Publications by authors named "Frank Staedtler"

40 Publications

Duplicated Enhancer Region Increases Expression of CTSB and Segregates with Keratolytic Winter Erythema in South African and Norwegian Families.

Am J Hum Genet 2017 May 27;100(5):737-750. Epub 2017 Apr 27.

Division of Human Genetics, School of Pathology and the Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa. Electronic address:

Keratolytic winter erythema (KWE) is a rare autosomal-dominant skin disorder characterized by recurrent episodes of palmoplantar erythema and epidermal peeling. KWE was previously mapped to 8p23.1-p22 (KWE critical region) in South African families. Using targeted resequencing of the KWE critical region in five South African families and SNP array and whole-genome sequencing in two Norwegian families, we identified two overlapping tandem duplications of 7.67 kb (South Africans) and 15.93 kb (Norwegians). The duplications segregated with the disease and were located upstream of CTSB, a gene encoding cathepsin B, a cysteine protease involved in keratinocyte homeostasis. Included in the 2.62 kb overlapping region of these duplications is an enhancer element that is active in epidermal keratinocytes. The activity of this enhancer correlated with CTSB expression in normal differentiating keratinocytes and other cell lines, but not with FDFT1 or NEIL2 expression. Gene expression (qPCR) analysis and immunohistochemistry of the palmar epidermis demonstrated significantly increased expression of CTSB, as well as stronger staining of cathepsin B in the stratum granulosum of affected individuals than in that of control individuals. Analysis of higher-order chromatin structure data and RNA polymerase II ChIA-PET data from MCF-7 cells did not suggest remote effects of the enhancer. In conclusion, KWE in South African and Norwegian families is caused by tandem duplications in a non-coding genomic region containing an active enhancer element for CTSB, resulting in upregulation of this gene in affected individuals.
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http://dx.doi.org/10.1016/j.ajhg.2017.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420352PMC
May 2017

Novel mutation in the CHST6 gene causes macular corneal dystrophy in a black South African family.

BMC Med Genet 2016 07 20;17(1):47. Epub 2016 Jul 20.

Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, 2050, Johannesburg, Gauteng, South Africa.

Background: Macular corneal dystrophy (MCD) is a rare autosomal recessive disorder that is characterized by progressive corneal opacity that starts in early childhood and ultimately progresses to blindness in early adulthood. The aim of this study was to identify the cause of MCD in a black South African family with two affected sisters.

Methods: A multigenerational South African Sotho-speaking family with type I MCD was studied using whole exome sequencing. Variant filtering to identify the MCD-causal mutation included the disease inheritance pattern, variant minor allele frequency and potential functional impact.

Results: Ophthalmologic evaluation of the cases revealed a typical MCD phenotype and none of the other family members were affected. An average of 127 713 variants per individual was identified following exome sequencing and approximately 1.2 % were not present in any of the investigated public databases. Variant filtering identified a homozygous E71Q mutation in CHST6, a known MCD-causing gene encoding corneal N-acetyl glucosamine-6-O-sulfotransferase. This E71Q mutation results in a non-conservative amino acid change in a highly conserved functional domain of the human CHST6 that is essential for enzyme activity.

Conclusion: We identified a novel E71Q mutation in CHST6 as the MCD-causal mutation in a black South African family with type I MCD. This is the first description of MCD in a black Sub-Saharan African family and therefore contributes valuable insights into the genetic aetiology of this disease, while improving genetic counselling for this and potentially other MCD families.
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http://dx.doi.org/10.1186/s12881-016-0308-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4955246PMC
July 2016

The use of haplotype-specific transcripts improves sample annotation consistency.

Biomark Res 2014 30;2:17. Epub 2014 Sep 30.

Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.

Background: Exact sample annotation in expression microarray datasets is essential for any type of pharmacogenomics research.

Results: Candidate markers were explored through the application of Hartigans' dip test statistics to a publically available human whole genome microarray dataset. The marker performance was tested on 188 serial samples from 53 donors and of variable tissue origin from five public microarray datasets. A qualified transcript marker panel consisting of three probe sets for human leukocyte antigens HLA-DQA1 (2 probe sets) and HLA-DRB4 identified sample donor identifier inconsistencies in six of the 188 test samples. About 3% of the test samples require root-cause analysis due to unresolvable inaccuracies.

Conclusions: The transcript marker panel consisting of HLA-DQA1 and HLA-DRB4 represents a robust, tissue-independent composite marker to assist control donor annotation concordance at the transcript level. Allele-selectivity of HLA genes renders them good candidates for "fingerprinting" with donor specific expression pattern.
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http://dx.doi.org/10.1186/2050-7771-2-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184161PMC
October 2014

Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study.

Nat Methods 2014 Aug 29;11(8):809-15. Epub 2014 Jun 29.

Center for Medical Genetics, Ghent University, Ghent, Belgium.

MicroRNAs are important negative regulators of protein-coding gene expression and have been studied intensively over the past years. Several measurement platforms have been developed to determine relative miRNA abundance in biological samples using different technologies such as small RNA sequencing, reverse transcription-quantitative PCR (RT-qPCR) and (microarray) hybridization. In this study, we systematically compared 12 commercially available platforms for analysis of microRNA expression. We measured an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples and synthetic spikes from microRNA family members with varying homology. We developed robust quality metrics to objectively assess platform performance in terms of reproducibility, sensitivity, accuracy, specificity and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which help to guide informed selection of a quantitative microRNA gene expression platform for particular study goals.
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http://dx.doi.org/10.1038/nmeth.3014DOI Listing
August 2014

Gene expression profiling of immunomagnetically separated cells directly from stabilized whole blood for multicenter clinical trials.

Clin Transl Med 2014 13;3:36. Epub 2014 Nov 13.

Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland.

Background: Clinically useful biomarkers for patient stratification and monitoring of disease progression and drug response are in big demand in drug development and for addressing potential safety concerns. Many diseases influence the frequency and phenotype of cells found in the peripheral blood and the transcriptome of blood cells. Changes in cell type composition influence whole blood gene expression analysis results and thus the discovery of true transcript level changes remains a challenge. We propose a robust and reproducible procedure, which includes whole transcriptome gene expression profiling of major subsets of immune cell cells directly sorted from whole blood.

Methods: Target cells were enriched using magnetic microbeads and an autoMACS® Pro Separator (Miltenyi Biotec). Flow cytometric analysis for purity was performed before and after magnetic cell sorting. Total RNA was hybridized on HGU133 Plus 2.0 expression microarrays (Affymetrix, USA). CEL files signal intensity values were condensed using RMA and a custom CDF file (EntrezGene-based).

Results: Positive selection by use of MACS® Technology coupled to transcriptomics was assessed for eight different peripheral blood cell types, CD14+ monocytes, CD3+, CD4+, or CD8+ T cells, CD15+ granulocytes, CD19+ B cells, CD56+ NK cells, and CD45+ pan leukocytes. RNA quality from enriched cells was above a RIN of eight. GeneChip analysis confirmed cell type specific transcriptome profiles. Storing whole blood collected in an EDTA Vacutainer® tube at 4°C followed by MACS does not activate sorted cells. Gene expression analysis supports cell enrichment measurements by MACS.

Conclusions: The proposed workflow generates reproducible cell-type specific transcriptome data which can be translated to clinical settings and used to identify clinically relevant gene expression biomarkers from whole blood samples. This procedure enables the integration of transcriptomics of relevant immune cell subsets sorted directly from whole blood in clinical trial protocols.
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http://dx.doi.org/10.1186/s40169-014-0036-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424390PMC
May 2015

High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions.

Microbiol Res 2014 Feb-Mar;169(2-3):107-20. Epub 2013 Dec 1.

Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.

Due to evolutionary conservation of biology, experimental knowledge captured from genetic studies in eukaryotic model organisms provides insight into human cellular pathways and ultimately physiology. Yeast chemogenomic profiling is a powerful approach for annotating cellular responses to small molecules. Using an optimized platform, we provide the relative sensitivities of the heterozygous and homozygous deletion collections for nearly 1800 biologically active compounds. The data quality enables unique insights into pathways that are sensitive and resistant to a given perturbation, as demonstrated with both known and novel compounds. We present examples of novel compounds that inhibit the therapeutically relevant fatty acid synthase and desaturase (Fas1p and Ole1p), and demonstrate how the individual profiles facilitate hypothesis-driven experiments to delineate compound mechanism of action. Importantly, the scale and diversity of tested compounds yields a dataset where the number of modulated pathways approaches saturation. This resource can be used to map novel biological connections, and also identify functions for unannotated genes. We validated hypotheses generated by global two-way hierarchical clustering of profiles for (i) novel compounds with a similar mechanism of action acting upon microtubules or vacuolar ATPases, and (ii) an un-annotated ORF, YIL060w, that plays a role in respiration in the mitochondria. Finally, we identify and characterize background mutations in the widely used yeast deletion collection which should improve the interpretation of past and future screens throughout the community. This comprehensive resource of cellular responses enables the expansion of our understanding of eukaryotic pathway biology.
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http://dx.doi.org/10.1016/j.micres.2013.11.004DOI Listing
September 2014

Genetic diversity in black South Africans from Soweto.

BMC Genomics 2013 Sep 23;14:644. Epub 2013 Sep 23.

Division of Human Genetics, School of Pathology, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.

Background: Due to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap and 1000 Genomes Projects. Notably excluded, however, is the southern Africa region, which is inhabited predominantly by southeastern Bantu-speakers, currently suffering under the dual burden of infectious and non-communicable diseases. Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure. Here, we present the most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg).

Results: Participants were typed for ~4.3 million SNPs using the Illumina Omni5 beadchip. PCA and ADMIXTURE plots were used to compare the observed variation with that seen in selected populations worldwide. Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources. To assess the suitability of our sample as representative of Sowetans, we compared our results to participants in a larger rheumatoid arthritis case-control study. The control group showed good clustering with our sample, but among the cases were individuals who demonstrated notable admixture.

Conclusions: Sowetan population structure appears unique compared to other black Africans, and may have clinical implications. Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme.
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http://dx.doi.org/10.1186/1471-2164-14-644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3850641PMC
September 2013

Robust and tissue-independent gender-specific transcript biomarkers.

Biomarkers 2013 Aug 8;18(5):436-45. Epub 2013 Jul 8.

Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Basel, Switzerland.

Context: Correct gender assignment in humans at the molecular level is crucial in many scientific disciplines and applied areas.

Materials And Methods: Candidate gender markers were identified through supervised statistical analysis of genome wide microarray expression data from human blood samples (N = 123, 58 female, 65 male) as a training set. The potential of the markers to predict undisclosed tissue donor gender was tested on microarray data from 13 healthy and 11 cancerous human tissue collections (internal) and external datasets from samples of varying tissue origin. The abundance of some genes in the marker panel was quantified by RT-PCR as alternative analytical technology.

Results: We identified and qualified predictive, gender-specific transcript markers based on a set of five genes (RPS4Y1, EIF1AY, DDX3Y, KDM5D and XIST).

Conclusion: Gene expression marker panels can be used as a robust tissue- and platform-independent predictive approach for gender determination.
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http://dx.doi.org/10.3109/1354750X.2013.811538DOI Listing
August 2013

Increased survival despite failure of transplanted human hepatocyte implantation into liver parenchyma of nude mice with repeated lethal Jo2-induced liver deficiency.

Cell Transplant 2014 29;23(12):1557-72. Epub 2013 Apr 29.

EA 3921, IFR 133, Faculté de Médecine et de Pharmacie, Besançon, France.

We recently found that rat hepatocyte transplantation was efficient (liver repopulation: 2.4%) in a sublethal nude mouse model (less than 33% mortality) of repeated liver injury generated using Jo2, a mouse-specific anti-Fas antibody, at sublethal dose of 250 µg/kg for 3 weeks. Genomic analysis of the livers revealed cell cycle blockade and an antiproliferative status of circadian genes, suggesting a selective advantage. By contrast, in the present study, freshly isolated human hepatocyte transplantation performed in the same mouse model resulted in implantation of less than 6,000 cells per liver (about 0.006% repopulation) in all animals. Genomic analysis of nude mouse livers revealed a lack of P21 upregulation, while a signature of stimulation of liver regeneration was observed, including upregulation of early response genes and upregulation of circadian genes. When we translated this sublethal model to a lethal model (65% mortality) by increasing the Jo2 repeated doses to 375 µg/kg, human hepatocyte engraftment was still very low; however, animal mortality was corrected by transplantation (only 20% mortality). Genomic findings in livers from the mice of the lethal Jo2 transplanted group were similar to those of the sublethal Jo2 transplanted group, that is, no selective advantage genomic signature and signature of mouse liver regeneration. In conclusion, transplanted human hepatocytes acted as if they modified nude mouse liver responses to Jo2 by stimulating liver regeneration, leading to an increased survival rate.
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http://dx.doi.org/10.3727/096368913X667501DOI Listing
September 2015

Perturbation of microRNAs in rat heart during chronic doxorubicin treatment.

PLoS One 2012 31;7(7):e40395. Epub 2012 Jul 31.

Discovery and Investigative Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland.

Anti-cancer therapy based on anthracyclines (DNA intercalating Topoisomerase II inhibitors) is limited by adverse effects of these compounds on the cardiovascular system, ultimately causing heart failure. Despite extensive investigations into the effects of doxorubicin on the cardiovascular system, the molecular mechanisms of toxicity remain largely unknown. MicroRNAs are endogenously transcribed non-coding 22 nucleotide long RNAs that regulate gene expression by decreasing mRNA stability and translation and play key roles in cardiac physiology and pathologies. Increasing doses of doxorubicin, but not etoposide (a Topoisomerase II inhibitor devoid of cardiovascular toxicity), specifically induced the up-regulation of miR-208b, miR-216b, miR-215, miR-34c and miR-367 in rat hearts. Furthermore, the lowest dosing regime (1 mg/kg/week for 2 weeks) led to a detectable increase of miR-216b in the absence of histopathological findings or alteration of classical cardiac stress biomarkers. In silico microRNA target predictions suggested that a number of doxorubicin-responsive microRNAs may regulate mRNAs involved in cardiac tissue remodeling. In particular miR-34c was able to mediate the DOX-induced changes of Sipa1 mRNA (a mitogen-induced Rap/Ran GTPase activating protein) at the post-transcriptional level and in a seed sequence dependent manner. Our results show that integrated heart tissue microRNA and mRNA profiling can provide valuable early genomic biomarkers of drug-induced cardiac injury as well as novel mechanistic insight into the underlying molecular pathways.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040395PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409211PMC
April 2013

Selective and specific inhibition of the plasmodium falciparum lysyl-tRNA synthetase by the fungal secondary metabolite cladosporin.

Cell Host Microbe 2012 Jun;11(6):654-63

Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, Basel, Switzerland.

With renewed calls for malaria eradication, next-generation antimalarials need be active against drug-resistant parasites and efficacious against both liver- and blood-stage infections. We screened a natural product library to identify inhibitors of Plasmodium falciparum blood- and liver-stage proliferation. Cladosporin, a fungal secondary metabolite whose target and mechanism of action are not known for any species, was identified as having potent, nanomolar, antiparasitic activity against both blood and liver stages. Using postgenomic methods, including a yeast deletion strains collection, we show that cladosporin specifically inhibits protein synthesis by directly targeting P. falciparum cytosolic lysyl-tRNA synthetase. Further, cladosporin is >100-fold more potent against parasite lysyl-tRNA synthetase relative to the human enzyme, which is conferred by the identity of two amino acids within the enzyme active site. Our data indicate that lysyl-tRNA synthetase is an attractive, druggable, antimalarial target that can be selectively inhibited.
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http://dx.doi.org/10.1016/j.chom.2012.04.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3391680PMC
June 2012

The virtuous technology cycle concept and its application in next-generation sequencing.

Drug Discov Today 2012 Sep 12;17(17-18):1015-22. Epub 2012 Apr 12.

Novartis Institutes of Biomedical Research (NIBR), Biomarker Development (BMD), Basel, Switzerland.

External access to scientific technology plays an increasingly important part in pharmaceutical R&D. One advantage of accessing technology externally is the avoidance of costs associated with purchase and the reduced time required for developing new methods; in addition, access to external scientific expertise can be beneficial. However, few conceptual frameworks exist for achieving an optimal mix of internal and external technology access. In this review, we describe the virtuous technology cycle (VTC) concept and exemplify its application to next-generation sequencing (NGS). Based on selected examples, we show that the VTC concept can greatly enhance the number of technologies accessed and thus significantly increase flexibility and efficiency in drug discovery. We also discuss the challenges of externally accessing NGS technologies.
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http://dx.doi.org/10.1016/j.drudis.2012.04.003DOI Listing
September 2012

Genome-wide association mapping of quantitative traits in outbred mice.

G3 (Bethesda) 2012 Feb 1;2(2):167-74. Epub 2012 Feb 1.

Recent developments in high-density genotyping and statistical analysis methods that have enabled genome-wide association studies in humans can also be applied to outbred mouse populations. Increased recombination in outbred populations is expected to provide greater mapping resolution than traditional inbred line crosses, improving prospects for identifying the causal genes. We carried out genome-wide association mapping by using 288 mice from a commercially available outbred stock; NMRI mice were genotyped with a high-density single-nucleotide polymorphism array to map loci influencing high-density lipoprotein cholesterol, systolic blood pressure, triglyceride levels, glucose, and urinary albumin-to-creatinine ratios. We found significant associations (P < 10(-5)) with high-density lipoprotein cholesterol and identified Apoa2 and Scarb1, both of which have been previously reported, as candidate genes for these associations. Additional suggestive associations (P < 10(-3)) identified in this study were also concordant with published quantitative trait loci, suggesting that we are sampling from a limited pool of genetic diversity that has already been well characterized. These findings dampen our enthusiasm for currently available commercial outbred stocks as genetic mapping resources and highlight the need for new outbred populations with greater genetic diversity. Despite the lack of novel associations in the NMRI population, our analysis strategy illustrates the utility of methods that could be applied to genome-wide association studies in humans.
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http://dx.doi.org/10.1534/g3.111.001792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284324PMC
February 2012

Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples.

PLoS One 2011 16;6(11):e27156. Epub 2011 Nov 16.

Biomarker Development, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America.

Large-scale molecular profiling technologies have assisted the identification of disease biomarkers and facilitated the basic understanding of cellular processes. However, samples collected from human subjects in clinical trials possess a level of complexity, arising from multiple cell types, that can obfuscate the analysis of data derived from them. Failure to identify, quantify, and incorporate sources of heterogeneity into an analysis can have widespread and detrimental effects on subsequent statistical studies.We describe an approach that builds upon a linear latent variable model, in which expression levels from mixed cell populations are modeled as the weighted average of expression from different cell types. We solve these equations using quadratic programming, which efficiently identifies the globally optimal solution while preserving non-negativity of the fraction of the cells. We applied our method to various existing platforms to estimate proportions of different pure cell or tissue types and gene expression profilings of distinct phenotypes, with a focus on complex samples collected in clinical trials. We tested our methods on several well controlled benchmark data sets with known mixing fractions of pure cell or tissue types and mRNA expression profiling data from samples collected in a clinical trial. Accurate agreement between predicted and actual mixing fractions was observed. In addition, our method was able to predict mixing fractions for more than ten species of circulating cells and to provide accurate estimates for relatively rare cell types (<10% total population). Furthermore, accurate changes in leukocyte trafficking associated with Fingolomid (FTY720) treatment were identified that were consistent with previous results generated by both cell counts and flow cytometry. These data suggest that our method can solve one of the open questions regarding the analysis of complex transcriptional data: namely, how to identify the optimal mixing fractions in a given experiment.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027156PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217948PMC
March 2012

Integrated epigenetics of human breast cancer: synoptic investigation of targeted genes, microRNAs and proteins upon demethylation treatment.

PLoS One 2011 4;6(11):e27355. Epub 2011 Nov 4.

Laboratory for Gynecological Oncology, Department of Biomedicine/Women's Hospital, University of Basel, Basel, Switzerland.

Background: The contribution of aberrant DNA methylation in silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations are reversible, it became of interest to determine the effects of the 5-aza-2'-deoxycytidine (DAC) demethylation therapy in breast cancer at different molecular levels.

Methods And Findings: Here we investigate a synoptic model to predict complete DAC treatment effects at the level of genes, microRNAs and proteins for several human breast cancer lines. The present study assessed an effective treatment dosage based on the cell viability, cytotoxicity, apoptosis and methylation assays for the investigated cell lines. A highly aggressive and a non-aggressive cell line were investigated using omics approaches such as MALDI-TOF MS, mRNA- and microRNA expression arrays, 2-D gel electrophoresis and LC-MS-MS. Complete molecular profiles including the biological interaction and possible early and late systematic stable or transient effects of the methylation inhibition were determined. Beside the activation of several epigenetically suppressed TSGs, we also showed significant dysregulation of some important oncogenes, oncomiRs and oncosuppressors miRNAs as well as drug tolerance genes/miRNAs/proteins.

Conclusions: In the present study, the results denote some new molecular DAC targets and pathways based on the chemical modification of DNA methylation in breast cancer. The outlined approach might prove to be useful as an epigenetic treatment model also for other human solid tumors in the management of cancer patients.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027355PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208622PMC
March 2012

A microarray analysis of full depth knee cartilage of ovariectomized rats.

BMC Res Notes 2011 Mar 15;4:63. Epub 2011 Mar 15.

Cartilage biology and biomarkers, Nordic Bioscience, Herlev, Denmark.

Background: This short communication focuses the on articular cartilage and the subchondral bone, both of which play important roles in the development of osteoarthritis (OA). There are indications that estrogen-deficiency, as the post-menopausal state, accelerate the development of OA.

Findings: We investigated, which extracellular matrix (ECM) protein, proteases and different pro-inflammatory factors was up- or down-regulated in the knee joint tissue in response to estrogen-deficiency in rats induced by ovariectomy. These data support previous findings that several metalloproteinases (MMPs) and cysteine proteases are co-regulated with numerous collagens and proteoglycans that are important for cartilage integrity. Furthermore quite a few pro-inflammatory cytokines were regulated by estrogen deprivation.

Conclusion: We found multiple genes where regulated in the joint by estrogen-deficiency, many of which correspond well with our current knowledge of the pathogenesis of OA. It supports that estrogen-deficiency (e.g. OVX) may accelerate joint deterioration. However, there are also data that draw attention the need for better understanding of the synergy between proteases and tissue turnover.
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http://dx.doi.org/10.1186/1756-0500-4-63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068969PMC
March 2011

Cross-study and cross-omics comparisons of three nephrotoxic compounds reveal mechanistic insights and new candidate biomarkers.

Toxicol Appl Pharmacol 2011 Apr 21;252(2):112-22. Epub 2010 Nov 21.

Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany.

The European InnoMed-PredTox project was a collaborative effort between 15 pharmaceutical companies, 2 small and mid-sized enterprises, and 3 universities with the goal of delivering deeper insights into the molecular mechanisms of kidney and liver toxicity and to identify mechanism-linked diagnostic or prognostic safety biomarker candidates by combining conventional toxicological parameters with "omics" data. Mechanistic toxicity studies with 16 different compounds, 2 dose levels, and 3 time points were performed in male Crl: WI(Han) rats. Three of the 16 investigated compounds, BI-3 (FP007SE), Gentamicin (FP009SF), and IMM125 (FP013NO), induced kidney proximal tubule damage (PTD). In addition to histopathology and clinical chemistry, transcriptomics microarray and proteomics 2D-DIGE analysis were performed. Data from the three PTD studies were combined for a cross-study and cross-omics meta-analysis of the target organ. The mechanistic interpretation of kidney PTD-associated deregulated transcripts revealed, in addition to previously described kidney damage transcript biomarkers such as KIM-1, CLU and TIMP-1, a number of additional deregulated pathways congruent with histopathology observations on a single animal basis, including a specific effect on the complement system. The identification of new, more specific biomarker candidates for PTD was most successful when transcriptomics data were used. Combining transcriptomics data with proteomics data added extra value.
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http://dx.doi.org/10.1016/j.taap.2010.11.006DOI Listing
April 2011

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Authors:
Leming Shi Gregory Campbell Wendell D Jones Fabien Campagne Zhining Wen Stephen J Walker Zhenqiang Su Tzu-Ming Chu Federico M Goodsaid Lajos Pusztai John D Shaughnessy André Oberthuer Russell S Thomas Richard S Paules Mark Fielden Bart Barlogie Weijie Chen Pan Du Matthias Fischer Cesare Furlanello Brandon D Gallas Xijin Ge Dalila B Megherbi W Fraser Symmans May D Wang John Zhang Hans Bitter Benedikt Brors Pierre R Bushel Max Bylesjo Minjun Chen Jie Cheng Jing Cheng Jeff Chou Timothy S Davison Mauro Delorenzi Youping Deng Viswanath Devanarayan David J Dix Joaquin Dopazo Kevin C Dorff Fathi Elloumi Jianqing Fan Shicai Fan Xiaohui Fan Hong Fang Nina Gonzaludo Kenneth R Hess Huixiao Hong Jun Huan Rafael A Irizarry Richard Judson Dilafruz Juraeva Samir Lababidi Christophe G Lambert Li Li Yanen Li Zhen Li Simon M Lin Guozhen Liu Edward K Lobenhofer Jun Luo Wen Luo Matthew N McCall Yuri Nikolsky Gene A Pennello Roger G Perkins Reena Philip Vlad Popovici Nathan D Price Feng Qian Andreas Scherer Tieliu Shi Weiwei Shi Jaeyun Sung Danielle Thierry-Mieg Jean Thierry-Mieg Venkata Thodima Johan Trygg Lakshmi Vishnuvajjala Sue Jane Wang Jianping Wu Yichao Wu Qian Xie Waleed A Yousef Liang Zhang Xuegong Zhang Sheng Zhong Yiming Zhou Sheng Zhu Dhivya Arasappan Wenjun Bao Anne Bergstrom Lucas Frank Berthold Richard J Brennan Andreas Buness Jennifer G Catalano Chang Chang Rong Chen Yiyu Cheng Jian Cui Wendy Czika Francesca Demichelis Xutao Deng Damir Dosymbekov Roland Eils Yang Feng Jennifer Fostel Stephanie Fulmer-Smentek James C Fuscoe Laurent Gatto Weigong Ge Darlene R Goldstein Li Guo Donald N Halbert Jing Han Stephen C Harris Christos Hatzis Damir Herman Jianping Huang Roderick V Jensen Rui Jiang Charles D Johnson Giuseppe Jurman Yvonne Kahlert Sadik A Khuder Matthias Kohl Jianying Li Li Li Menglong Li Quan-Zhen Li Shao Li Zhiguang Li Jie Liu Ying Liu Zhichao Liu Lu Meng Manuel Madera Francisco Martinez-Murillo Ignacio Medina Joseph Meehan Kelci Miclaus Richard A Moffitt David Montaner Piali Mukherjee George J Mulligan Padraic Neville Tatiana Nikolskaya Baitang Ning Grier P Page Joel Parker R Mitchell Parry Xuejun Peng Ron L Peterson John H Phan Brian Quanz Yi Ren Samantha Riccadonna Alan H Roter Frank W Samuelson Martin M Schumacher Joseph D Shambaugh Qiang Shi Richard Shippy Shengzhu Si Aaron Smalter Christos Sotiriou Mat Soukup Frank Staedtler Guido Steiner Todd H Stokes Qinglan Sun Pei-Yi Tan Rong Tang Zivana Tezak Brett Thorn Marina Tsyganova Yaron Turpaz Silvia C Vega Roberto Visintainer Juergen von Frese Charles Wang Eric Wang Junwei Wang Wei Wang Frank Westermann James C Willey Matthew Woods Shujian Wu Nianqing Xiao Joshua Xu Lei Xu Lun Yang Xiao Zeng Jialu Zhang Li Zhang Min Zhang Chen Zhao Raj K Puri Uwe Scherf Weida Tong Russell D Wolfinger

Nat Biotechnol 2010 Aug 30;28(8):827-38. Epub 2010 Jul 30.

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA.

Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. 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, >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. We 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.
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http://dx.doi.org/10.1038/nbt.1665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315840PMC
August 2010

A panel of urinary biomarkers to monitor reversibility of renal injury and a serum marker with improved potential to assess renal function.

Nat Biotechnol 2010 May;28(5):486-94

Department of Investigative Laboratory Sciences, Safety Assessment, Merck Research Laboratories, West Point, Pennsylvania, USA.

The Predictive Safety Testing Consortium's first regulatory submission to qualify kidney safety biomarkers revealed two deficiencies. To address the need for biomarkers that monitor recovery from agent-induced renal damage, we scored changes in the levels of urinary biomarkers in rats during recovery from renal injury induced by exposure to carbapenem A or gentamicin. All biomarkers responded to histologic tubular toxicities to varied degrees and with different kinetics. After a recovery period, all biomarkers returned to levels approaching those observed in uninjured animals. We next addressed the need for a serum biomarker that reflects general kidney function regardless of the exact site of renal injury. Our assay for serum cystatin C is more sensitive and specific than serum creatinine (SCr) or blood urea nitrogen (BUN) in monitoring generalized renal function after exposure of rats to eight nephrotoxicants and two hepatotoxicants. This sensitive serum biomarker will enable testing of renal function in animal studies that do not involve urine collection.
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http://dx.doi.org/10.1038/nbt.1627DOI Listing
May 2010

Urinary clusterin, cystatin C, beta2-microglobulin and total protein as markers to detect drug-induced kidney injury.

Nat Biotechnol 2010 May;28(5):463-9

Novartis Institutes for BioMedical Research, Novartis, Basel, Switzerland.

Earlier and more reliable detection of drug-induced kidney injury would improve clinical care and help to streamline drug-development. As the current standards to monitor renal function, such as blood urea nitrogen (BUN) or serum creatinine (SCr), are late indicators of kidney injury, we conducted ten nonclinical studies to rigorously assess the potential of four previously described nephrotoxicity markers to detect drug-induced kidney and liver injury. Whereas urinary clusterin outperformed BUN and SCr for detecting proximal tubular injury, urinary total protein, cystatin C and beta2-microglobulin showed a better diagnostic performance than BUN and SCr for detecting glomerular injury. Gene and protein expression analysis, in-situ hybridization and immunohistochemistry provide mechanistic evidence to support the use of these four markers for detecting kidney injury to guide regulatory decision making in drug development. The recognition of the qualification of these biomarkers by the EMEA and FDA will significantly enhance renal safety monitoring.
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http://dx.doi.org/10.1038/nbt.1622DOI Listing
May 2010

Cell type-specific gene expression differences in complex tissues.

Nat Methods 2010 Apr 7;7(4):287-9. Epub 2010 Mar 7.

Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.

We describe cell type-specific significance analysis of microarrays (csSAM) for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. First, we validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejection, which revealed hundreds of differentially expressed genes that were otherwise undetectable.
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http://dx.doi.org/10.1038/nmeth.1439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699332PMC
April 2010

Performance of novel kidney biomarkers in preclinical toxicity studies.

Toxicol Sci 2010 Jul 29;116(1):8-22. Epub 2010 Jan 29.

Department of Toxicology, University of Würzburg, Würzburg, Germany.

The kidney is one of the main targets of drug toxicity, but early detection of renal damage is often difficult. As part of the InnoMed PredTox project, a collaborative effort aimed at assessing the value of combining omics technologies with conventional toxicology methods for improved preclinical safety assessment, we evaluated the performance of a panel of novel kidney biomarkers in preclinical toxicity studies. Rats were treated with a reference nephrotoxin or one of several proprietary compounds that were dropped from drug development in part due to renal toxicity. Animals were dosed at two dose levels for 1, 3, and 14 days. Putative kidney markers, including kidney injury molecule-1 (Kim-1), lipocalin-2 (Lcn2), clusterin, and tissue inhibitor of metalloproteinases-1, were analyzed in kidney and urine using quantitative real-time PCR, ELISA, and immunohistochemistry. Changes in gene/protein expression generally correlated well with renal histopathological alterations and were frequently detected at earlier time points or at lower doses than the traditional clinical parameters blood urea nitrogen and serum creatinine. Urinary Kim-1 and clusterin reflected changes in gene/protein expression and histopathological alterations in the target organ in the absence of functional changes. This confirms clusterin and Kim-1 as early and sensitive, noninvasive markers of renal injury. Although Lcn2 did not appear to be specific for kidney toxicity, its rapid response to inflammation and tissue damage in general may suggest its utility in routine toxicity testing.
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http://dx.doi.org/10.1093/toxsci/kfq029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886853PMC
July 2010

Transcriptome changes in renal allograft protocol biopsies at 3 months precede the onset of interstitial fibrosis/tubular atrophy (IF/TA) at 6 months.

Nephrol Dial Transplant 2009 Aug 27;24(8):2567-75. Epub 2009 Apr 27.

Novartis Pharma AG, Basel, Switzerland.

Background: Interstitial fibrosis and tubular atrophy (IF/TA) in renal transplants are the major morphological correlates of progressive graft deterioration. Early diagnosis of IF/TA is a pre-requisite for a timely therapeutic intervention in patients at risk. To evaluate events occurring before the overt onset of IF/TA, gene expression profiling of 3-month protocol biopsies from patients with IF/TA was performed in a patient group (n = 8) who developed mild IF/TA [chronic allograft nephropathy (CAN) grade I, by the Banff scoring system] in the subsequent 6-month protocol biopsy ('progressors'), and in 12 patients without IF/TA at 6 months ('non-progressors').

Methods: RNA was extracted, labelled and hybridized to human specific genome wide DNA microarrays. Normalized data were subjected to gene-centric and pathway-centric statistical methods.

Results: Compared to the non-progressors, the 3-month biopsies of the progressor group showed overexpression of several genes that are important in the T- and B-cell activation and immune response. Genes involved in pro-fibrotic processes were identified in the biopsies of the progressors that preceded the observed IF/TA at 6 months. Furthermore, several genes with transporter and metabolic functions were underrepresented in the progressors in the 3-month biopsies.

Conclusion: Gene expression profiling of early protocol biopsies identified changes in the transcriptome of grafts, which may be important for the development of IF/TA. Such early detection of transcriptome changes can facilitate the identification of patients at risk shifting the intervention time point well before the histological diagnosis of irreversible IF/TA.
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http://dx.doi.org/10.1093/ndt/gfp183DOI Listing
August 2009

The molecular signature of oxidative metabolism and the mode of macrophage activation determine the shift from acute to chronic disease in experimental arthritis: critical role of interleukin-12p40.

Arthritis Rheum 2008 Nov;58(11):3471-84

Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

Objective: Repeated injection of streptococcal cell wall (SCW) fragments results in chronic arthritis in mice. The objective of this study was to identify genes and pathways that determine disease progression based on gene expression profiling in this model.

Methods: Chronic arthritis was induced in mice by 4 injections of SCW fragments. RNA samples were isolated from synovial tissue obtained at various time points and were analyzed using mouse genome array and quantitative reverse transcription-polymerase chain reaction techniques. The functional role of potential key genes was evaluated in mice with specific gene deletions.

Results: Gene expression analyses revealed a shift in molecular signature. In contrast to an up-regulation of the inflammatory response pathway, the pathways involved in oxidative metabolism were significantly down-regulated during the chronic phase of arthritis. Since oxidative metabolism determines the mode of macrophage activation, we investigated phenotype switching in macrophages. Markers of alternatively activated macrophages, such as arginase 1, were at maximal levels during acute inflammation. In contrast, induction of markers of classically activated macrophages (M1), such as interleukin-1beta (IL-1beta) and inducible nitric oxide synthase (iNOS), was relatively low during the acute phase of disease, but highly increased toward the chronic phase. M1 polarization during the chronic phase was accompanied by a Th1 signature, characterized by IL-12p40, IL-12p35, and interferon-gamma. However, the absence of IL-12p40, but not IL-12p35, significantly inhibited the chronic phase of arthritis and was marked by a reduction in IL-17 and iNOS levels, as well as restored expression of oxidative metabolism genes.

Conclusion: M1 polarization accompanied by a decline in oxidative metabolism determine the chronic phase of arthritis. IL-12p40, most likely acting through the IL-23/IL-17 axis, plays a critical role in this process.
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http://dx.doi.org/10.1002/art.23956DOI Listing
November 2008

Improved xenogenic hepatocyte implantation into nude mouse liver parenchyma with acute liver failure when followed by repeated anti-Fas antibody (Jo2) treatment.

Cell Transplant 2008 ;17(5):507-24

EA 3921, IFR 133, Faculté de Médecine et de Pharmacie, Besançon, France.

Hepatocyte transplantation is a promising therapy for acute liver failure in humans. Recently, we succeeded in inducing various acute and chronic liver failures in nude mice. Engraftment of transplanted xenogeneic rat hepatocytes, visualized in the host liver by anti-MHC class I immunohistochemistry, revealed that liver repopulation was limited, and equivalent in nude mice with and without acute liver failure. In the present study, acute liver failure was induced in nude mice by a single injection of sublethal anti-Fas antibody Jo2, followed 24 h later by rat hepatocyte transplantation and than by a weekly repeated injection of Jo2. Rat hepatocyte engraftment into the recipient liver parenchyma 3 weeks following hepatocyte transplantation was about sevenfold increased when nude mice were subsequently subjected to weekly repeated Jo2 injection. Genomic analysis of these mice showed an overall transcriptome profile of upregulation of cellular cycle blocking transcripts, activation of liver injury inducing IFN-gamma/STAT1 pathway, and circadian transcript signature of antiproliferative cell status compared to mice submitted to hepatocyte transplantation only. The findings of the present study suggest that the induction of cell proliferation blockade in recipient livers could promote sufficient engraftment of transplanted hepatocytes to allow transient or definitive treatment of liver failure in humans.
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http://dx.doi.org/10.3727/096368908785096051DOI Listing
January 2009

Effects of long-term dietary intake of magnesium on rat liver transcriptome.

Magnes Res 2007 Dec;20(4):259-65

Laboratoire de biologie cellulaire, UFR des Sciences médicales et pharmaceutiques, EA 3921 OMC, Besançon, France.

In the present study we investigated the effect of a two-year treatment period with a diet containing 3.2g, 0.8 g and 0.15 g Mg/kg, on the rat liver transcriptome. At the end of the study, a treatment-dependent decrease in plasmatic Mg concentration was found (0.86 +/- 0.02 mmol/L, 0.70 +/- 0.02 mmol/L and 0.52 +/- 0.03 mmol/L for groups receiving 3.2g, 0.8 g and 0.15 g Mg/kg diet, respectively). No significant treatment-related effect on body and liver weights was observed, however a dietary Mg intake-dependent increase in mortality rate occurred in animals (11%, 25% and 38% death of animals). Mg content in the diet affected gene expression in rat livers, as assessed by rat specific DNA microarrays. We identified 11 genes up-regulated and 39 genes down-regulated by at least two-fold by a decrease in Mg content and grouped them within five functional pathways: metabolism 20%, cytoarchitecture (connective tissue/cell adhesion/cytoskeleton) 12%, channels/ transporters 20%, turn-over (nucleic acid and protein) 16%, and homeostasis (stress/DNA damage/apoptosis/ageing) 32%. The results of the present study confirm the pleiotropic effects of Mg and provide further evidence that a Mg decrease in the diet may be considered as a promoting factor for pathologies, especially in the liver, during ageing.
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December 2007

Effects of ceramide-1-phosphate on cultured cells: dependence on dodecane in the vehicle.

J Lipid Res 2007 Jan 3;48(1):66-76. Epub 2006 Oct 3.

Novartis Institutes for BioMedical Research, A-1235 Vienna, Austria.

Ceramide-1-phosphate (C1P), the product of ceramide kinase, is a sphingophospholipid with recently recognized signaling properties. In particular, it was reported to be mitogenic and capable of direct stimulation of cytosolic phospholipase A(2alpha). Much of the present knowledge has relied on the use of C1P of various acyl chain lengths, together with diverse protocols to deliver it to cultured cells. A mixture of ethanol (or methanol) with dodecane, as the vehicle, has become popular. However, the contribution of this solvent to the observed effects of C1P has not been documented. Here, we show that addition of C1P in ethanol-dodecane to culture medium leads to irreversible cytotoxic effects. These culminate in mitochondrial swelling, vacuole formation, and cell death. Not only the toxicity of C1P, but also its ability to trigger prostaglandin E2 release, is fully dependent upon addition of a premade C1P-dodecane mixture. Furthermore, we show that these effects are not restricted to C1P. They result from the capacity of dodecane to interact with phospholipids; hence, they go undetected with a vehicle control. This study should raise awareness about the use of dodecane for phospholipid delivery and, in turn, help in unraveling C1P signaling, which is still poorly understood.
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http://dx.doi.org/10.1194/jlr.M600399-JLR200DOI Listing
January 2007

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Authors:
Leming Shi Laura H Reid Wendell D Jones Richard Shippy Janet A Warrington Shawn C Baker Patrick J Collins Francoise de Longueville Ernest S Kawasaki Kathleen Y Lee Yuling Luo Yongming Andrew Sun James C Willey Robert A Setterquist Gavin M Fischer Weida Tong Yvonne P Dragan David J Dix Felix W Frueh Frederico M Goodsaid Damir Herman Roderick V Jensen Charles D Johnson Edward K Lobenhofer Raj K Puri Uwe Schrf Jean Thierry-Mieg Charles Wang Mike Wilson Paul K Wolber Lu Zhang Shashi Amur Wenjun Bao Catalin C Barbacioru Anne Bergstrom Lucas Vincent Bertholet Cecilie Boysen Bud Bromley Donna Brown Alan Brunner Roger Canales Xiaoxi Megan Cao Thomas A Cebula James J Chen Jing Cheng Tzu-Ming Chu Eugene Chudin John Corson J Christopher Corton Lisa J Croner Christopher Davies Timothy S Davison Glenda Delenstarr Xutao Deng David Dorris Aron C Eklund Xiao-hui Fan Hong Fang Stephanie Fulmer-Smentek James C Fuscoe Kathryn Gallagher Weigong Ge Lei Guo Xu Guo Janet Hager Paul K Haje Jing Han Tao Han Heather C Harbottle Stephen C Harris Eli Hatchwell Craig A Hauser Susan Hester Huixiao Hong Patrick Hurban Scott A Jackson Hanlee Ji Charles R Knight Winston P Kuo J Eugene LeClerc Shawn Levy Quan-Zhen Li Chunmei Liu Ying Liu Michael J Lombardi Yunqing Ma Scott R Magnuson Botoul Maqsodi Tim McDaniel Nan Mei Ola Myklebost Baitang Ning Natalia Novoradovskaya Michael S Orr Terry W Osborn Adam Papallo Tucker A Patterson Roger G Perkins Elizabeth H Peters Ron Peterson Kenneth L Philips P Scott Pine Lajos Pusztai Feng Qian Hongzu Ren Mitch Rosen Barry A Rosenzweig Raymond R Samaha Mark Schena Gary P Schroth Svetlana Shchegrova Dave D Smith Frank Staedtler Zhenqiang Su Hongmei Sun Zoltan Szallasi Zivana Tezak Danielle Thierry-Mieg Karol L Thompson Irina Tikhonova Yaron Turpaz Beena Vallanat Christophe Van Stephen J Walker Sue Jane Wang Yonghong Wang Russ Wolfinger Alex Wong Jie Wu Chunlin Xiao Qian Xie Jun Xu Wen Yang Liang Zhang Sheng Zhong Yaping Zong William Slikker

Nat Biotechnol 2006 Sep;24(9):1151-61

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA.

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.
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http://dx.doi.org/10.1038/nbt1239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272078PMC
September 2006

Progressive pulmonary sarcoidosis--a fibroproliferative process potentially triggered by EGR-1 and IL-6.

Sarcoidosis Vasc Diffuse Lung Dis 2006 Mar;23(1):38-50

Respiratory Medicine and Pulmonary Cell Research and Institute for Pathology, University Hospital, Basel, Switzerland.

Background And Aim Of The Work: Sarcoidosis is a chronic granulomatous disorder of unknown etiology. In most patients the disease is self-limited, although for reasons unclear, others progress or die from progressive organ fibrosis. Growth factors have been implicated in the pathogenesis of other fibrotic lung conditions. We have, therefore, examined the relationship between growth factor expression and disease phenotype in sarcoidosis.

Methods: Adopting a target gene approach utilizing gene expression arrays, growth factor gene expression profile was analyzed in the peripheral blood of 12 patients and 12 healthy controls. Expression, functional activity and the effect of oligonucleotide antisense treatment on selected proteins differentially expressed in progressive sarcoidosis were then tested in vitro on primary human lung fibroblasts.

Results: Genes regulating angiogenesis were preferentially upregulated in the self-limited form of disease, while early growth response-1 and interleukin-6 were predominantly activated in progressive sarcoidosis. Increased expression of early growth response-1 in sarcoid lung was confirmed by immunohistochemistry. Stimulated human fibroblasts also rapidly expressed interleukin-6 and early growth response-1 and these proteins were found to mediate serum-induced fibroblast proliferation as proliferation could be significantly abrogated with interleukin-6 and early growth response-1 antisense oligonucelotides.

Conclusion: We conclude that progressive pulmonary sarcoidosis is characterized by a fibroproliferative dysregulation potentially triggered by early growth response-1 and interleukin-6. Our disease model underlines the inability of steroids to prevent ongoing fibroproliferation in the lung.
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March 2006

Differentiation of spontaneous and induced mammary adenocarcinomas of the rat by gene expression profiling.

Exp Toxicol Pathol 2006 Nov 14;58(2-3):151-61. Epub 2006 Aug 14.

Preclinical Safety, Novartis Pharma AG, Basel, Switzerland.

The differentiation of spontaneous and induced adenocarcinomas is of interest in the setting of carcinogenicity studies. In the experiment reported here, a differentiation of morphologically similar spontaneous and induced mammary adenocarcinomas of the rat is achieved by gene expression profiling. By choosing one marker gene based on the gene expression profile for each tumour type, we were able to distinguish the tumours by real-time quantitative polymerase chain reaction (RT-QPCR) as well.
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http://dx.doi.org/10.1016/j.etp.2006.06.008DOI Listing
November 2006