Microarray Papers of Note Published July 2009
Journal: Acta Biomaterialia. 2010 Jul 1. [Epub ahead of print]
Title: A matrix micropatterning platform for cell localization and stem cell fate determination.
Authors: Huang N, et al.
Using a microscale direct writing technique, the authors of this paper characterized the generation of multicomponent cell-extracellular matrix microarrays for cellular micropatterning, localization, and stem cell fate determination. ECMs and other biomolecules of various geometries and sizes were printed onto epoxide-modified glass substrates to evaluate cell attachment by human endothelial cells. The endothelial cells displayed strong preferential attachment to the ECM patterned regions and aligned their cytoskeleton along the direction of the micropatterns. The authors next generated ECM microarrays that contained one or more ECM components and then cultured murine embryonic stem cells on the microarrays. The ESCs selectively attached to the micropatterned features and expressed markers associated with a pluripotent phenotype, such as E-cadherin and alkaline phosphatase, when maintained in growth medium containing leukemia inhibitory factor.
Journal: Biosensors and Bioelectronics. 2010 Jul 16. [Epub ahead of print]
Title: A generic surface chemistry for peptide microarrays implementation: application to the detection of anti-H3 antibody.
Authors: El Khoury G, et al.
Peptide microarrays can be created by immobilizing peptides on a solid support or by direct on-chip peptide synthesis. The authors of this study proposed a strategy where direct peptide on-chip synthesis and peptide immobilization are viewed as complementary approaches. In a first step, OCPS is envisioned for the screening and selection of biologically relevant peptides. In a second step, selected peptides would be synthesized on resin, qualified and immobilized for implementing microarrays. A versatile surface chemistry for both OCPS and peptide immobilization was developed allowing for an identical physico-chemical environment for both implementation strategies, the authors noted. In this paper, they describe the synthesis of a 16-mer peptide corresponding to the human histone H3 epitope on an amino-functionalized support.
Journal: Cancer Research. 2010 Jul 1;70(13):5207-12.
Title: Distinct genomic alterations in prostate cancers in Chinese and Western populations suggest alternative pathways of prostate carcinogenesis.
Authors: Mao X, et al.
The authors of this paper used a genome-wide approach to reveal the genomic alterations in Chinese prostate cancers. They found a significant reduction in the frequency of certain somatic genomic changes that are commonly found in Western prostate cancers, including the 21q22.2-22.3 deletion, which involves the TMPRSS2:ERG fusion gene, and 10q deletion, which causes PTEN inactivation. Array results were confirmed by PCR-based molecular copy-number counting in selected samples. The different frequencies of these genomic changes were further evaluated by fluorescent in situ hybridization and immunohistochemistry analyses of tissue microarray samples. The authors suggest that tumors arise in Western and Chinese populations by alternative pathogenetic mechanisms.
Journal: Comparative Biochemistry and Physiology. 2010 Jul 8. [Epub ahead of print]
Title: Microarray technology is an effective tool for identifying genes related to the aquacultural improvement of Japanese flounder, Paralichthys olivaceus.
Authors: Aoki T, et al.
Expressed sequence tag-based microarrays were constructed for cultured fish and shellfish species including Japanese flounder, Paralichthys olivaceus. Using the flounder microarray, the efficacy of two DNA vaccines derived from pathogenic viruses, hirame rhabdovirus and viral hemorrhagic septicemia virus, was evaluated through gene-expression profiles. The study results suggest that both DNA vaccines were effective in protecting the flounder from HIRRV and VHSV.
Journal: Foodborne Pathogens and Disease. 2010 Jul;7(7):763-73.
Title: Microarray analysis and draft genomes of two Escherichia coli O157:H7 lineage II cattle isolates FRIK966 and FRIK2000 investigating lack of Shiga toxin expression.
Authors: Dowd S, et al.
The existence of two separate genetic lineages of Escherichia coli O157:H7 has previously been reported, and research indicates that lineage I could be more pathogenic toward human hosts than lineage II. The autors have previously shown that lineage I as a group expresses higher levels of Shiga toxin 2 than lineage II. To help evaluate why lineage II strains do not express appreciable levels of this toxin, whole-genome microarray studies were performed using Agilent custom microarrays. Gene expression of the two representative bovine lineage II strains was compared with gene expression of E. coli O157:H7 EDL933. Missing or differentially expressed genes and pathways were identified. Quantitative RT-PCR was performed to validate the microarray data. Draft genomes of FRIK966 and FRIK2000 were sequenced using Roche Applied Science/454 GS-FLX technology shotgun and paired-end approaches followed by de novo assembly. The results of the analysis support the hypothesis that lineage II strains may be less of a risk as human foodborne pathogens, according to the authors.
Journal: Genes, Chromosomes, and Cancer. 2010 Jul;49(7):610-9.
Title: Combined classical cytogenetics and microarray-based genomic copy number analysis reveal frequent 3;5 rearrangements in clear cell renal cell carcinoma.
Authors: Pei J, et al.
The authors of this study compared karyotypic analysis and genomic copy number analysis with SNP-based microarrays with regard to the detection of recurrent genomic imbalances in 20 clear cell renal cell carcinomas. Genomic imbalances were identified in 19 of 20 tumors by DNA copy number analysis and in 15 tumors by classical cytogenetics. A statistically significant correlation was observed between the number of genomic imbalances and tumor stage. The most common genomic imbalances were loss of 3p and gain of 5q. According to the authors, the data suggest that DNA copy number analysis will supplant karyotypic analysis of tumor types such as ccRCC that are characterized by recurrent genomic imbalances, rather than balanced rearrangements. They argue that their findings also suggest that the 5q duplication/3p deficiency resulting from unbalanced 3;5 translocations conveys a proliferative advantage of particular importance in ccRCC tumorigenesis.
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Journal: International Journal of Cancer. 2010 Jul 15. [Epub ahead of print]
Title: Common alleles in candidate susceptibility genes associated with risk and development of epithelial ovarian cancer.
Authors: Notaridou M, et al.
Common germline genetic variation in the population is associated with susceptibility to epithelial ovarian cancer, according to the authors of this study. Microcell-mediated chromosome transfer and expression microarray analysis identified nine genes associated with functional suppression of tumorogenicity in ovarian cancer cell lines; AIFM2, AKTIP, AXIN2, CASP5, FILIP1L, RBBP8, RGC32, RUVBL1 and STAG3. Sixty-three tagging SNPs in these genes were first genotyped in 1,799 invasive ovarian cancer cases and 3,045 controls to look for associations with disease risk. Two SNPs in RUVBL1, rs13063604 and rs7650365, were associated with increased risk of serous ovarian cancer. The authors genotyped rs13063604 and rs7650365 in an additional 4,590 cases and 6,031 controls from 10 sites from the US, Europe, and Australia. However, they found that neither SNP was significant in stage 2. They also evaluated the potential role of tSNPs in these nine genes in ovarian cancer development by testing for allele-specific loss of heterozygosity in 286 primary ovarian tumors. The authors found frequent LOH for tSNPs in the AXIN2, AKTIP and RGC32 and one SNP, rs1637001, in STAG3 showed, allele-specific LOH with loss of the common allele in 94 percent of informative tumors.
Journal: Journal of the American Chemical Society. 2010 Jul 28;132(29):9963-5.
Title: Synthesis of glycopolymers for microarray applications via ligation of reducing sugars to a poly(acryloyl hydrazide) scaffold.
Authors: Godula K, et al.
The authors describe a general synthetic strategy for the assembly of glycopolymers that relies on the reactivity of reducing glycans toward hydrazides to form stable cyclic N-glycosides. They developed a poly(acryloyl hydrazide) scaffold to which they conjugated a variety of reducing glycans ranging in structure from simple mono- and disaccharides to considerably more complex human milk and blood oligosaccharides. Using a biotin-terminated PAH scaffold prepared via RAFT polymerization, they also assembled a panel of glycopolymers that were then microarrayed on streptavidin-coated glass. The authors also demonstrated that in these microarrays, the glycopolymer ligands bind lectins according to the structures of their pendant glycans.
Journal: Journal of Virology Methods. 2010 Jul 27. [Epub ahead of print]
Title: Human papillomavirus detection and typing in thin prep cervical cytologic specimens comparing the Digene Hybrid Capture II Assay, the Roche Linear Array HPV Genotyping Assay, and the Kurabo GeneSquare Microarray Assay.
Authors: Ermel A, et al.
Three methods for the detection of human papillomavirus DNA were compared in cervical cytologic specimens: the Digene Hybrid Capture II Assay, the Roche Linear Array HPV Genotyping Assay, and the Kurabo GeneSquare Microarray. The main goals of the study were to correlate cytology with HPV detection and to determine agreement between assay pairs for HPV detection. Thin-prep Pap smears were performed and supernates were tested by the Digene, Roche, and Kurabo assays. For specimens reacting with the HPV 52/33/35/58 probe in the Roche assay, type-specific PCR was performed for HPV types 52, 33, 35, or 58. Binomial proportions and kappa coefficients were calculated for agreement between assays. Cytology results and supernatant were available for 202 subjects. HPV detection increased with worsening cytologic abnormality in all three assays. For all cytologic groups, Roche and Kurabo detected more HPV than Digene. However, for the detection of oncogenic HPV types represented in all three assays, differences between assays were less pronounced. The highest agreement was between Roche and Kurabo.
Journal: Langmuir. 2010 Jul 28. [Epub ahead of print]
Title: Plasma nanotextured PMMA surfaces for protein arrays: increased protein binding and enhanced detection sensitivity.
Authors: Tsougeni K, et al.
Poly(methyl methacrylate) substrates were nanotextured through treatment in oxygen plasma to create substrates with increased surface area for protein microarray applications. Conditions of plasma treatment were found for maximum uniform protein adsorption on these nanotextured PMMA surfaces. Similar results were obtained using both a high-density plasma and a low-density reactive ion etcher, suggesting independence from the plasma reactor type, according to the authors. The protein binding was evaluated by studying the adsorption of two model proteins, namely, biotinylated bovine serum albumin and rabbit gamma-globulins. The immobilization of these proteins onto the surfaces was quantitatively determined through reaction with fluorescently labeled binding molecules. It was found that the adsorption of both proteins was increased up to six-fold with plasma treatment compared to untreated surfaces and up to four-fold compared to epoxy-coated glass slides.
Journal: Nature. 2010 Jul 28. [Epub ahead of print]
Title: Diverse somatic mutation patterns and pathway alterations in human cancers.
Authors: Kan Z, et al.
The authors of this study report the identification of 2,576 somatic mutations across approximately 1,800 megabases of DNA representing 1,507 coding genes from 441 tumors comprising breast, lung, ovarian, and prostate cancer types and subtypes. Using Affymetrix GeneChips, they found that mutation rates and the sets of mutated genes varied substantially across tumor types and subtypes. Statistical analysis identified 77 significantly mutated genes including protein kinases, G-protein-coupled receptors such as GRM8, BAI3, AGTRL1, and LPHN3, and other druggable targets. Integrated analysis of somatic mutations and copy number alterations identified another 35 significantly altered genes including GNAS, indicating an expanded role for G-alpha subunits in multiple cancer types, according to the authors. Additionally, their experimental analyses demonstrated the functional roles of mutant GNAO1 and mutant MAP2K4 in oncogenesis.
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Journal: Nature Biotechnology. 2010 Jul 30. [Epub ahead of print]
Title: The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
Authors: MAQC Consortium, et al.
In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma, or neuroblastoma in humans. In total, more than 30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. The consortium found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis, according to the consortium.
Journal: Nature Genetics. 2010 Jul 25. [Epub ahead of print]
Title: Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia.
Authors: Johansen C, et al.
Genome-wide association studies have identified multiple loci associated with plasma lipid concentrations, but common variants at these loci together explain less than 10 percent of variation in each lipid trait. In this study, the authors showed an accumulation of rare variants, or a mutation skew, in GWAS-identified genes in individuals with hypertriglyceridemia. Through GWAS, they identified common variants in APOA5, GCKR, LPL, and APOB associated with HTG. Resequencing of these genes revealed a significant burden of 154 rare missense or nonsense variants in 438 individuals with HTG, compared to 53 variants in 327 controls. Considering rare variants in these genes incrementally increased the proportion of genetic variation contributing to HTG, according to the authors.
Journal: New England Journal of Medicine. 2010 Jul 22;363(4):321-30.
Title: Genetic ancestry in lung-function predictions.
Authors: Kumar R, et al.
The authors assessed the ancestry of 777 participants self-identified as African American in the Coronary Artery Risk Development in Young Adults study and evaluated the relation between pulmonary function and ancestry by means of linear regression. They performed similar analyses of Affymetrix SNP 6.0 array data for two independent cohorts of subjects identifying themselves as African American: 813 participants in the Health, Aging, and Body Composition study and 579 participants in the Cardiovascular Health Study. The authors compared the fit of two types of models to lung-function measurements: models based on the covariates used in standard prediction equations and models incorporating ancestry. They also evaluated the effect of the ancestry-based models on the classification of disease severity in two asthma-study populations. According to the authors, African ancestry was inversely related to forced expiratory volume in 1 second and forced vital capacity in the CARDIA cohort. These relations were also seen in the HABC and CHS cohorts. In predicting lung function, the ancestry-based model fit the data better than standard models.
Journal: Nucleic Acids Research. 2010 Jul 14. [Epub ahead of print]
Title: Shielding effect of monovalent and divalent cations on solid-phase DNA hybridization: surface plasmon resonance biosensor study.
Authors: Springer T, et al.
In this study, the authors investigate the simultaneous effect of monovalent and divalent cations on the hybridization of fully complementary or partly mismatched DNA targets to DNA probes immobilized on the surface of a surface plasmon resonance sensor. Their results demonstrated that the hybridization process is "substantially influenced" by the cation-shielding effect and that this effect differs for solid-phase hybridization, due to the high surface density of negatively charged probes, and hybridization in a solution.
Journal: PLoS One. 2010 Jul 9;5(7):e11504.
Title: A genome-wide association study of neuroticism in a population-based sample.
Authors: Calboli F, et al.
The authors of this paper performed a genome-wide association study in 2,235 participants drawn from a population-based study of neuroticism. Neuroticism was first measured by the Eysenck Personality Questionnaire. After quality control, the authors analyzed 430,000 autosomal SNPs together with an additional 1.2 million SNPs imputed with high quality from the Hap Map CEU samples. They found a very small effect of population stratification, corrected using one principal component, and some cryptic kinship that required no correction. NKAIN2 showed suggestive evidence of association with neuroticism as a main effect and GPC6 showed suggestive evidence for interaction with age, according to the authors. They also found support for one previously reported association, but failed to replicate other recent reports. The authors suggest common SNP variation does not strongly influence neuroticism.
Journal: PLoS One. 2010 Jul 26;5(7):e11804.
Title: Genotyping with a 198 mutation arrayed primer extension array for hereditary hearing loss: assessment of its diagnostic value for medical practice.
Authors: Rodriguez-Paris J, et al.
This paper described the Hereditary Hearing Loss Arrayed Primer Extension microarray, which the authors claim can enable the analysis of 198 mutations across eight genes — GJB2, GJB6, GJB3, GJA1, SLC26A4, SLC26A5, MTRNR1, and MTTS1 — in a single test. To evaluate the array for an ethnically diverse patient population, the authors tested 144 individuals with congenital sensorineural hearing loss who were negative for biallelic GJB2 or GJB6 mutations. The array successfully detected all GJB2 changes previously identified in the study group. Additional mutations were identified in the SLC26A4, SLC26A5 and MTRNR1 genes of 12 out of 144 individuals, four of whom had genotypes consistent with pathogenicity. The authors suggest that the current format of the microarray falls short of adding diagnostic value beyond the customary testing of GJB2, perhaps reflecting the array's limitations on the number of mutations included for each gene, but more likely resulting from unknown genetic contributors to this phenotype.
Journal: Proceedings of the National Academy of Sciences. 2010 Jul 13;107(28):12587-92.
Title: High-throughput method for analyzing methylation of CpGs in targeted genomic regions.
Authors: Nautiyal S, et al.
The paper describes a microarray-based method for determining the extent of DNA methylation. The method relies on a selective enrichment of the regions to be assayed by target amplification by capture and ligation. Using the assay, the methylation status of more than 145,000 CpGs from 5,472 promoters in 221 samples was measured. The methylation levels of nearby CpGs were correlated, but the correlation falls off over several hundred base pairs. In some instances, the authors found that nearby CpGs have different levels of methylation. Comparison of normal and tumor samples indicated that, in tumors, the promoter regions of genes involved in differentiation and signaling are preferentially hypermethylated, while those of housekeeping genes remain hypomethylated.