RhoB and the cellular response to farnesyltransferase inhibitors: the search for clues to cell death mechanisms.
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Alkyl and Aryl Transferases↗
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Results for “Biomarker Profiling”
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Clinically validated benchmarking of normalisation techniques for two-colour oligonucleotide spotted microarray slides.
Acquisition of microarray data is prone to systematic errors. A correction, called normalisation, must be applied to the data before further analysis is performed. With many normalisation techniques published and in use, the best way of executing this correction remains an open question. In this study, a variety of single-slide normalisation techniques, and different parameter settings for these techniques, were compared over many replicated microarray experiments. Different normalisation techniques were assessed through the distribution of the standard deviation of replicates from one biological sample across different slides. It is shown that local normalisation outperformed global normalisation, and intensity-based 'LOWESS' outperformed trimmed mean and median normalisation techniques. Overall, the top performing normalisation technique was a print-tip-based LOWESS with zero robust iterations. Lastly, we validated this evaluation methodology by examining the ability to predict oestrogen receptor-positive and -negative breast cancer samples with data that had been normalised using different techniques.
Algorithms↗
Peculiarities of molecular events in human glial tumors revealed by serial analysis of gene expression (SAGE).
AIM: To enhance glioblastoma (GB) marker discovery we compared gene expression in glioblastoma with human normal brain (NB). METHODS: Serial analysis of gene expression (SAGE) was used to determine the genes differentially expressed between glioblastoma and human NB by accessing SAGEmap NCBI web site. RESULTS: Of 117 genes with more than 5-fold difference (P less, not similar 0.05) found by comparison of five GB vs. two NB SAGE libraries, 24 had an increased expression in GB. High expression of 10 genes in GB as well as in GB cell lines suggested that expression in the bulk tumors originated from transformed cells. CONCLUSION: Since the highest expression levels of these 24 genes were mostly found in GB, they can be viewed as molecular markers in the analysis of malignant progression of astrocytic tumors.
Astrocytoma↗
Integration of genomic and metabonomic data in systems biology--are we 'there' yet?
The measurement of genes, proteins and metabolites has gained increasing acceptance as a means by which to study the response of an organism to stimuli, whether they are environmental, genetic, pharmacological, toxicological, etc. Typically referred to as genomics, proteomics, and metabonomics or metabolomics, respectively, these methods as independent entities have undoubtedly provided new biological insight that was not attainable a decade ago. Not surprisingly, scientists continue to push the boundaries to extract knowledge from data, and it is currently recognized that the full realization of these technologies is limited by a lack of tools to enable data integration. Integration of these 'omic datasets, or integromics, is desirable as it links the individual biological elements together to provide a more complete understanding of dynamic biological processes. Accordingly, in addition to developing new data analysis methods to extract further details from each of the high-content datasets individually, effort is also being expended to create or improve statistical methods, databases, annotations and pathway mapping to maximize our learning. There are several recent examples, in both mammalian and non-mammalian systems, in which genes, proteins and/or metabolites have been integrated using either biology- or data-driven strategies. Herein, key findings are reviewed, gaps in our current tools and technologies are identified and illustrated, and perspective is provided on the potential of integromics in biological research.
Acetaminophen↗
Quantitative profiling of drug-associated proteomic alterations by combined 2-nitrobenzenesulfenyl chloride (NBS) isotope labeling and 2DE/MS identification.
The identification of drug-responsive biomarkers in complex protein mixtures is an important goal of quantitative proteomics. Here, we describe a novel approach for identifying such drug-induced protein alterations, which combines 2-nitrobenzenesulfenyl chloride (NBS) tryptophan labeling with two-dimensional gel electrophoresis (2DE)/mass spectrometry (MS). Lysates from drug-treated and control samples are labeled with light or heavy NBS moiety and separated on a common 2DE gel, and protein alterations are identified by MS through the differential intensity of paired NBS peptide peaks. Using NBS/2DE/MS, we profiled the proteomic alterations induced by tamoxifen (TAM) in the estrogen receptor (ER) positive MCF-7 breast cancer cell line. Of 88 protein spots that significantly changed upon TAM treatment, 44 spots representing 23 distinct protein species were successfully identified with NBS-paired peptides. Of these 23 TAM-altered proteins, 16 (70%) have not been previously associated with TAM or ER activity. We found the NBS labeling procedure to be both technically and biologically reproducible, and the NBS/2DE/MS alterations exhibited good concordance with conventional 2DE differential protein quantitation, with discrepancies largely due to the comigration of distinct proteins in the regular 2DE gels. To validate the NBS/2DE/MS results, we used immunoblotting to confirm GRP78, CK19, and PA2G4 as bona fide TAM-regulated proteins. Furthermore, we demonstrate that PA2G4 expression can serve as a novel prognostic factor for disease-free survival in two independent breast cancer patient cohorts. To our knowledge, this is the first report describing the proteomic changes in breast cancer cells induced by TAM, the most commonly used selective estrogen receptor modulator (SERM). Our results indicate that NBS/2DE/MS may represent a more reliable approach for cellular protein quantitation than conventional 2DE approaches.
Cell Line, Tumor↗
Transcriptional profiling of peripheral blood cells in clinical pharmacogenomic studies.
Peripheral blood represents an attractive tissue source in clinical pharmacogenomic studies, given the feasibility of its collection from patients and its potential as a sentinel tissue to monitor perturbations of physiology in many disease states. The hypothesis is that the circulating blood cells monitor the physiological state of the organism and alter their transcriptome in response to this surveillance. However, the successful implementation of transcriptional profiling of peripheral blood cells in clinical trials represents a tremendous technical challenge for several reasons, including controlling the pre-analytical variables associated with sample processing and the interpretation of gene expression signatures generated from the complex mixture of cell types in blood. Multiple approaches for identifying transcriptomes in peripheral blood cells exist and each method is associated with significant advantages and disadvantages. Nonetheless, a growing number of studies are rapidly identifying transcriptional biomarkers in peripheral blood cells that may function as biomarkers of disease, evidence of pharmacodynamic effect, or even predictors of clinical outcomes and risk of toxicity. This review highlights the major approaches employed in global transcriptional profiling of peripheral blood cells and summarizes the available literature of initial studies in the growing field of hemogenomics. The overall purpose of the review is to focus on the development and application of technologies for the use of peripheral blood cells as a sentinel or surrogate tissue to measure disease state and drug response.
Animals↗
[Hepatocarcinogenesis in human liver].
Due to the development of the imaging techniques and liver surgery, pathologists are encountered more frequently with preneoplastic liver lesions. Well-defined stages of human hepatocarcinogenesis have been distinguished recently. Dysplastic foci represent the earliest stage of this process. Small-cell dysplastic foci are tumor precursors, but the large-cell form of this lesion does not progress further. The next stage is the dysplastic nodule, this larger lesion can be recognized by imaging techniques and gross examination of the specimen. Low- and high-risk forms are distinguished based on the level of cytological and structural atypia. The small hepatocellular carcinomas have a diameter of less than 2 cm by definition. The small HCC of indistinctly nodular type is equivalent of in situ carcinomas in other organs and designated sometimes as early HCC. The small HCC of the distinctly nodular type can be interpreted as advanced cancer despite its small size. The distinction between these lesions can be facilitated by ancillary techniques. The so-called capillarization of the liver sinusoids during the progression is characterized by the increased expression of endothelial markers as CD31 and CD34. Immunostaining for CD44, beta-catenin and p53 has prognostic value. Molecular biological techniques reveal gradual epigenetic and DNA changes during the process of hepatocarcinogenesis. Global gene expression profiling of hepatocellular carcinomas may result in a new classification of this tumor and can reveal new potential therapeutic targets.
Biomarkers, Tumor↗
Identification and classification of differentially expressed genes in non-small cell lung cancer by expression profiling on a global human 59.620-element oligonucleotide array.
Improvements in detection, treatment and prognosis for patients with non-small cell lung cancer (NSCLC) depend on the molecular understanding of tumor development and progression. Using Affymetrix GeneChips comprising 59,620 elements, we determined the gene expression profiles of 89 NSCLC and 15 normal lung samples. We found 187 (0.3%) genes, which are at least 2-fold overexpressed and 157 (0.3%) genes 2-fold less expressed in NSCLC compared with normal lung. Cell cycle regulation, cell adhesion and nucleotide metabolism were the major biological processes connected to a large proportion of genes up-regulated in NSCLC. Down-regulated genes were frequently involved in metabolic/catabolic processes and signal transduction. The expression of specific genes revealed reliable differentiation of tumor from normal lung tissues, as well as the classification of both NSCLC subtypes squamous cell carcinoma and adenocarcinoma. In this context, collagens (COL7, 17) and cytokeratins (CK6, 15, 17) are preferentially induced in squamous cell carcinoma, whereas several transcription factors (TTF1, DAT1, TF-2) are exclusively elevated in adenocarcinomas. Some gene products involved in the metastatic process [matrixmetalloproteinase 12 (MMP-12) and urokinase plasminogen activator alpha (uPA)] were found as prognostic markers for the recurrence free interval and survival. Particularly, the simultaneous use of the MMP-12 and uPA expression predicted relapse-free and global survival of the patients. Screening of NSCLC with a genome-wide array revealed diagnostic, prognostic and potential therapeutic targets that might be suitable for an individual risk profile by tumor specific arrays.
Aged↗
Protein expression profiles in adenocarcinomas and squamous cell carcinomas of the lung generated using tissue microarrays.
With the appearance of defect-targeted therapies, the definition of tumour protein expression profiles has gained increasing importance. Two lung carcinoma tissue microarrays, one including 75 primary adenocarcinomas (ACs) and the other comprising 67 primary squamous cell carcinomas (SQCCs), were generated in the present study. On both arrays, each tumour was represented by an average of five cores. In addition, one punch of normal lung parenchyma adjacent to each tumour was included in the array. Immunohistochemical expression of 86 proteins was evaluated and the results were analysed by non-parametric tests, hierarchical clustering, and principal component analysis. In both tumour entities, parenchyma and tumours were clearly separated by hierarchical clustering. By the same statistical approach, it was possible to distinguish ACs from SQCCs with 98% accuracy and to distinguish parenchyma adjacent to ACs from that adjacent to SQCCs with 96% accuracy. It was also possible to separate ACs into three groups that significantly differed in survival. Cathepsin E and hsp105 were identified as previously unknown predictors of survival in lung AC. In summary, this study has shown that protein profiles are feasible tools for anticipating biological behaviour.
Adenocarcinoma↗
Human galectin-2: expression profiling by RT-PCR/immunohistochemistry and its introduction as a histochemical tool for ligand localization.
Sugar-encoded information of glyco-conjugates is translated into cellular responses by endogenous lectins. Galectins stand out against other lectin families due to their wide range of functions including cell adhesion, tissue invasion or growth regulation exerted at extracellular, membrane, cytoplasmic and nuclear sites. This remarkable versatility warrants close scrutiny of their emerging network, in this study with focus on homodimeric human galectin-2. We first detected presence of specific mRNA in various tissue types by processing post mortem and surgical specimens by RT-PCR protocols. Overlap of gene expression was noted with proto-type galectins-1 and -7 and also family members from the other two subgroups. To monitor expression on the level of protein a polyclonal anti-galectin-2 antibody was raised. Immunopositivity was semi-quantitatively assessed in sections of 209 human samples establishing an array both of normal tissues and samples with inflammation or benign/malignant growth. In general, positivity was predominantly epithelial without restriction of staining to certain tissue types, as fittingly indicated by our RT-PCR analysis. Staining was not limited to the cytoplasm but also included nuclear sites. To examine the suitability of the labeled lectin as a histochemical probe we biotinylated galectin-2 under activity-preserving conditions and introduced it to tissue profiling. Specific cytoplasmic staining proved the validity of the concept. Our results encourage systematic histopathologic studies by immuno- and lectin histochemistry, especially by adding galectin-2 as study object to galectin fingerprinting which has already yielded prognostic information on galectins-1, -3, -4 and -8 and hereby contributed to define functional overlap/divergence in this lectin family.
Antibodies↗
Biomarkers for melanoma.
PURPOSE OF REVIEW: Given the capricious nature of melanoma, biomarkers that provide significant insight into the behavior of melanoma would greatly aid in identifying patients at risk for disease progression, those whose disease has progressed subclinically, and those who would benefit from currently available systemic therapies. This review focuses on molecular prognostic markers in primary melanoma, markers that aid in the detection of metastatic melanoma, and markers predictive of systemic therapy. RECENT FINDINGS: Significant advances have been made in the field of melanoma biomarkers. Utilization of paraffin-embedded tissue and multiple markers have improved the RT-PCR assays for detection of melanoma cells in lymph node tissue as well as peripheral blood. Lymphangiogenesis has been identified as a novel mechanism for melanoma progression, and candidate markers in the NF-kappaB signaling pathway have been identified to play a key role in melanoma: tumor vasculature interactions. Loss of heterozygosity has been used to identify potential candidates for biochemotherapy. Furthermore, serum S100B protein has been shown to be superior to lactate dehydrogenase in predicting prognosis and response to treatment for patients with advanced melanoma. SUMMARY: Although recent studies have contributed greatly to the development of melanoma markers, it is anticipated that the application of gene expression profiling and proteomics techniques to melanocytic neoplasms will result in the identification of even more effective biomarkers for melanoma than those currently in clinical use.
Biomarkers, Tumor↗
Metabolic profiling--IBC's inaugural meeting. Using metabolomics to accelerate drug discovery and development. 14-15 November 2005, Durham, NC, USA.
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Animals↗
Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma.
Systematic detection of low-abundance proteins in human blood that may be putative disease biomarkers is complicated by an extremely wide range of protein abundances. Hence, depletion of major proteins is one potential strategy for enhancing detection sensitivity in serum or plasma. This study compared a recently commercialized HPLC column containing antibodies to six of the most abundant blood proteins ("Top-6 depletion") with either older Cibacron blue/Protein A or G depletion methods or no depletion. In addition, a prototype spin column version of the HPLC column and an alternative prototype two antibody spin column were evaluated. The HPLC polyclonal antibody column and its spin column version are very promising methods for substantially simplifying human serum or plasma samples. These columns show the lowest nonspecific binding of the depletion methods tested. In contrast other affinity methods, particularly dye-based resins, yielded many proteins in the bound fractions in addition to the targeted proteins. Depletion of six abundant proteins removed about 85% of the total protein from human serum or plasma, and this enabled 10- to 20-fold higher amounts of depleted serum or plasma samples to be applied to 2-D gels or alternative protein profiling methods such as protein array pixelation. However, the number of new spots detected on 2-D gels was modest, and most newly visualized spots were minor forms of relatively abundant proteins. The inability to detect low-abundance proteins near expected 2-D staining limits was probably due to both the highly heterogeneous nature of most plasma or serum proteins and masking of many low-abundance proteins by the next series of most abundant proteins. Hence, non2-D methods such as protein array pixelation are more promising strategies for detecting lower abundance proteins after depleting the six abundant proteins.
Animals↗
Proteomic analysis of the allograft response.
BACKGROUND: As transcriptional profiling techniques appear to provide a useful means to evaluate the allograft response, we have now initiated an attempt to use proteomics to examine the allograft response. METHODS: To this end, we have evaluated the use of Protein Chip technology, coupled with bioinformatics analysis towards discovery of allograft response biomarkers in a mouse skin transplant model. To compare samples obtained from acutely rejecting allograft recipients at days 7, 9, and 21, we treated one group with a potent antirejection regimen. Mean survival time in the fully MHC-mismatched skin graft model using this protocol is more than 100 days. We also studied recipients of nontreated syngenetic grafts. We applied Protein Chip technology toward discovery of allograft response markers in this model. RESULTS: At days 7 and 9, before the clinical appearance of rejection at day 10, several protein biomarker candidates were detected, based on their molecular mass that clearly differentiated between rejection and the nonrejection groups. CONCLUSIONS: Protein profiling of serum as a means to characterize the allografts response of a given host deserves further testing in clinical studies.
Abatacept↗
Anti-glycan antibodies as biomarkers for diagnosis and prognosis.
Glycans (sugars or carbohydrates) are predominant surface components of cells such as erythrocytes, immune cells and microorganisms. As such, they give rise to high levels of anti-glycan antibodies of all classes. Antibodies to certain defined mono, di and oligosaccharides that are common in bacterial, fungal and parasite cells exist in human sera and can be profiled using glycan arrays. The use of glycan arrays for systematic screening of blood samples from multiple sclerosis (MS) and Crohn's disease (CD) patients in versus to blood samples from control groups, have lead to the discovery of a few anti glycan antibodies biomarkers enabling diagnosis and prognosis in MS and CD patients. Anti-Glc(alpha1,4)Glc(alpha) IgM antibodies were found to be specific for MS patients, enabling differentiation between MS patients and patients with other neurological diseases, with 54% sensitivity and 85% specificity. Anti-Glc(alpha1,4)Glc(alpha) IgM were found to be predictive for the conversion of patients in first acute neurological event to clinically defined MS. Anti-laminaribioside (ALCA), anti-mannobioside (AMCA) and anti-chitobioside (ACCA) antibodies were found to be specific for CD. The combined use of these antibodies enables improved diagnosis of CD versus ulcerative colitis and other gastrointestinal diseases, as well as stratification of CD patients with a more complicated disease and high risk for surgery. Anti-glycan antibodies profiling (AGAP) is a new and promising approach for development of biomarkers for diagnosis and prognosis.
Antibodies↗
Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease.
Multiple sclerosis (MS) and other T cell-mediated autoimmune diseases develop in individuals carrying a complex susceptibility trait, probably following exposure to various environmental triggers. Owing to the presumed weak influence of single genes on disease predisposition and the recognized genetic heterogeneity of autoimmune disorders in humans, candidate gene searches in MS have been difficult. In an attempt to identify molecular markers indicative of disease status rather than susceptibility genes for MS, we show that gene expression profiling of peripheral blood mononuclear cells by cDNA microarrays can distinguish MS patients from healthy controls. Our findings support the concept that the activation of autoreactive T cells is of primary importance for this complex organ-specific disorder and prompt further investigations on gene expression in peripheral blood cells aimed at characterizing disease phenotypes.
Adult↗
Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases.
Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS) is a proteomic technique that enables the profiling of proteins present in any biological material studied. We used this approach to identify new biomarkers of hepatocellular carcinoma (HCC) in the sera of patients with cirrhosis. Sera from 82 patients with cirrhosis, either without (n = 38) or with (n = 44) HCC, were analyzed by SELDI-TOF MS, and the results of the two groups were compared. The most efficient protein peaks leading to discrimination of patients with HCC were selected (receiver operative characteristic curves). The highest-scoring peak combination was established in a first group of serum samples (multinomial regression) and was tested in an independent group. The protein corresponding to the highest discrimination was purified and characterized further. The intensity of 30 protein peaks significantly differed between cirrhotic patients with and without HCC. An algorithm including the six highest-scoring peaks allowed correct classification (presence or absence of HCC) of 92.5% of patients in the test sample set and 90% in the validation sample set. The highest discriminating peak (8900 Da) was purified further and was characterized as the C-terminal part of the V10 fragment of vitronectin. An in vitro study suggested that the increase of the 8900-Da fragment in the serum of patients with HCC may proceed from the cleavage of native vitronectin with metalloproteases, a family of enzymes whose activity is enhanced in HCC. In conclusion, global protein profiling is an efficient approach that enabled us to identify a catalytic fragment ofvitronectin as a new serum marker of HCC in patients with chronic liver diseases.
Aged↗
Circulating microRNA panels for multi-cancer detection and gastric cancer screening: leveraging a network biology approach.
BACKGROUND: Screening tests, particularly liquid biopsy with circulating miRNAs, hold significant potential for non-invasive cancer detection before symptoms manifest. METHODS: This study aimed to identify biomarkers with high sensitivity and specificity for multiple and specific cancer screening. 972 Serum miRNA profiles were compared across thirteen cancer types and healthy individuals using weighted miRNA co-expression network analysis. To prioritize miRNAs, module membership measure and miRNA trait significance were employed. Subsequently, for specific cancer screening, gastric cancer was focused on, using a similar strategy and a further step of preservation analysis. Machine learning techniques were then applied to evaluate two distinct miRNA panels: one for multi-cancer screening and another for gastric cancer classification. RESULTS: The first panel (hsa-miR-8073, hsa-miR-614, hsa-miR-548ah-5p, hsa-miR-1258) achieved 96.1% accuracy, 96% specificity, and 98.6% sensitivity in multi-cancer screening. The second panel (hsa-miR-1228-5p, hsa-miR-1343-3p, hsa-miR-6765-5p, hsa-miR-6787-5p) showed promise in detecting gastric cancer with 87% accuracy, 90% specificity, and 89% sensitivity. CONCLUSIONS: Both panels exhibit potential for patient classification in diagnostic and prognostic applications, highlighting the significance of liquid biopsy in advancing cancer screening methodologies.
Neoplasms↗