Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene.

Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis

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

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12881-016-0308-0) contains supplementary material, which is available to authorized users

Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene.

Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis

112(4).Tox.Pt2.MON.417-510

Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis. minimal expression of single-cell necrosis with minimal mononuclear infiltrate without associated changes in clinical chemistry parameters Male Sprague-Dawley rats were obtained from Charles River Laboratories, Inc. (Wilmington, MA). Rats were 57 days old and weighed 233.4-274.0 g at the start of the treatment. Upon arrival to Abbott Laboratories (Abbott Park, IL), all rats were acclimated for 6 days before treatment began. The two treatment groups comprising four rats each received the test compound at a concentration of 10 or 100 mg/kg, respectively. Animals in the equally sized control group received vehicle only. Rats were dosed once daily by gavage for 7 days. The dose volume was 10 mL/kg. Doses were milligram salt per kilogram per day and were calculated for each rat on the basis of the most recent body weight data available. Rats were fasted overnight after their last treatment, euthanized under halothane anesthesia and submitted for necropsy. Each rat received its last treatment approximately 24 hr before scheduled necropsy. In vivo observations, pathology, and sampling. All rats were observed twice each day during the pretreatment and treatment periods for survival and general condition. Blood samples were drawn from all rats, and clinical chemistry parameters were obtained for alanine aminotransferase (ALT), aspartate aminotransferase (AST), sorbitol dehydrogenase (SDH), alkaline phosphatase (ALKPHOS), total bilirubin (TBIL), glucose (GLU), and triglycerides (TRIG). At necropsy, liver was weighed and the percent of body weight of each organ was calculated. One part of the liver (left lateral lobe) was fixed for potential histopathology in 10% formalin and subsequently sectioned and stained with hematoxylin and eosin, while the rest of the organ was rinsed in phosphate-buffered saline, immediately flashfrozen in liquid nitrogen, and kept frozen for subsequent RNA isolation. RNA Isolation and Distribution Approximately 100 mg of tissue from each liver was placed into TRIzol reagent (Invitrogen Corp., Carlsbad, CA) and homogenized. Total RNA isolation was performed exactly according to the TRIzol reagent protocol. The remaining portion of the liver was retained frozen. Following isolation, the RNA was quantitated using a BioRad SmartSpec 3000 spectrophotometer (BioRad, Hercules, CA), and the integrity of the RNA was determined using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). The RNA from the four animals in each treatment group was then pooled using equivalent amounts from each sample. The RNA was aliquoted and precipitated in ethanol and ammonium acetate for shipment to the participating DNA microarray users. In addition, RNA from individual animals was shipped to some of the DNA microarray analysis laboratories. DNA microarray analysis. RNA samples were analyzed independently by five different Affymetrix users: Boehringer-Ingelheim Pharmaceuticals, Novartis, Pfizer Inc, F. Hoffmann-La Roche AG, and Schering AG using rat RGU34A expression probe arrays (Affymetrix, Santa Clara, CA), containing 8,799 probe sets interrogating primarily annotated genes. The rat sequences used for the design of the RGU34A expression probe array were derived from Build 34 of the UniGene database (http://www.ncbi. nih.gov/UniGene/; created from Genbank 107/dbEST 11/18/98) and supplemented with additional annotated gene sequences from Genbank 110 (http://www.ncbi. nih.gov/GenBank/). UniGene clusters are represented by an example sequence that is the most complete and most 3´sequence in the cluster. The oligonucleotide probes are 25mers and 16 probe pairs per sequence are used. Processing of RNA and GeneChip experiments was carried out basically as recommended by Affymetrix, with some userspecific variations Data analysis. Tab-delimited files obtained from the Affymetrix Microarray Suite software, version 4.0, (*.chp files) and containing data on signal intensity [average difference (Avg Diff)] and categorical expression-level measurement (Absolute Call) were used for analysis. Data were normalized and further analyzed using Roche in-house developed software (RACE-A; F. Hoffmann-La Roche AG, Mannheim, Germany). Briefly, this software performs a normalization step on the signal intensities based on the average signal (Mean Avg Diff) of each microarray before calculating additional parameters. In the cases where biological replicates were included, RACE-A was also used to calculate the average signal (arithmetic mean), and SD for each probe set. Also, comparative analysis between control and treated was performed including fold change (Avg Diff Treated/Avg Diff Control) and a significance value (p-value), calculated using a two-tailed, unpaired t-test. Once the required statistical parameters were calculated, data were filtered and exported to MS-Excel 2002 (Microsoft, Corp., Bellevue, WA) or additional software for visualization and further analysis. In addition, methods comprising more sophisticated algorithms and designed et al. 1999). Unsupervised methods such as clustering algorithms and PCA are commonly used to determine if gene expression patterns allow the discrimination of natural subpopulations that might bear a biological meaning such as treated/untreated or healthy/diseased. PCA is a mathematical technique that reduces the dimensionality of highly multivariate data. The reduced dimensions (or components) actually describe the major part of the variation in the samples and separate natural subpopulations without a priori knowledge Cluster analysis is a method used to organize primary data. Pairwise average-linkage cluster is a form of unsupervised hierarchical clustering commonly used for the analysis of microarray data. Relationships among objects such as experimental conditions or genes are represented by a tree whose branch lengths reflect the degree of similarity between the objects as assessed by a pairwise similarity function based on correlation coefficients The complete data set is currently being submitted to ArrayExpress (EMBLEuropean Bioinformatics Institute, Hinxton, UK; http://www.ebi.ac.uk/arrayexpress) and will be available for public download by the second quarter of 2004. Accession numbers referencing this data set will be available on the HESI website (http://hesi.ilsi.org/ index.cfm?pubentityid=120). Results Clinical chemistry and histopathology. A significant change in both body weight and food consumption compared to that of control groups was seen in the high-dose, but not in the low-dose group (data not shown). Clinical chemistry values confirmed liver toxicity occurred in the high-dose rats No compound-related histopathological changes were found for the low-dose group, whereas several compound-related changes were seen in livers from rats treated at the high-dose level. These included cytoplasmic vacuolation of periportal hepatocytes, minimal to mild necrosis of periportal hepatocytes, increased infiltration of portal tracts by mononuclear inflammatory cells, and hyperplasia of oval cells along portal tracts. Comparisons across users. After microarray analysis of the RNA, it was determined that different users obtained comparable results despite possible variation in the sample processing [from total RNA up to fragmented IVT (in vitro transcript)] and microarray hybridization protocols. In a preliminary round of analysis using rigid cutoff values to assess which genes were modulated, the number of genes detected as regulated in the pooled samples (2-fold increase or decrease) by each user were strikingly different Further microarray results demonstrated that when individual animals were analyzed, as opposed to pooled samples, the number of genes detected as induced/ repressed was generally reduced

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.

Contains fulltext : 70716.pdf (publisher's version ) (Closed access)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

Performance- and stimulus-dependent oscillations in monkey prefrontal cortex during short-term memory

Short-term memory requires the coordination of sub-processes like encoding, retention, retrieval and comparison of stored material to subsequent input. Neuronal oscillations have an inherent time structure, can effectively coordinate synaptic integration of large neuron populations and could therefore organize and integrate distributed sub-processes in time and space. We observed field potential oscillations (14-95Hz) in ventral prefrontal cortex of monkeys performing a visual memory task. Stimulus-selective and performance-dependent oscillations occurred simultaneously at 65-95Hz and 14-50Hz, the latter being phase-locked throughout memory maintenance. We propose that prefrontal oscillatory activity may be instrumental for the dynamical integration of local and global neuronal processes underlying short-term memory