In Print: Jul 14, 2009

Microarray-related Papers of Note Published in June 2009

Journal: American Journal of Obstetrics & Gynecology. 2009 Jun;200(6):661.e1-7.

Title: Differential expression profile of microRNAs in human placentas from preeclamptic pregnancies vs. normal pregnancies.

Authors: X Zhu; T Han; I Sargent; G Yin; Y Yao

The purpose of this study was to perform a comprehensive analysis of the microRNA expression profile in placentas from preeclamptic pregnancies versus normal placentas. Placentas were obtained from patients with mild preeclampsia and severe preeclampsia and in a normal control group with elective cesarean delivery. MiRNA expression profiles were assessed using microarray and RT-PCR analysis. The authors found that 34 miRNAs were expressed differentially in preeclamptic placentas, compared with normal placentas. Of these, 11 miRNAs were overexpressed, and 23 were underexpressed in preeclamptic pregnancies. The authors suggest that the findings show the involvement of these miRNAs in the pathogenesis of preeclampsia.

Journal: Analytica Chimica Acta. 2009 Jun 30;644(1-2):95-103.

Title: New 3D microarray platform based on macroporous polymer monoliths.

Authors: M Rober; J Walter; E Vlakh; F Stahl; C Kasper; T Tennikova

Polymer macroporous monoliths are used as sorbents in different, mostly dynamic, interphase processes. In this paper, the authors showed that monolithic materials bound strongly to inert glass surfaces, and suggest could serve as operative matrices at the development of three-dimensional microarrays. During this process, several rigid macroporous copolymers differed by reactivity and hydrophobic-hydrophilic properties were synthesized and tested. The constructed devices were used as platforms for constructing protein microarray and a model mouse IgG-goat anti-mouse IgG affinity pair was used to determine the potential of the developed test systems, as well as to optimize microanalytical conditions. The array platforms were applied to detect the bone tissue marker osteopontin directly in cell culture medium.

Journal: Analytical Chemistry. 2009 Jun 1;81(11):4296-301.

Title: In situ microarray fabrication and analysis using a microfluidic flow cell array integrated with surface plasmon resonance microscopy.

Authors: J Liu; M Eddings; A Miles; R Bukasov; B Gale; J Shumaker-Parry

The authors describe the integration of a microfluidic flow cell array with surface plasmon resonance microscopy supporting in situ microarray fabrication and multichannel analysis of biomolecule probe-target interactions. More specifically, they demonstrated the use of the MFCA for delivery of sample solutions with continuous flow in 24 channels in parallel for microarray creation and binding analysis while using SPRM for real-time monitoring of these processes. The label-free measurement of antibody-antibody interactions demonstrates the capabilities of the integrated MFCA-SPRM system and is the first step towards the authors' goal of making a high-throughput, label-free immunogenicity assay, they noted.

Journal: Analytical Chemistry. 2009 Jun 23. [Epub ahead of print]

Title: Microsphere-based rolling circle amplification microarray for the detection of DNA and proteins in a single assay.

Authors: T Konry; R Hayman; D Walt

The authors describe a high-density microarray for simultaneous detection of proteins and DNA in a single test. The system, rolling circle amplification, can be used as a signal amplification method for both protein and nucleic acid detection. The authors tested the microsphere sensors with synthetic DNA and purified recombinant protein analytes. They designed a target DNA sequence from a conserved gene that encodes the outer membrane protein P6 (OMP-P6) of both typeable and nontypeable strains of Haemophilus influenzae. The proinflammatory mediators IL-6 and IL-8 were selected as target proteins. Capture antibodies were first immobilized on fluorescently encoded microspheres. The microspheres were then loaded into the etched microwells of an imaging optical fiber bundle. A sandwich assay was performed for target proteins IL-6 and IL-8 using biotin-labeled secondary antibodies. Biotinylated capture DNA probes were then attached to the detection antibodies via an avidin bridge. A padlock probe, complementary to the target sequence, was subsequently hybridized to the capture probe. In the presence of the target sequence, the padlock probe was ligated, and this circular sequence was used for RCA. Following RCA, multiple fluorescently labeled signal probes were hybridized to each amplified sequence, and the microarray was imaged using an epi-fluorescence microscope. Using this assay, detection was achieved for proteins and target DNA.

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Journal: Biosensors and Bioelectronics. 2009 Jun 15;24(10):2997-3002.

Title: High-performance UV-curable epoxy resin-based microarray and microfluidic immunoassay devices.

Authors: L Yu; Y Liu; Y Gan; C Li

The authors fabricated Immunoassay devices including microarray and microfluidic systems using a UV-curable resin by an approach which they claim can not only produce a 3-dimensional patterned structure, but also introduce functional epoxide groups for protein immobilization. The authors also improved the performance of the epoxy resin-based microarray by optimizing the printing buffer, probe concentration, and immobilization time. They claim the developed microfluidic immunoassay can be used to colorimetrically detect proteins for immunoassays.

Journal: BMC Genomics. 2009 Jun 12;10:264.

Title: Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing.

Authors: S Mane; C Evans; K Cooper; O Crasta; O Folkerts; S Hutchison; T Harkins; D Thierry-Mieg; J Thierry-Mieg; R Jensen

The authors used second-generation sequencers to sequence cDNA synthesized from the Microarray Quality Control project's reference RNA samples using Roche's 454 Genome Sequencer FLX. They generated more than 3.6 million sequence reads of average length 250 basepairs for the MAQC samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90 percent of the reads mapped to the human genome and 64 percent of the reads mapped to the RefSeq database of well-annotated genes. The authors measured gene expression levels in the samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and quantitative RT-PCR from the MAQC studies. They concluded that, using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed "excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRT-PCR."

Title: Integrated analysis of DNA copy number and gene expression microarray data using gene sets.

Authors: R Menezes; M Boetzer; M Sieswerda; G Ommen; J Boer

The authors chose to analyze copy number and expression array data using gene sets, rather than individual genes, and analyzed two publicly available datasets to illustrate their approach. The two selected independent breast cancer datasets yielded similar patterns of association between gene dosage and gene expression levels, in spite of different platforms having been used, the authors found. They argue in this paper that there is an advantage to using sets of genes' expressions to detect associations with long-spanning, low-amplitude copy number aberrations. The model allows for additional explanatory variables and does not require mapping between copy number and expression probes, they wrote.

Journal: BMC Bioinformatics. 2009 Jun 30;10(1):204.

Title: Comparison of sequence-dependent tiling array normalization approaches.

Authors: H Chung; M Vingron

According to the authors, tiling arrays contain a high number of small probes covering genomic loci, but to achieve high coverage the probe sequences cannot be selected for their hybridization properties. The affinity of the probes towards their targets therefore varies in a sequence-dependent manner. Some current approaches developed to remove this bias use a peak detection algorithm that is different from the one used previously. The authors argue that the resulting enhancement of detection is due to the peak detection algorithm rather than the sequence-dependent normalization. To test this, the authors compared three different sequence-dependent probe level normalization procedures to a naive sequence-independent normalization technique. They used normalized intensity values as input to a single peak detection algorithm and a spike-in data set served as benchmark for the performance. The authors found that sequence-dependent normalization of microarray data did not improve the detection of enriched DNA or RNA fragments. Instead, they argue that the success of the sequence-independent naive approach is only possible due to the control experiment and requires proper scaling of the measured intensities.

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Journal: Cancer Research. 2009 Jun 1;69(11):4851-60.

Title: Genomic profiling of microRNAs in bladder cancer: miR-129 is associated with poor outcome and promotes cell death in vitro.

Authors: L Dyrskjøt; M Ostenfeld; J Bramsen; A Silahtaroglu; P Lamy; R Ramanathan; N Fristrup; J Jensen; C Andersen; K Zieger; S Kauppinen; B Ulhøi; J Kjems; M Borre; T Orntoft

The authors profiled the expression of 290 unique human microRNAs in 11 normal and 106 bladder tumor samples using spotted locked nucleic acid-based oligonucleotide microarrays. They identified several differentially expressed miRNAs between normal urothelium and cancer and between the different disease stages. They also identified miRNAs that correlated to the presence of concomitant carcinoma in situ and identified several miRNAs with prognostic potential for predicting disease progression. The authors argue that these results indicate that several miRNAs are differentially regulated in bladder cancer and may form a basis for clinical development of new biomarkers for bladder cancer.

Journal: Genes, Chromosomes, & Cancer. 2009 Jun;48(6):521-31.

Title: Integrative high-resolution microarray analysis of human myeloma cell lines reveals deregulated miRNA expression associated with allelic imbalances and gene expression profiles.

Authors: M Lionetti; L Agnelli; L Mosca; S Fabris; A Andronache; K Todoerti; D Ronchetti; G Deliliers; A Neri

Seeking to understand microRNA deregulation in multiple myeloma, the authors profiled global miRNA expression in a panel of molecularly well-characterized human myeloma cell lines using high-resolution microarrays, and then used integrative analyses to identify altered patterns correlated with DNA copy-number or gene-expression profiles. The authors identified 16 miRNAs mapped to chromosomal regions frequently involved in numerical imbalances in MM, whose expression correlated with the CN of the corresponding miRNA genes.The expression of some of the miRNAs was validated by quantitative RT-PCR. A number of the identified miRNAs were previously reported to play roles in tumorigenesis.

Journal: Journal of Biomolecular Screening. 2009 Jun 12. [Epub ahead of print]

Title: Development of a fluorescence-based, ultra high-throughput screening platform for nanoliter-scale cytochrome P450 microarrays.

Authors: S Sukumaran; B Potsaid; M Lee; D Clark; J Dordick

The authors describe a high-throughput, integrated screening platform for CYP450 assays combining enzyme encapsulation techniques, microarraying methods, and wide-field imaging. They fabricated alginate-containing microarrays consisting of up to 1,134 CYP450 reaction elements on functionalized glass slides and imaged them to yield endpoint activity, stability, and kinetic data. They claim the system enables a "significant miniaturization of CYP enzyme assays with significant conservation of assay reagents, greatly increased throughput, and no apparent loss of enzyme activity or assay sensitivity."

Journal: Journal of Clinical Investigation. 2009 Jun;119(6):1714-26.

Title: High throughput digital quantification of mRNA abundance in primary human acute myeloid leukemia samples.

Authors: J Payton; N Grieselhuber; L Chang; M Murakami; G Geiss; D Link; R Nagarajan; M Watson; T Ley

According to the authors, acute promyelocytic leukemia is characterized by the t(15;17) chromosomal translocation, which results in fusion of the retinoic acid receptor alpha gene to another gene, most commonly promyelocytic leukemia . The resulting fusion protein, PML-RARA, initiates APL, which is a subtype of acute myeloid leukemia called M3. In this paper, the authors identified a gene-expression signature that is specific to M3 samples, and used NanoString Technologies' nCounter system to validate the signature for a larger number of genes.

Journal: Journal of Experimental Botany. 2009 Jun 26. [Epub ahead of print]

Title: Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage.

Authors: P Guo; M Baum; S Grando; S Ceccarelli; G Bai; R Li; M von Korff; R Varshney; A Graner; J Valkoun

The authors used the 22K Affymetrix Barley 1 microarray to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1, and one drought-sensitive genotype, Moroc9-75, to monitor the changes in gene expression at the transcriptional level in barley leaves during the reproductive stage under drought conditions. The authors found that 17 genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and believe that their encoded proteins may play roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism, generating protectants against reactive-oxygen-species scavenging, and stabilizing membranes and proteins. 17 other genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were possibly constitutively expressed in drought-tolerant genotypes. Additionally, 18 genes were differentially expressed in all genotypes under drought. The authors said these genes are more likely to be drought-responsive genes in barley.

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Journal: Journal of Peptide Science. 2009 Jun;15(6):393-7.

Title: Immobilization strategies for small molecule, peptide and protein microarrays.

Author: M Köhn

This review describes chemical preparation methods for protein, peptide, and small-molecule microarrays with a focus on site-selective and bioorthogonal immobilization reactions, particularly the Staudinger ligation and the thiolene reaction. The paper also describes the application of peptide microarrays, which were prepared by Staudinger ligation, to substrate specificity mapping.

Journal: Molecular Cancer Therapeutics. 2009 Jul 7. [Epub ahead of print]

Title: Response prediction to a multitargeted kinase inhibitor in cancer cell lines and xenograft tumors using high-content tyrosine peptide arrays with a kinetic readout.

Authors: M Versele; W Talloen; C Rockx; T Geerts; B Janssen; T Lavrijssen; P King; H Göhlmann; M Page; T Perera

Multitargeted kinase inhibitors have shown clinical efficacy in a range of cancer types, but problems associated with these drugs include the low fraction of patients for which these treatments provide initial clinical benefit and the occurrence of resistance during prolonged therapy, according to the authors. In this paper, they described the development of a response prediction platform that does not require prior knowledge of the relevant kinases targeted by the inhibitor. Instead, phosphotyrosine peptide profiles were created using PamGene peptide arrays with a kinetic readout in lysates in the presence and absence of a kinase inhibitor. The authors argue the approach allows for the stratification of responders and nonresponders to a multitargeted kinase inhibitor.

Journal: Nucleic Acids Research. 2009 Jun;37(11):e79.

Title: Text-based over-representation analysis of microarray gene lists with annotation bias.

Authors: H Leong; D Kipling

The authors evaluated over-representation analysis, a method that uses a hypergeometric test to determine whether a particular functionally defined group of genes is represented more than expected by chance within a gene list. The authors found that a feature of experimentally derived gene lists is that the constituents have more annotation associated with them, as they have been studied for a longer period of time. They argue that this bias is a result of patterns of research activity within the biomedical community, and is a problem for classical hypergeometric test-based ORA approaches. In response, the authors developed three approaches to overcome the bias, and demonstrate in the paper their usability in a range of published datasets covering different species.

Journal: The Plant Journal. 2009 Jun;58(6):1054-67.

Title: A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.

Authors: D Drost; E Novaes; C Boaventura-Novaes; C Benedict; R Brown; T Yin; G Tuskan; M Kirst

The authors have developed methods for high-throughput microarray-based genotyping in yeast and several inbred plant species species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. The analysis resulted in genotypes for 719 single-feature polymorphism and 1,014 gene-expression marker candidates. Using these genotypes and an established microsatellite framework map, the authors produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. Using gene-based markers, the authors localized over 35 million base pairs of previously unplaced whole-genome shotgun scaffold sequence to putative locations in the genome of P. trichocarpa.

Journal: PLoS One. 2009 Jun 3;4(6):e5775.

Title: Gene expression profiling of lymphoblasts from autistic and nonaffected sib pairs: altered pathways in neuronal development and steroid biosynthesis.

Authors: V Hu; A Nguyen; K Kim; M Steinberg; T Sarachana; M Scully; S Soldin; T Luu; N Lee

This case-control study sought to better understand the molecular basis of autism spectrum disorders based on large-scale gene-expression profiling. Array analyses were conducted on lymphoblastoid cell lines from over 20 sib pairs where one sibling had a diagnosis of autism and the other was not affected in order to identify biochemical and signaling pathways which are differentially regulated in cells from autistic and nonautistic siblings. Bioinformatics and gene ontological analyses of the data implicated genes which are involved in nervous system development, inflammation, and cytoskeletal organization, in addition to genes which may be relevant to gastrointestinal or other physiological symptoms often associated with autism. Additionally, the authors said the data suggests that these processes may be modulated by cholesterol/steroid metabolism, especially at the level of androgenic hormones.

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Journal: PLoS One. 2009 Jun 17;4(6):e5943.

Title: Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays.

Authors: G Thomassen; A Rowe; K Lagesen; J Lindvall; T Rognes

The authors describe the design of tiling arrays for transcriptome analysis and detail the normalization and analysis procedures. They created a design method to make two 280,000-feature microarrays covering the entire genome of the bacterial species Escherichia coli and Neisseria meningitidis, as well as the use of multiple copies of control probe-sets on tiling microarrays. The authors also developed a normalization and background estimation procedure for tiling arrays along with a method for array analysis focused on detection of short transcripts.

Journal: Transgenic Research. 2009 Jun 16. [Epub ahead of print]

Title: Fuzzy-logic based strategy for validation of multiplex methods: example with qualitative GMO assays.

Authors: G Bellocchi; V Bertholet; S Hamels; W Moens; J Remacle; G Van den Eede

The authors in this paper argue that there are advantages that a fuzzy-based aggregation method could bring into the validation of a multiplex method for GMO detection. Fuzzy logic allows the summarizing of information obtained by independent validation statistics into one synthetic indicator of overall method performance. The authors argue that using array technology, specifically Eppendorf's DualChip GMO kit, poses specific validation issues, such as patterns of performance for a variety of GMOs at different concentrations. According to the authors, fuzzy-logic based rules were shown to be applicable to improve interpretation of results and facilitate overall evaluation of the array-based method.