Robust estimation of protein expression ratios with lysate microarray technology

Mircean, Cristian; Shmulevich, Ilya; Cogdell, David; Choi, Woonyoung; Jia, Yu; Tăbuş, Ioan; Hamilton, Stanley R.; Zhang, Wei

doi:10.1093/bioinformatics/bti258

Cited by 40 publications

(24 citation statements)

References 4 publications

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“…BSA has numerous biochemical applications, including protein microarray technology [3], lysate microarray technology [4], enzyme-linked immunosorbent assay (ELISA) [5,6], immunoblots as a blocking agent during western blotting to reduce background and non-specific binding [7], and immunohistochemistry [8]. Moreover, it is generally used in vaccine delivery studies as a model protein [9][10][11][12][13][14], owing to its ease of assay, well-known immunogenicity pattern, well-known physicochemical properties, low cost, and general availability.…”

Section: Introductionmentioning

confidence: 99%

Highly Sensitive Chemiluminescent Analysis of Residual Bovine Serum Albumin (BSA) Based on a Pair of Specific Monoclonal Antibodies and Peroxyoxalate–glyoxaline–PHPPA Dimer Chemiluminescent System in Vaccines

Xue

Zhang

et al. 2012

Appl Biochem Biotechnol

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Enzyme-linked immunosorbent assay (ELISA), horseradish peroxidase (HRP)-catalyzed fluorescent reaction, and oxalate chemiluminescence analysis have been combined to develop a highly sensitive, simple, and rapid method for analysis of bovine serum albumin (BSA) based on a pair of specific monoclonal antibodies in vaccines. A typical "sandwich type" immunoassay was used. Reaction of 3-(4-hydroxyphenyl propionate) (PHPPA) with hydrogen peroxide-urea, catalyzed by HRP, produced fluorescence of 3-(4-hydroxyphenyl propionate) dimer, which was detected by chemiluminescence analysis with the bis(2,4,6-trichlorophenyl)oxalate (TCPO)-H(2)O(2)-glyoxaline-PHPPA dimer chemiluminescent system. This method exhibited high performance with a linear correlation between response and amount of bovine serum albumin (BSA) in the range 0.1 to 100.0 ng mL(-1) (r = 0.9988), and the detection limit was 0.03 ng mL(-1) (S/N = 3). Intra- and interassay coefficient variations were all lower than 9.0% at three concentrations (1.0, 20.0, and 80.0 ng mL(-1)). The proposed method has been used for successful analysis of the amount of residual BSA in vaccines. The results obtained compared well with those obtained by conventional colorimetric ELISA and luminol chemiluminescent ELISA.

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Section: Introductionmentioning

confidence: 99%

Highly Sensitive Chemiluminescent Analysis of Residual Bovine Serum Albumin (BSA) Based on a Pair of Specific Monoclonal Antibodies and Peroxyoxalate–glyoxaline–PHPPA Dimer Chemiluminescent System in Vaccines

Xue

Zhang

et al. 2012

Appl Biochem Biotechnol

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“…The introduction of a universal reference standard on each RPPM has been suggested as one solution to compensate for the variability introduced by different instruments and experimental factors (Sheehan et al, 2005). Data analysis of RPPMs, especially those with serial sample dilutions, is somewhat more complex than in DNA microarrays (Mircean et al, 2005). As in ELISA applications, standard curves must be generated for each antibody.…”

Section: Challenges Of Rppmsmentioning

confidence: 99%

Microarrays as Validation Strategies in Clinical Samples: Tissue and Protein Microarrays

Aguilar‐Mahecha

Hassan

Ferrario

et al. 2006

OMICS: A Journal of Integrative Biology

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The widespread use of DNA microarrays has led to the discovery of many genes whose expression profile may have significant clinical relevance. The translation of this data to the bedside requires that gene expression be validated as protein expression, and that annotated clinical samples be available for correlative and quantitative studies to assess clinical context and usefulness of putative biomarkers. We review two microarray platforms developed to facilitate the clinical validation of candidate biomarkers: tissue microarrays and reverse-phase protein microarrays. Tissue microarrays are arrays of core biopsies obtained from paraffin-embedded tissues, which can be assayed for histologically-specific protein expression by immunohistochemistry. Reverse-phase protein microarrays consist of arrays of cell lysates or, more recently, plasma or serum samples, which can be assayed for protein quantity and for the presence of post-translational modifications such as phosphorylation. Although these platforms are limited by the availability of validated antibodies, both enable the preservation of precious clinical samples as well as experimental standardization in a high-throughput manner proper to microarray technologies. While tissue microarrays are rapidly becoming a mainstay of translational research, reverse-phase protein microarrays require further technical refinements and validation prior to their widespread adoption by research laboratories.

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“…Mapping in vitro phosphoprotein signaling pathways using RPMA RPMA has demonstrated the sensitivity necessary to distinguish protein expression ratios of low abundance protein species in whole cell lysates and in rare cell populations [25, 100,105,[125][126][127]. Wei et al recently utilized RPMA to evaluate nucleotide excision repair (NER) proteins in lymphocyte cell lines derived from patients with newly diagnosed squamous cell carcinomas of the head and neck (SCCHN), and compared these protein expression levels to those of clinically matched normal controls [126,127].…”

Section: Analytical Challengesmentioning

confidence: 99%

“…Wei et al recently utilized RPMA to evaluate nucleotide excision repair (NER) proteins in lymphocyte cell lines derived from patients with newly diagnosed squamous cell carcinomas of the head and neck (SCCHN), and compared these protein expression levels to those of clinically matched normal controls [126,127]. When NER protein levels were stimulated by transfection with damaged and undamaged plasmid DNA, it was found that lymphocytes derived from SCCHN patients had significantly lower overall levels of NER protein expression, suggesting that SCCHN maintain a higher tolerance to DNA damage.…”

Section: Analytical Challengesmentioning

confidence: 99%

Clinical phosphoproteomic profiling for personalized targeted medicine using reverse phase protein microarray

et al. 2006

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Healthcare providers are increasingly incorporating information gleaned from genomics and proteomics in the diagnosis and treatment of cancer. These lines of inquiry are providing greater insight into why patients with similar histological tumor classification and staging often demonstrate dissimilar clinical outcomes, and are illuminating distinct diagnostic subgroups that are more responsive to specific treatment modalities. Clearer understanding of genes, gene products, and signaling pathways holds great promise for the personalization of molecular medicine. While the origins of oncologic disease are genetically encoded, the disease process is largely mediated through altered protein function. Recent investigations suggest that each individual patient's tumor possesses unique kinasedriven cell signaling derangements, and that these derangements derive, in part, from the tumor's relationship with its host microenvironment. Identification of signaling derangements and mapping functional protein-protein interactions via phosphoproteomic profiling offers great promise for the precise targeting of therapeutic agents, identifying new therapeutic targets, devising effective combinatorial therapies, monitoring treatment efficacy and toxicity, and ultimately predicting treatment outcome. This review focuses on advances in clinical phosphoproteomic profiling of cancer using the emerging technology of reverse phase protein microarrays, and highlights the translational roles this technology is playing in laying the foundations for personalized molecular therapeutics.

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Robust estimation of protein expression ratios with lysate microarray technology

Abstract: http://www.cs.tut.fi/~mirceanc/lysate_array_bioinformatics.htm

Cited by 40 publications

References 4 publications

Highly Sensitive Chemiluminescent Analysis of Residual Bovine Serum Albumin (BSA) Based on a Pair of Specific Monoclonal Antibodies and Peroxyoxalate–glyoxaline–PHPPA Dimer Chemiluminescent System in Vaccines

Highly Sensitive Chemiluminescent Analysis of Residual Bovine Serum Albumin (BSA) Based on a Pair of Specific Monoclonal Antibodies and Peroxyoxalate–glyoxaline–PHPPA Dimer Chemiluminescent System in Vaccines

Microarrays as Validation Strategies in Clinical Samples: Tissue and Protein Microarrays

Clinical phosphoproteomic profiling for personalized targeted medicine using reverse phase protein microarray

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