverse phenotypes and endotypes with distinct pathophysiological mechanisms, significant challenges arise in its clinical diagnosis and treatment. The discovery of potential biomarkers of asthma has significant implications for its clinical classification and precise treatment. The purpose of this study is to identify potential biomarkers for asthma, providing a foundation for its diagnosis and treatment.MethodsWe constructed an ovalbumin (OVA)-sensitized asthmatic mice model and used isobaric Tags for Relative and Absolute Quantitation (iTRAQ) labeling and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) technology to identify differentially expressed proteins (DEPs) in lung tissues. We then performed enrichment analyses of the DEPs using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and constructed protein-protein interaction (PPI) networks.ResultsWe identified 242 DEPs in the asthmatic mice model and showed that heat shock protein family A (Hsp70) member 5 (HSPA5) is a central protein in asthma. Consistent with our bioinformatics analysis, our western blot validation confirmed that the protein levels of arginase 1 (ARG1), chitinase-like protein 3 (CHIL3), chloride channel accessory 1 (CLCA1), and bactericidal/permeability-increasing protein (BPI) fold-containing family B member 1 (BPIFB1) were significantly increased in asthma group compared to the control group. Thus, we found that CLCA1 and BPIFB1 were the most promising potential biomarkers of asthma.ConclusionsOur iTRAQ analysis and western blot verification of asthmatic mice showed that HSPA5 is a central protein in asthma, and CLCA1 and BPIFB1 are novel potential biomarkers that could play significant roles in the diagnosis and treatment of asthma.
| S-EPMC11565350 | biostudies-literature
Project description:One of the main causations of the poor prognosis of pancreatic cancer is the lack of effective chemotherapies. Gemcitabine is a widely used chemotherapeutic drug, but limited therapeutic efficacy is achieved due to chemoresistance. Recent studies demonstrated that the presence of cancer stem cells may lead to the failure of chemotherapy. Moreover, gemcitabine can promote the stemness of pancreatic cancer cells. We detected the alterations in protein phosphorylation and signaling pathways in pancreatic cancer cells after gemcitabine treatment using iTRAQ labeling LC-MS/MS, because it was featured with the advantages of strong separation ability and analysis range. A total of 232 differentially expressed phosphorylated proteins were identified in this study. Gene Ontology analysis revealed that nuclear lumen, nuclear part and organelle lumen were enriched for cell components and protein binding, poly (A) RNA binding and RNA binding were enriched for molecular function. A variety of signaling pathways were enriched based on KEGG analysis. AMPK, mTOR and PI3K/Akt pathways were verified after gemcitabine exposure. Moreover, we found there were complex interactions of phosphorylated proteins in modulating cancer stemness induced by gemcitabine exposure based on PPIs map. Our experiments may identify potential targets and strategies for sensitizing pancreatic cancer cells to gemcitabine.
| S-EPMC5634998 | biostudies-literature
Project description:Glioblastoma (GBM) is the most aggressive form of astrocytoma and is difficult to diagnose at early stage. In this study, our goal is to find and validate biomarkers for GBM through serum proteome expression profiling, which would assist in the early diagnosis, and management of GBMs. In the discovery phase, we performed shotgun proteomics of control and GBM pooled serum samples using untargeted 4-plex iTRAQ (isobaric Tags for Relative and Absolute Quantitation) mass spectrometry to identify candidate biomarkers with differential abundance The two candidates, S100A8 and S100A9 were prioritized for verification based on their maximal abundance in GBM serum in our discovery phase.
2019-03-04 | PXD012207 | Pride
Project description:Non-Hodgkin's lymphoma (NHL) is the third most common malignant tumor among children. However, at initial NHL diagnosis, most cases are at an advanced stage because of nonspecific clinical manifestations and currently limited diagnostic methods. This study aimed to screen and verify potential serum biomarkers of pediatric NHL using isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis. Serum protein expression profiles from children with B-NHL (n=20) and T-NHL (n=20) and healthy controls (n=20) were detected by utilizing iTRAQ in combination with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) and analyzed by applying Ingenuity Pathway Analysis (IPA). The candidate biomarkers S100A8 and LRG1 were further validated by using enzyme-linked immunosorbent assays (ELISAs). Receiver operating characteristic (ROC) analysis based on ELISA data was used to evaluate diagnostic efficacy. In total, 534 proteins were identified twice using iTRAQ combined with 2D LC-MS/MS. Further analysis identified 79 and 73 differentially expressed proteins in B-NHL and T-NHL serum, respectively, compared with control serum according to our defined criteria; 34 proteins were overexpressed and 45 proteins underexpressed in B-NHL, whereas 45 proteins were overexpressed and 28 proteins underexpressed in T-NHL (p < 0.05). IPA demonstrated a variety of signaling pathways, including acute phase response signaling and liver X receptor/retinoid X receptor (LXR/RXR) activation, to be strongly associated with pediatric NHL. S100A8 and LRG1 were elevated in NHL patients compared to normal controls according to ELISA (p < 0.05), which was consistent with iTRAQ results. The areas under the ROC curves of S100A8, LRG1, and the combination of S100A8 and LRG1 were 0.873, 0.898 and 0.970, respectively. Our findings indicate that analysis of the serum proteome using iTRAQ combined with 2D LC-MS/MS is a feasible approach for biomarker discovery. Serum S100A8 and LRG1 are promising candidate biomarkers for pediatric NHL, and these differential proteins illustrate a novel pathogenesis and may be clinically helpful for NHL diagnosis in the future.
| S-EPMC8970600 | biostudies-literature
Project description:ObjectivesSepsis is the major cause of death for critically ill patients. Recent progress in proteomics permits a thorough characterization of the mechanisms associated with critical illness. The purpose of this study was to screen potential biomarkers for early prognostic assessment of patients with sepsis.MethodsFor the discovery stage, 30 sepsis patients with different prognoses were selected. Urinary proteins were identified using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS. Mass spec instrument analysis were performed with Mascot software and the International Protein Index (IPI); bioinformatic analyses were used by the algorithm of set and the Gene Ontology (GO) Database. For the verification stage, the study involved another 54 sepsis-hospitalized patients, with equal numbers of patients in survivor and non-survivor groups based on 28-day survival. Differentially expressed proteins were verified by Western Blot.ResultsA total of 232 unique proteins were identified. Proteins that were differentially expressed were further analyzed based on the pathophysiology of sepsis and biomathematics. For sepsis prognosis, five proteins were significantly up-regulated: selenium binding protein-1, heparan sulfate proteoglycan-2, alpha-1-B glycoprotein, haptoglobin, and lipocalin; two proteins were significantly down-regulated: lysosome-associated membrane proteins-1 and dipeptidyl peptidase-4. Based on gene ontology clustering, these proteins were associated with the biological processes of lipid homeostasis, cartilage development, iron ion transport, and certain metabolic processes. Urinary LAMP-1 was down-regulated, consistent with the Western Blot validation.ConclusionThis study provides the proteomic analysis of urine to identify prognostic biomarkers of sepsis. The seven identified proteins provide insight into the mechanism of sepsis. Low urinary LAMP-1 levels may be useful for early prognostic assessment of sepsis.Trial registrationClinicalTrial.gov NCT01493492.
| S-EPMC3553154 | biostudies-literature
Project description:BackgroundProteomics may help us better understand the changes of multiple proteins involved in oncogenesis and progression of prostate cancer(PCa) and identify more diagnostic and prognostic biomarkers. The aim of this study was to screen biomarkers of PCa by the proteomics analysis using isobaric tags for relative and absolute quantification(iTRAQ).MethodsThe patients undergoing prostate biopsies were classified into 3 groups according to pathological results: benign prostate hyperplasia (BPH, n = 20), PCa(n = 20) and BPH with local prostatic intraepithelial neoplasm(PIN, n = 10). Then, all the specimens from these patients were analyzed by iTRAQ and two-dimensional liquid chromatography-tandem mass spectrometry (2DLC-MS/MS). The Gene Ontology(GO) function and the transcription regulation networks of the differentially expressed were analyzed by MetaCore software. Western blotting and Immunohistochemical staining were used to analyze the interesting proteins.ResultA total of 760 proteins were identified from 13787 distinct peptides, including two common proteins that enjoy clinical application: prostate specific antigen (PSA) and prostatic acid phosphatase(PAP). Proteins that expressed differentially between PCa and BPH group were further analyzed. Compared with BPH, 20 proteins were significantly differentially up-regulated (>1.5-fold) while 26 were significantly down-regulated in PCa(<0.66-fold). In term of GO database, the differentially expressed proteins were divided into 3 categories: cellular component(CC), molecular function (MF) and biological process(BP). The top 5 transcription regulation networks of the differentially expressed proteins were initiated through activation of SP1, p53, YY1, androgen receptor(AR) and c-Myc The overexpression of periostin in PCa was verified by western blotting and immunohistochemical staining.ConclusionOur study indicates that the iTRAQ technology is a new strategy for global proteomics analysis of the tissues of PCa. A significant up-regulation of periostin in PCa compared to BPH may provide clues for not only a promising biomarker for the prognosis of PCa but also a potential target for therapeutical intervention.
| S-EPMC3100237 | biostudies-literature
Project description:We analyzed gene expression profiles of human testicular biopsies in men with idiopathic nonobstructive azoospermia. Using new generation oligonucleotide microarray platform GeneChipM-BM-. Human Gene 1.0 ST, we identified genes which could be potential biomarkers of azoospermia and molecular indicators that could determine a particular stage of impaired spermatogenesis. Thus, we shed light on genes which were had so far been weakly characterized and which were had never related to infertility before. These studies also included the comparative analysis of the hierarchical clustering of gene expression profile with histopathological data provided for azoospermic patients. We analyzed 31 testicular biopsy samples with Affymetrix Human Gene 1.0 ST microarrays. 27 of them were obtained from patients with various types of NOA and 4 with normal spermatogenesis.
2013-09-16 | E-GEOD-45885 | biostudies-arrayexpress