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PubMed2026

Identification of Immune Response-Related Proteomic Biomarkers in Moyamoya Disease Using Serum Olink Proteomics.

Moyamoya disease, a rare chronic cerebrovascular disorder, requires invasive digital subtraction angiography (DSA) for diagnosis. This study employed high-throughput proteomics to identify plasma biomarkers for Moyamoya disease diagnosis. We conducted immunopanel analysis using the Olink platform to evaluate 92 immune-related proteins in plasma samples from 88 Moyamoya disease patients and 88 healthy controls. Key proteins were identified through differential expression analysis, GO, and KEGG enrichment analysis. A diagnostic model was constructed using LASSO regression, Boruta algorithm, and machine learning models including random forest and XGBoost. Validation of these proteins was performed using GEO external data sets, followed by prediction of potential therapeutic drugs and molecular docking validation through pharmacogenomic databases. A total of 44 differentially expressed proteins were identified through the Olink immunopanel, with 12 downregulated and 32 upregulated. GO and KEGG analyses revealed significant enrichment of these proteins in innate immune responses and signaling pathways such as NF-kB and MAPK. Through LASSO, random forest, and protein under-area analysis, four potential biomarkers for Moyamoya disease (MGMT, SIT1, PRDX1, TRAF2) were identified. A diagnostic model using these proteins showed the highest AUC value with the XGBoost model. Additionally, TRAF2 and PRDX1 exhibited significant expression differences in Moyamoya disease patients within the GEO data set. Our study revealed the immune landscape of Moyamoya disease, identified four biomarkers, and established a variety of diagnostic models.

Humans↗

PubMed2001

Proteomic profiling of the cancer microenvironment by antibody arrays.

Critical changes in protein expression that enable tumors to initiate and progress originate in the local tissue microenvironment, and there are increasing indications that these microenvironmental alterations in protein expression play critical roles in shaping and directing this process. As a model to better understand how patterns of protein expression shape the tissue microenvironment, we analyzed protein expression in tissue derived from squamous cell carcinoma of the oral cavity through an antibody microarray approach for high-throughput proteomic analysis. Utilizing laser capture microdissection to procure total protein from specific microscopic cellular populations, we demonstrate that quantitative, and potentially qualitative, differences in expression patterns of multiple proteins within epithelial cells reproducibly correlate with oral cavity tumor progression. Furthermore, differential expression of multiple proteins was also found in stromal cells surrounding and adjacent to regions of diseased epithelium that directly correlated with tumor progression of the epithelium. Most of the proteins identified in both cell types are involved in signal transduction pathways, thus we hypothesize that extensive molecular communication involving complex cellular signaling between epithelium and stroma play a key role in driving oral cavity cancer progression.

Antibodies, Neoplasm↗

PubMed2002

Comparison of protein expression profiles between monolayer and spheroid cell culture of HT-29 cells revealed fragmentation of CK18 in three-dimensional cell culture.

The use of three-dimensional cell culture models, so-called multicellular tumor spheroids, is a special approach in experimental cancer research, because spheroids are similar to in vivo tumors in structural as well as functional sense. Cells grown in spheroids exhibit alterations of cell cycle regulation, induction of apoptosis and differentiation and can acquire multidrug resistance. In this study we investigated the protein expression in human colorectal cancer cells grown in monolayer and in spheroid cultures using proteomics. Evaluation by computer-assisted image analysis revealed overexpression of three cytokeratin 18 fragments that were generated in vivo. Cytokeratin 18 has previously been described as a target for caspase-mediated cleavage during apoptosis and our results indicate that apoptosis may take place in spheroids. Other proteins upregulated in spheroids include calreticulin precursor, a rho GDP dissociation inhibitor variant, several cytokeratins and peroxiredoxin 4. Some of these proteins have already been linked to chemoresistance and apoptotic phenomena.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2006

Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes.

A critical step in protein biomarker discovery is the ability to contrast proteomes, a process referred generally as quantitative proteomics. While stable-isotope labeling (e.g., ICAT, 18O- or 15N-labeling, or AQUA) remains the core technology used in mass spectrometry-based proteomic quantification, increasing efforts have been directed to the label-free approach that relies on direct comparison of peptide peak areas between LC-MS runs. This latter approach is attractive to investigators for its simplicity as well as cost effectiveness. In the present study, the reproducibility and linearity of using a label-free approach to highly complex proteomes were evaluated. Various amounts of proteins from different proteomes were subjected to repeated LC-MS analyses using an ion trap or Fourier transform mass spectrometer. Highly reproducible data were obtained between replicated runs, as evidenced by nearly ideal Pearson's correlation coefficients (for ion's peak areas or retention time) and average peak area ratios. In general, more than 50% and nearly 90% of the peptide ion ratios deviated less than 10% and 20%, respectively, from the average in duplicate runs. In addition, the multiplicity ratios of the amounts of proteins used correlated nicely with the observed averaged ratios of peak areas calculated from detected peptides. Furthermore, the removal of abundant proteins from the samples led to an improvement in reproducibility and linearity. A computer program has been written to automate the processing of data sets from experiments with groups of multiple samples for statistical analysis. Algorithms for outlier-resistant mean estimation and for adjusting statistical significance threshold in multiplicity of testing were incorporated to minimize the rate of false positives. The program was applied to quantify changes in proteomes of parental and p53-deficient HCT-116 human cells and found to yield reproducible results. Overall, this study demonstrates an alternative approach that allows global quantification of differentially expressed proteins in complex proteomes. The utility of this method to biomarker discovery is likely to synergize with future improvements in the detecting sensitivity of mass spectrometers.

Amino Acid Sequence↗

PubMed2006

Proteome analysis of the sarcoplasmic fraction of pig semimembranosus muscle: implications on meat color development.

Two-dimensional electrophoresis was used to investigate sarcoplasmic protein expression in pig Semimembranosus muscles sampled 20 min after slaughter. Two groups (light and dark) of 12 animals were selected from 1000 pigs, based on meat L values measured 36 h postmortem. Twenty-two proteins or fragments (p < 0.05) were differentially expressed. Muscles leading to darker meat had a more oxidative metabolism, indicated by more abundant mitochondrial enzymes of the respiratory chain, hemoglobin, and chaperone or regulator proteins (HSP27, alphaB-crystallin, and glucose-regulated protein 58 kDa). Conversely, enzymes of glycolysis were overexpressed in the lighter group. Such samples were also characterized by higher levels of glutathione S-transferase omega, which can activate the RyR calcium channels, and higher levels of cyclophilin D. This protein pattern is likely to have severe implications on postmortem metabolism, namely, acceleration of ATP depletion and pH fall and subsequent enhanced protein denaturation, well-known to induce discoloration.

Animals↗

PubMed2006

Proteome analysis of multidrug resistance in vincristine-resistant human gastric cancer cell line SGC7901/VCR.

In order to elucidate the mechanisms of multidrug resistance (MDR) of vincristine-resistant human gastric carcinoma cell line SGC7901/VCR, 2-DE was used to separate the total proteins of SGC7901/VCR and its parental cell line SGC7901. PDQuest software was applied to analyze 2-DE images, and the differential protein spots were identified by both MALDI-TOF-MS and ESI-Q-TOF-MS. Then the differential expressional levels of partially identified proteins were determined by Western blot analysis and real-time RT-PCR. Furthermore, the association of heat shock protein (HSP27), one of the highly expressed proteins in sgc7901/vcr, with MDR was analyzed using antisense inhibition of HSP27. In this study, the well-resolved, reproducible 2-DE patterns of SGC7901/VCR and SGC7901 were established, and yielded about 1100 protein-spots each. All the 24 differential proteins between the two cell lines were identified, and the differential expression levels of the partial proteins were confirmed. The suppression of HSP27 expression by HSP27 antisense oligonucleotides could enhance vincristine chemosensitivity in sgc7901/vcr and induce the cells to exhibit apoptotic morphological features after vincristine treatment. The differentially expressed proteins could be divided into six groups based on their functions: calcium-binding proteins, chaperones, proteins involved in drug detoxification or repair of DNA damage, metabolic enzymes, proteins related to cellular structure, and proteins relative to signal transduction, some of which may contribute to MDR of human gastric carcinoma cell line SGC7901/VCR. These data will be valuable for further study of the mechanisms of MDR in human gastric cancer.

Amino Acid Sequence↗

PubMed2003

Chinese hamster ovary K2 cell lipid droplets appear to be metabolic organelles involved in membrane traffic.

The principal lipids in animal cell lipid droplets are cholesterol, cholesterol ester, and triglyceride, but the protein composition of this compartment is largely unknown. Here we report on the proteomic analysis of lipid droplets. Using a combination of mass spectrometry and immunoblotting, we identify nearly 40 specifically associated proteins in droplets isolated from Chinese hamster ovary K2 cells grown in normal medium. The proteins fall in to five groups: structural molecules of the droplet-like adipose differentiation-related protein; multiple enzymes involved in the synthesis, storage, utilization, and degradation of cholesterol esters and triglycerides; multiple, different Rab GTPases known to be involved in regulating membrane traffic; signaling molecules such as p50RhoGAP; and a group of proteins that do not fit any classification but include proteins often found in caveolae/rafts such as caveolin-1 and 2 and flotillin-1. The proteome of droplets isolated from cells grown in the presence of oleate is largely the same except for an increase in the amount of adipose differentiation-related protein, caveolin-1, and a protein thought to be involved in phospholipid recycling called CGI-58. Based on the protein profile, the lipid droplet appears to be a complex, metabolically active organelle that is directly involved in membrane traffic and possibly phospholipid recycling. We propose the name adiposome for this organelle.

Animals↗

PubMed2006

Protein microarrays for the detection of biomarkers in head and neck squamous cell carcinomas.

Protein microarrays are of increasing importance for high-throughput screening of fresh tissues. In our study, protein microarrays were generated by printing antibodies onto membranes to characterize protein profiles expressed by head and neck squamous cell carcinomas (HNSCCs). Cellular proteomes of 30 matched normal squamous epithelial cells and carcinoma specimens were analyzed after tissue microdissection using microarrays composed of 83 different antibodies. As controls, Western blot analysis and tissue microarrays (TMAs) containing 98 HNSCC specimens were used. Of the 83 proteins examined, 14 showed differential expression between HNSCCs and normal epithelium. The protein microarray approach revealed an upregulation of 8 proteins and a downregulation of 6 proteins. Bag-1, Cox-2, Hsp-70, Stat3, pescadillo, MMP-7 (matrilysin), IGF-2, and cyclin D1 were identified to be significantly upregulated, whereas suppressor of cytokine signaling 1, thrombospondin, TGF-beta1, Jun, Fos, and Fra-2 were downregulated. The differential expression of these proteins was confirmed using Western blot and TMA. Upon correlation of differentially regulated proteins with the clinicopathologic data of our patients, MMP-7 (matrilysin) was found to be associated with survival in univariate, but not multivariate, analysis. These data indicate that our protein arrays provide protein information in a systematic, reproducible, and also high-throughput fashion.

Biomarkers, Tumor↗

PubMed2003

Proteomics of the dissimilatory iron-reducing bacterium Shewanella oneidensis MR-1, using a matrix-assisted laser desorption/ionization-tandem-time of flight mass spectrometer.

Shewanella oneidensis MR-1 is a gram-negative facultative aerobic bacterium living at oxic-anoxic interfaces in nature. The plasticity of terminal electron-acceptors used under anaerobic conditions is huge, but the adaptation to these different environmental conditions remains unclear. In this work, we used a proteomic approach to study the protein content when the organism is grown under anaerobic respiration conditions on insoluble ferric oxide. By analysis of two-dimensional gel patterns of soluble protein extracts, we discovered 20 differentially displayed proteins. The protein spots were further analyzed by mass spectrometry for which we used, in addition to nano-high-performance liquid chromatography coupled to an electrospray ionization-quadrupole-time of flight instrument, a recently introduced matrix-assisted laser desorption/ionization (MALDI) tandem-time of flight mass spectrometer. The instrument allows the acquisition of high quality spectra, in both the mass spectrometry and tandem mass spectrometry mode, and is therefore able to identify protein spots unambiguously. Advantageous to electrospray ionization is a minimised sample handling, inherent to MALDI ionization, and the presence of high energy fragmentation ions, generating sequence information that also can differentiate isobaric amino acids. With this strategy, we could point out a regulatory protein that is up-regulated under iron(III) respiration. This protein, the aerobic respiration control protein (ArcA), has been reported as being a regulator during anaerobiosis in other species. To our knowledge, this is the first report of the possible involvement of ArcA from S. oneidensis MR-1 in the reduction of ferric oxide.

Bacterial Proteins↗

PubMed2001

FindTarget: software for subtractive genome analysis.

In silico subtractive/differential genome analysis is a powerful approach for identifying genus- or species-specific genes, or groups of genes that are responsible for a unique phenotype. By this method, one searches for genes present in one group of bacteria and absent in another group. A software package has been developed, named FindTarget, that has a user-friendly web interface to facilitate differential genome analysis. The user chooses the genomes to compare, the similarity criteria and the thresholds to decide if a gene has a counterpart in another genome. The searches are based on BLASTP comparisons of proteomes. FindTarget also includes access to sequences, coloured multiple alignments, phylogenetic trees of conserved proteins and links to public annotated databases which provide a means for validation of the results. To illustrate this approach, a FindTarget search for genes putatively involved in the specificity of cell envelope synthesis of Gram-negative bacteria is presented. The results show that most of the identified genes are clearly involved in cell wall processes, underlining the power of such an approach in general and that of FindTarget in particular.

Bacterial Proteins↗

PubMed2007

Evaluation of an in vitro model of androgen ablation and identification of the androgen responsive proteome in LNCaP cells.

Proteins responsive to androgen and anti-androgen may be involved in the development and progression of prostate cancer and the ultimate failure of androgen-ablation therapy. These proteins represent potential diagnostic and therapeutic targets for improved management of prostate cancer. We have investigated the effect of androgen (R1881) and anti-androgen (bicalutamide) on the androgen-responsive prostate cancer LNCaP cell line using a quantitative gel-based proteomic approach. Prior to analysis, the in vitro system was evaluated for reproducibility and validated by appropriate molecular responses to treatment. Six replicate samples were independently generated and analysed by 2-D DIGE. According to strict statistical criteria, 197 spots were differentially expressed, of which we have successfully identified 165 spots corresponding to 125 distinct proteins. Following androgen supplementation, 108 spots (68 proteins) were increased and 57 spots (39 proteins) were decreased. Essentially no difference was observed between control and anti-androgen-treated samples, confirming the absence of "off-target" effects of bicalutamide. Identified proteins were involved in diverse processes including the stress response and intracellular signalling. The potential contribution to disease of these processes and identified constituent proteins are discussed. This rigorous, statistically supported study of androgen responses has provided a number of potential candidates for development as diagnostic/prognostic markers and drug targets.

Androgens↗

PubMed2005

Heat-shock protein 27: a potential biomarker for hepatocellular carcinoma identified by serum proteome analysis.

Hepatocellular carcinoma (HCC) is the third leading cause of cancer mortality worldwide and ranks second in China. The prognosis of HCC remains dismal mainly because of its late diagnosis, especially in patients with coexisting chronic liver diseases. To identify serum biomarkers for HCC, sera from 20 healthy volunteers, 20 hepatitis B virus (HBV) infected patients and 20 HCC patients were selected for screening study and same number of sera into the same three groups were used for validation study. A strategy including sonication, albumin and immunoglobulin G (IgG) depletion and desalting was optimized for screening differentially expressed proteins of low abundance in serum. By 2-DE image analysis and MALDI-TOF-MS/MS identification, eight proteins including heat-shock protein 27 (HSP27), alpha-fetoprotein (AFP), alpha-1 antitrypsin, clusterin, caeruloplasmin, haptoglobin alpha2 chain, tranferrin and transthyretin were found significantly changed among the healthy, HBV and HCC groups. Further validation study by Western blot showed the detection of HSP27 in 90% HCC sera and two HBV sera, but in none of normal sera. Thus, 2-DE based serum proteome analysis can be useful in the screening of serum biomarkers for HCC and HSP27 could aid in the diagnosis of HCC though further validation is needed.

Adult↗

PubMed2005

Proteomic analysis of sera from hepatocellular carcinoma patients after radiofrequency ablation treatment.

Comparative proteomic analysis was used to search for characteristic alterations in the sera of hepatocellular carcinoma (HCC) patients who had undergone curative radiofrequency ablation treatment. Serum samples collected from eight patients before and after treatment were subjected to 2-DE. Eighty-eight protein spots differentially expressed with the treatment were selected by clustering analysis, and the proteins were identified by MS based on MALDI-TOF/TOF analysis and public database searches. The statistical analysis suggested that four proteins decreased after treatment (pro-apolipoprotein, alpha2-HS glycoprotein, apolipoprotein A-IV precursor, and PRO1708/PRO2044, which is the carboxy terminal fragment of albumin) and that seven proteins were increased after treatment, including leucine-rich alpha2-glycoprotein and alpha1-antitrypsin. These data facilitate the identification of differentially expressed proteins that are involved in HCC carcinogenesis and provide candidate biomarkers for the development of diagnostic and therapeutic tools.

Apolipoproteins A↗

PubMed2006

Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometry.

MOTIVATION: Using stable isotopes in global proteome scans, labeled molecules from one sample are pooled with unlabeled molecules from another sample and subsequently subjected to mass-spectral analysis. Stable-isotope methodologies make use of the fact that identical molecules of different stable-isotope compositions are differentiated in a mass spectrometer and are represented in a mass spectrum as distinct isotopic clusters with a known mass shift. We describe two multivariable linear regression models for (16)O/(18)O stable-isotope labeled data that jointly model pairs of resolved isotopic clusters from the same peptide and quantify the abundance present in each of the two biological samples while concurrently accounting for peptide-specific incorporation rates of the heavy isotope. The abundance measure for each peptide from the two biological samples is then used in down-stream statistical analyses, e.g. differential expression analysis. Because the multivariable regression models are able to correct for the abundance of the labeled peptide that appear as an unlabeled peptide due to the inability to exchange the natural C-terminal oxygen for the heavy isotope, they are particularly advantageous for a two-step digestion/labeling procedure. We discuss how estimates from the regression model are used to quantify the variability of the estimated abundance measures for the paired samples. Although discussed in the context of (16)O/(18)O stable-isotope labeled data, the multivariable regression models are generalizable to other stable-isotope labeled technologies.

Algorithms↗

PubMed2006

Proteomic analysis of acute promyelocytic leukemia: PML-RARalpha leads to decreased phosphorylation of OP18 at serine 63.

In the present study, we employed 2-DE to characterize the effect of the acute promyelocytic leukemia (APL)-specific PML-RARalpha fusion protein on the proteome. Differentially expressed proteins, a number of which are related to the cell cycle function, including oncoprotein18 (OP18), heat shock protein70, glucose-regulated protein75, and peptidyl-prolyl isomerase, were identified by MS. Subsequent bioinformatic pathway discovery revealed an integrated network constituting SMARCB1, MYC, and TP53-regulated pathways. The data from the DNA microarray and proteomic experiments demonstrated the correlation between the translocation and higher expression of OP18 at mRNA and protein levels. Transient cotransfection assay revealed that PML-RARalpha is a potent activator of OP18 promoter and this transcriptional activation is retinoic acid sensitive. PML-RARalpha induction also leads to decreased phosphorylation on Ser63 residue of OP18, which is okadaic acid sensitive suggesting the involvement of a phosphatase pathway. Overexpression of a constitutively phosphorylated Ser63 mutant of OP18 in PML-RARalpha expressing APL patient, PR9, and NB4 cells led to a G2/M-phase arrest in contrast to a phosphorylation-deficient Ser63 mutant and untransfected control. Taken together, our results demonstrate the significance of decreased Ser63 phosphorylation of OP18 in PML-RARalpha-mediated effects on cell cycle.

Cell Line↗

PubMed2004

Proteome analysis reveals a distinct molecular profile of cellular stress following incubation of DDT1-MF2 smooth muscle cells in the presence of a high concentration of hyperforin.

The acylphloroglucinol derivative hyperforin is a major constituent of St. John's wort extracts ( Hypericum perforatum L.), which has been demonstrated to contribute to the antidepressant action of this herbal drug. In previous investigations we observed that hyperforin causes a rapid stimulation of intracellular calcium mobilization and enhances extracellular acidification in the hamster vas deferens smooth muscle cell line DDT (1)-MF2. To obtain further insight into its mode of action, we have now examined if these effects are accompanied by changes in protein expression. Cells were incubated with hyperforin for 15 min at a concentration of 1 microg/mL. Proteome analysis in cell lysates was accomplished by two-dimensional gel electrophoresis (2D-PAGE) and proteins were visualized by silver staining. Differences in the expression pattern between hyperforin- and vehicle-treated cells were displayed by computer-assisted differential display and identification of selected protein spots was performed by peptide mass fingerprinting after digestion with trypsin. Following incubation with hyperforin marked changes in the expression of several proteins were evident. A particularly strong change was observed for 6 proteins, which were identified as tubulin-beta, enolase 3, SYNCRIP, endoplasmin, elongation factor 2 and HSP84. As these proteins are known to be involved in cellular responses to stress by regulating energy metabolism as well as synthesis, intracellular transport and folding of proteins, our results suggest that the effects observed are not components of the normal pharmacological activity profile of hyperforin but are rather indicative of cellular stress promoting activity at higher concentrations.

Animals↗

PubMed2006

The use of microarrays to define functionally-related genes that are differentially expressed in the cycling pig uterus.

In swine and other livestock, the uterine endometrium exhibits dramatic morphological and secretory changes throughout the oestrous cycle and during pregnancy. Such physiological changes are a reflection of extremely complex interactions between gene products (RNA and protein). The recent development of genomics and proteomics methods, as well as associated bioinformatics tools, has provided the means to begin characterising such interactions. Indeed, the analysis of the transcriptome and proteome of cells and tissues now comprises a new field of study known as 'systems biology'. Currently, the most powerful technique available to the systems biologist is the microarray. These platforms represent oligonucleotide or cDNA fragments spotted in a specified high-density pattern on a solid support. Hybridisation of fluorescently-tagged cDNAs from different tissue sources permits the measurement of thousands of RNAs in parallel. The method permits the identification of genes that are present at different amounts between the two tissues and, more importantly, it permits the identification of groups of genes (clusters) that are expressed in comparable patterns. Results from a recent expression profiling experiment are described. The goal of the profiling experiment was to define genes that are differentially expressed in endometrium during the oestrous cycle. The experiment used an in-house cDNA microarray with > 14,000 distinct cDNAs cloned from reproductive tissues. Total RNAs from cyclic endometrium (Days 0, 3, 6, 10, 12, 14 and 18 post-oestrus) were reverse transcribed into cDNAs, labelled with fluorescent dye and hybridised to the arrays along with cDNAs derived from a reference RNA pool. A total of 4,827 genes were found to differ significantly at some time during the oestrous cycle. Clustering methods were able to define numerous groups of similarly expressed genes. These data will help to define the complex patterns of endometrial genes acting in concert to create the environments required for fertilisation, embryo growth and conceptus development in swine.

Animals↗

PubMed2006

[Proteomic analysis of proteins related to retinoid acid resistance].

OBJECTIVE: To evaluate the applicability of proteomic methods for shedding light on the mechanisms of All-trans retinoic acid resistance. METHODS: The expression of cellular proteins in the retinoid acid sensitive cell line NB4 and retinoid acid resistant cell line MR2 was analyzed using the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Differentially expressed proteins were analyzed by mass spectrometry for peptide mass finger and identified by SWISS-PROT protein database. RESULTS: Approximately 600 spots appeared in an sodium dod(SDS-GEL). The match of the expression of cellular proteins between NB4 and MR2 was better. Three significantly differentially expressed proteins were screened and identified to DJ-1 and HSP70, as well as KIAA1289 of which the function is not yet known. CONCLUSION: The utilization of 2D-PAGE, coupled with mass spectrometry is effective in screening the drug resistance-associated proteins and could provide molecular targets for the elucidation of resistance mechanisms.

Antineoplastic Agents↗