scholarly journals Protein Microarrays for Personalized Medicine

2010 ◽  
Vol 56 (3) ◽  
pp. 376-387 ◽  
Author(s):  
Xiaobo Yu ◽  
Nicole Schneiderhan-Marra ◽  
Thomas O Joos
Keyword(s):  
Personalized Medicine ◽  
Protein Function ◽  
Dna Microarrays ◽  
Biomarker Discovery ◽  
Protein Microarray ◽  
Disease Diagnosis ◽  
Protein Microarrays ◽  
Nucleotide Polymorphisms ◽  
Single Experiment

Abstract Background: Over the last 10 years, DNA microarrays have achieved a robust analytical performance, enabling their use for analyzing the whole transcriptome or for screening thousands of single-nucleotide polymorphisms in a single experiment. DNA microarrays allow scientists to correlate gene expression signatures with disease progression, to screen for disease-specific mutations, and to treat patients according to their individual genetic profiles; however, the real key is proteins and their manifold functions. It is necessary to achieve a greater understanding of not only protein function and abundance but also their role in the development of diseases. Protein concentrations have been shown to reflect the physiological and pathologic state of an organ, tissue, or cells far more directly than DNA, and proteins can be profiled effectively with protein microarrays, which require only a small amount of sample material. Content: Protein microarrays have become well-established tools in basic and applied research, and the first products have already entered the in vitro diagnostics market. This review focuses on protein microarray applications for biomarker discovery and validation, disease diagnosis, and use within the area of personalized medicine. Summary: Protein microarrays have proved to be reliable research tools in screening for a multitude of parameters with only a minimal quantity of sample and have enormous potential in applications for diagnostic and personalized medicine.

scholarly journals Human lymphoblastoid cell lines: a valuable tool for personalized medicine research

2016 ◽  
Vol 38 (1) ◽  
pp. 6-9
Author(s):  
David Gurwitz
Keyword(s):  
Personalized Medicine ◽  
Cell Lines ◽  
Biological Samples ◽  
Biomarker Discovery ◽  
Disease Diagnosis ◽  
Lymphoblastoid Cell Lines ◽  
Medicine Research ◽  
Human Lymphoblastoid Cell ◽  
The Right ◽  
Human Lymphoblastoid Cell Lines

Over the last two decades, and in particular since the completion of the Human Genome Project, medicine has been slowly but persistently moving towards personalized medicine – medical treatments tailored for the individual patient based on genetic and genomic information derived from patients' biological samples (blood samples and biopsied tissues). A major aim of this approach is to prescribe the right drug at the right dosage and right time for each patient. Another key aim of precision medicine is allowing earlier disease diagnosis, so that patients are treated with preventive therapeutics before the disease has caused irreparable damage. However, personalized medicine research is often hampered by high costs and lack of high-quality biological samples. Human lymphoblastoid cell lines (LCLs) are an affordable research tool that can be of high value for disease and drug response biomarker discovery in the context of personalized medicine exploration and can be obtained from many human biobanks.

scholarly journals Functional and structural analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the MYB oncoproteins associated with human cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shu Wen Lim ◽  
Kennet JunKai Tan ◽  
Osman Mohd Azuraidi ◽  
Maran Sathiya ◽  
Ee Chen Lim ◽  
...  
Keyword(s):  
Dna Binding ◽  
Single Nucleotide Polymorphisms ◽  
Cancer Progression ◽  
Posttranslational Modifications ◽  
Protein Function ◽  
Biomarker Discovery ◽  
Human Cancer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cancer Management

AbstractMYB proteins are highly conserved DNA-binding domains (DBD) and mutations in MYB oncoproteins have been reported to cause aberrant and augmented cancer progression. Identification of MYB molecular biomarkers predictive of cancer progression can be used for improving cancer management. To address this, a biomarker discovery pipeline was employed in investigating deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in predicting damaging and potential alterations on the properties of proteins. The nsSNP of the MYB family; MYB, MYBL1, and MYBL2 was extracted from the NCBI database. Five in silico tools (PROVEAN, SIFT, PolyPhen-2, SNPs&GO and PhD-SNP) were utilized to investigate the outcomes of nsSNPs. A total of 45 nsSNPs were predicted as high-risk and damaging, and were subjected to PMut and I-Mutant 2.0 for protein stability analysis. This resulted in 32 nsSNPs with decreased stability with a DDG score lower than − 0.5, indicating damaging effect. G111S, N183S, G122S, and S178C located within the helix-turn-helix (HTH) domain were predicted to be conserved, further posttranslational modifications and 3-D protein analysis indicated these nsSNPs to shift DNA-binding specificity of the protein thus altering the protein function. Findings from this study would help in the field of pharmacogenomic and cancer therapy towards better intervention and management of cancer.

scholarly journals Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases

2021 ◽  
Vol 12 ◽  
Author(s):  
Siting Li ◽  
Guang Song ◽  
Yina Bai ◽  
Ning Song ◽  
Jiuliang Zhao ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Biomarker Discovery ◽  
Protein Microarray ◽  
Protein Microarrays ◽  
Microarray Technology ◽  
Serum Samples ◽  
Future Studies ◽  
Key Issues

Dysregulated autoantibodies and cytokines were deemed to provide important cues for potential illnesses, such as various carcinomas and autoimmune diseases. Increasing biotechnological approaches have been applied to screen and identify the specific alterations of these biomolecules as distinctive biomarkers in diseases, especially autoimmune diseases. As a versatile and robust platform, protein microarray technology allows researchers to easily profile dysregulated autoantibodies and cytokines associated with autoimmune diseases using various biological specimens, mainly serum samples. Here, we summarize the applications of protein microarrays in biomarker discovery for autoimmune diseases. In addition, the key issues in the process of using this approach are presented for improving future studies.

scholarly journals A Pre-Processing Pipeline to Quantify, Visualize and Reduce Technical Variation in Protein Microarray Studies

2021 ◽  
Author(s):  
Sophie Bérubé ◽  
Tamaki Kobayashi ◽  
Amy Wesolowski ◽  
Douglas E. Norris ◽  
Ingo Ruczinski ◽  
...  
Keyword(s):  
Dna Microarrays ◽  
Protein Microarray ◽  
Protein Microarrays ◽  
Serum Samples ◽  
Fluorescent Intensity ◽  
Processing Pipeline ◽  
Infectious Disease Diagnostics ◽  
Using Data ◽  
Downstream Analysis ◽  
Microarray Studies

AbstractTechnical variation, or variation from non-biological sources, is present in most laboratory assays. Correcting for this variation enables analysts to extract a biological signal that informs questions of interest. However, each assay has different sources and levels of technical variation and the choice of correction methods can impact downstream analyses. Compared to similar assays such as DNA microarrays, relatively few methods have been developed and evaluated for protein microarrays, a versatile tool for measuring levels of various proteins in serum samples. Here, we propose a pre-processing pipeline to correct for some common sources of technical variation in protein microarrays. The pipeline builds upon an existing normalization method by using controls to reduce technical variation. We evaluate our method using data from two protein microarray studies, and by simulation. We demonstrate that pre-processing choices impact the fluorescent-intensity based ranks of proteins, which in turn, impact downstream analysis.1Impact StatementProtein microarrays are in wide use in cancer research, infectious disease diagnostics and biomarker identification. To inform research and practice in these and other fields, technical variation must be corrected using normalization and pre-processing. Current protein microarray studies use a variety of normalization methods, many of which were developed for DNA microarrays, and therefore are based on assumptions and data that are not ideal for protein microarrays. To address this issue, we develop, evaluate, and implement a pre-processing pipeline that corrects for technical variation in protein microarrays. We show that pre-processing and normalization directly impact the validity of downstream analysis, and protein-specific approaches are essential.

scholarly journals Systematic identification of Celastrol-binding proteins reveals that Shoc2 is inhibited by Celastrol

2018 ◽  
Vol 38 (6) ◽  
Author(s):  
Huang Xiao-pei ◽  
Chen Ji-kuai ◽  
Wei Xue ◽  
Yi-Fan Dong ◽  
Lang Yan ◽  
...  
Keyword(s):  
Protein Microarray ◽  
Microarray Experiment ◽  
Protein Microarrays ◽  
Down Regulation ◽  
Underlying Mechanisms ◽  
And Migration ◽  
Systematic Identification ◽  
First Time

Colorectal cancer (CRC) is the third most commonly diagnosed cancer. Celastrol exhibits anti-tumor activities in a variety of cancers. However, the effect of Celastrol on human CRC and the underlying mechanisms still need to be elucidated. The present study aimed to use in vitro and in vivo methods to clarify the anti-tumor effect of Celastrol and use protein microarrays to explore its mechanisms. We demonstrated that Celastrol effectively inhibited SW480 CRC cell proliferation. Two weeks of Celastrol gavage significantly inhibited the growth of xenografts in nude mice. A total of 69 candidate proteins were identified in the protein microarray experiment, including the most highly enriched protein Shoc2, which is a scaffold protein that modulates cell motility and metastasis through the ERK pathway. Celastrol significantly inhibited ERK1/2 phosphorylation in cell lines and xenograft tumors. Down-regulation of Shoc2 expression using Shoc2 siRNA also inhibited ERK1/2 phosphorylation. Furthermore, down-regulation of Shoc2 expression also significantly inhibited proliferation, colony formation, and migration functions of tumor cells. In addition, the LD0 of Celastrol by gavage is equal or more than 80 mg/kg in C57 male mice. In summary, we unraveled the anti-CRC function of Celastrol and confirmed for the first time that it inhibited the ERK1/2 pathway through binding to Shoc2.

scholarly journals Plasmodium falciparum serology: A comparison of two protein production methods for analysis of antibody responses by protein microarray

2020 ◽  
Author(s):  
Tate Oulton ◽  
Joshua Obiero ◽  
Isabel Rodriguez ◽  
Isaac Ssewanyana ◽  
Rebecca A Dabbs ◽  
...  
Keyword(s):  
High Throughput ◽  
Protein Microarray ◽  
Expression System ◽  
Protein Microarrays ◽  
In Vitro Transcription ◽  
Antibody Responses ◽  
Dependent Manner ◽  
Expression Systems ◽  
Protein Antigens

The evaluation of protein antigens as putative serologic biomarkers of infection has increasingly shifted to high-throughput, multiplex approaches such as the protein microarray. In vitro Transcription/Translation (IVTT) systems (a similarly high-throughput protein expression method) are already widely utilised in the production of protein microarrays, though purified recombinant proteins derived from more traditional whole cell based expression systems also play an important role in biomarker characterisation. Here we have performed a side-by-side comparison of antigen-matched protein targets from an IVTT and purified recombinant system, on a protein microarray. The magnitude and range of antibody responses to purified recombinants was found to be greater than that of IVTT proteins, and responses between targets from opposing expression systems did not clearly correlate. However, responses between amino acid sequence-matched targets from each expression system were more closely correlated. Despite the lack of a clearly defined relationship between antigen-matched targets produced in each expression system, our data indicate that protein microarrays produced using either method can be used confidently, in a context dependent manner, though care should be taken when comparing data derived from contrasting approaches.

scholarly journals Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nurul Ain Khoruddin ◽  
Mohd NurFakhruzzaman Noorizhab ◽  
Lay Kek Teh ◽  
Farida Zuraina Mohd Yusof ◽  
Mohd Zaki Salleh
Keyword(s):  
Protein Function ◽  
Association Studies ◽  
Whole Genome Sequence ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Bioinformatic Pipeline ◽  
Orang Asli ◽  
Pathogenic Variants ◽  
Allosteric Sites

AbstractSingle-nucleotide polymorphisms (SNPs) are the most common genetic variations for various complex human diseases, including cancers. Genome-wide association studies (GWAS) have identified numerous SNPs that increase cancer risks, such as breast cancer, colorectal cancer, and leukemia. These SNPs were cataloged for scientific use. However, GWAS are often conducted on certain populations in which the Orang Asli and Malays were not included. Therefore, we have developed a bioinformatic pipeline to mine the whole-genome sequence databases of the Orang Asli and Malays to determine the presence of pathogenic SNPs that might increase the risks of cancers among them. Five different in silico tools, SIFT, PROVEAN, Poly-Phen-2, Condel, and PANTHER, were used to predict and assess the functional impacts of the SNPs. Out of the 80 cancer-related nsSNPs from the GWAS dataset, 52 nsSNPs were found among the Orang Asli and Malays. They were further analyzed using the bioinformatic pipeline to identify the pathogenic variants. Three nsSNPs; rs1126809 (TYR), rs10936600 (LRRC34), and rs757978 (FARP2), were found as the most damaging cancer pathogenic variants. These mutations alter the protein interface and change the allosteric sites of the respective proteins. As TYR, LRRC34, and FARP2 genes play important roles in numerous cellular processes such as cell proliferation, differentiation, growth, and cell survival; therefore, any impairment on the protein function could be involved in the development of cancer. rs1126809, rs10936600, and rs757978 are the important pathogenic variants that increase the risks of cancers among the Orang Asli and Malays. The roles and impacts of these variants in cancers will require further investigations using in vitro cancer models.

Anti-Diabetic Activity of a Mineraloid Isolate, in vitro and in Genetically Diabetic Mice

2011 ◽  
Vol 81 (1) ◽  
pp. 34-42 ◽  
Author(s):  
Joel Deneau ◽  
Taufeeq Ahmed ◽  
Roger Blotsky ◽  
Krzysztof Bojanowski
Keyword(s):  
Dna Microarrays ◽  
Human Fibroblasts ◽  
Diabetic Animal ◽  
In Vitro Tests ◽  
Diabetic Mice ◽  
Fossil Material ◽  
Expression Of Genes ◽  
Enhanced Expression ◽  
Genetically Diabetic Mice

Type II diabetes is a metabolic disease mediated through multiple molecular pathways. Here, we report anti-diabetic effect of a standardized isolate from a fossil material - a mineraloid leonardite - in in vitro tests and in genetically diabetic mice. The mineraloid isolate stimulated mitochondrial metabolism in human fibroblasts and this stimulation correlated with enhanced expression of genes coding for mitochondrial proteins such as ATP synthases and ribosomal protein precursors, as measured by DNA microarrays. In the diabetic animal model, consumption of the Totala isolate resulted in decreased weight gain, blood glucose, and glycated hemoglobin. To our best knowledge, this is the first description ever of a fossil material having anti-diabetic activity in pre-clinical models.

scholarly journals Important Role for Phylogenetically Invariant PP2Acα Active Site and C-Terminal Residues Revealed by Mutational Analysis in Saccharomyces cerevisiae

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 21-29 ◽  
Author(s):  
David R H Evans ◽  
Brian A Hemmings
Keyword(s):  
Protein Interactions ◽  
Active Site ◽  
Protein Function ◽  
Mutational Analysis ◽  
Yeast Cells ◽  
Temperature Sensitive ◽  
Active Site Residues ◽  
Catalytic Function

Abstract PP2A is a central regulator of eukaryotic signal transduction. The human catalytic subunit PP2Acα functionally replaces the endogenous yeast enzyme, Pph22p, indicating a conservation of function in vivo. Therefore, yeast cells were employed to explore the role of invariant PP2Ac residues. The PP2Acα Y127N substitution abolished essential PP2Ac function in vivo and impaired catalysis severely in vitro, consistent with the prediction from structural studies that Tyr-127 mediates substrate binding and its side chain interacts with the key active site residues His-118 and Asp-88. The V159E substitution similarly impaired PP2Acα catalysis profoundly and may cause global disruption of the active site. Two conditional mutations in the yeast Pph22p protein, F232S and P240H, were found to cause temperature-sensitive impairment of PP2Ac catalytic function in vitro. Thus, the mitotic and cell lysis defects conferred by these mutations result from a loss of PP2Ac enzyme activity. Substitution of the PP2Acα C-terminal Tyr-307 residue by phenylalanine impaired protein function, whereas the Y307D and T304D substitutions abolished essential function in vivo. Nevertheless, Y307D did not reduce PP2Acα catalytic activity significantly in vitro, consistent with an important role for the C terminus in mediating essential protein-protein interactions. Our results identify key residues important for PP2Ac function and characterize new reagents for the study of PP2A in vivo.

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