A statistical approach in using cDNA array analysis to determine modest changes in gene expression in several brain regions after neurotoxic insult

Methamphetamine Modulates Gene Expression Patterns in Monocyte Derived Mature Dendritic Cells

BACKGROUND

The US is currently experiencing a grave epidemic of methamphetamine use as a recreational drug, and the risk for HIV-1 infection attributable to methamphetamine use continues to increase. Recent studies show a high prevalence of HIV infection among methamphetamine users. Dendritic cells (DCs) are potent antigen presenting cells that are the initial line of defense against HIV-1 infection. In addition, DCs also serve as reservoirs for HIV-1 and function at the interface between the adaptive and the innate immune systems, which recognize and internalize pathogens and subsequently activate T cells. Exposure to methamphetamine results in modulation of immune functional parameters that are necessary for host defense. Chronic methamphetamine use can cause psychiatric co-morbidity, neurological complications, and can alter normal biological processes and immune functions. Limited information is available on the mechanisms by which methamphetamine may influence immune function. This study explores the effect of methamphetamine on a specific array of genes that may modulate immune function. We hypothesize that methamphetamine treatment results in the immunomodulation of DC functions, leading to dysregulation of the immune system of the infected host. This suggests that methamphetamine has a role as a cofactor in the pathogenesis of HIV-1.

METHODS

We used the high-throughput technology of gene microarray analysis to understand the molecular mechanisms underlying the genomic changes that alter normal biological processes when DCs are treated with methamphetamine. Additionally, we validated the results obtained from microarray experiments using a combination of quantitative real-time PCR and Western blot analysis.

RESULTS

These data are the first evidence that methamphetamine modulates DC expression of several genes. Methamphetamine treatment alters categories of genes that are associated with chemokine regulation, cytokinesis, signal transduction mechanisms, apoptosis, and cell cycle regulation. This report focuses on a selected group of genes that are significantly modulated by methamphetamine treatment and that have been associated with HIV-1 pathogenesis.

DISCUSSION/CONCLUSION

The purpose of this study was to identify genes that are unique and/or specific to the complex immunomodulatory mechanisms that are altered as a result of methamphetamine abuse in HIV-1-infected patients. These studies will help to identify the molecular mechanisms that underlie methamphetamine toxicity, and several functionally important classes of genes have emerged as targets in methamphetamine-mediated immunopathogenesis of HIV-1. Identification of novel DC-specific and methamphetamine-responsive genes that modulate several biological, molecular, and signal transduction functions may serve as methamphetamine- and/or HIV-1-specific drug targets.

Designing Toxicogenomics Studies that use DNA Array Technology

Background

Bioassays are routinely used to evaluate the toxicity of test agents. Experimental designs for bioassays are largely encompassed by fixed effects linear models. In toxicogenomics studies where DNA arrays measure mRNA levels, the tissue samples are typically generated in a bioassay. These measurements introduce additional sources of variation, which must be properly managed to obtain valid tests of treatment effects.

Results

An analysis of covariance model is developed which combines a fixed-effects linear model for the bioassay with important variance components associated with DNA array measurements. These models can accommodate the dominant characteristics of measurements from DNA arrays, and they account for technical variation associated with normalization, spots, dyes, and batches as well as the biological variation associated with the bioassay. An example illustrates how the model is used to identify valid designs and to compare competing designs.

Conclusions

Many toxicogenomics studies are bioassays which measure gene expression using DNA arrays. These studies can be designed and analyzed using standard methods with a few modifications to account for characteristics of array measurements, such as multiple endpoints and normalization. As much as possible, technical variation associated with probes, dyes, and batches are managed by blocking treatments within these sources of variation. An example shows how some practical constraints can be accommodated by this modelling and how it allows one to objectively compare competing designs.

Molecular Changes Associated With the Endolymphatic Hydrops Model

HYPOTHESIS

Hearing loss and cochlear degeneration in the guinea pig model of endolymphatic hydrops (ELH) results, in part, from toxic levels of excitatory amino acids (EAAs) such as glutamate, which in turn leads to changes in the expression of genes linked to intracellular glutamate homeostasis and apoptosis, leading to neuronal cell death.

BACKGROUND

EAAs have been shown to play a role in normal auditory signal transmission in mammalian cochlea, but have also been implicated in neurotoxicity when levels are elevated. Changes in the expression of specific genes involved in the glutamatergic and apoptotic pathway would serve as evidence for excitotoxicity linked to elevated levels of glutamate.

METHODS

Guinea pigs underwent surgical obliteration of the endolymphatic duct, and then a timed harvest of the treated (right) and control (left) cochlea and subsequent quantification of gene expression via real-time quantitative polymerase chain reaction.

RESULTS

Quantitative polymerase chain reaction data show significant upregulation of glutamate aspartate transporter and neuronal nitric oxide synthase mRNA levels 3 weeks postsurgery and Caspase 3 mRNA levels 1 week postsurgery. No significant changes were detected in glutamine synthetase expression levels.

CONCLUSION

Upregulation of genes involved in glutamate homeostasis and the apoptotic pathway in animals treated with endolymphatic duct obstruction (usually associated with secondary ELH) support the hypothesis that EAAs may play a role in the pathophysiology of ELH-related cochlear injury. Inhibitors to these pathways can be useful for the study of new avenues to delay or prevent ELH-related hearing loss.

Biomarkers of adult and developmental neurotoxicity

Neurotoxicity may be defined as any adverse effect on the structure or function of the central and/or peripheral nervous system by a biological, chemical, or physical agent. A multidisciplinary approach is necessary to assess adult and developmental neurotoxicity due to the complex and diverse functions of the nervous system. The overall strategy for understanding developmental neurotoxicity is based on two assumptions: (1) significant differences in the adult versus the developing nervous system susceptibility to neurotoxicity exist and they are often developmental stage dependent; (2) a multidisciplinary approach using neurobiological, including gene expression assays, neurophysiological, neuropathological, and behavioral function is necessary for a precise assessment of neurotoxicity. Application of genomic approaches to developmental studies must use the same criteria for evaluating microarray studies as those in adults including consideration of reproducibility, statistical analysis, homogenous cell populations, and confirmation with non-array methods. A study using amphetamine to induce neurotoxicity supports the following: (1) gene expression data can help define neurotoxic mechanism(s), (2) gene expression changes can be useful biomarkers of effect, and (3) the site-selective nature of gene expression in the nervous system may mandate assessment of selective cell populations.

Methamphetamine modulation of gene expression in the brain: analysis using customized cDNA microarray system with the mouse homologues of KIAA genes

Amphetamine abuse may be associated with adaptive changes in gene expression. In the present study, we used a newly developed cDNA array system comprising mouse KIAA (mKIAA) cDNA clones to examine changes in gene expression after chronic methamphetamine (MAP) treatment. Mice were daily treated with saline or MAP (2 mg/kg, ip) for 2 weeks. Approximately 800 mKIAA clones were blotted onto a nylon membrane and hybridized with 33P-labeled DNA derived from mRNAs from mouse whole brain. MAP-induced changes were found in several clones by using whole brain mRNA. Since gene expression of Per2, one of the period protein-related proteins, was the most affected by MAP treatment, its expression was further analyzed in pooled hippocampi from 20 mice that had been treated with saline or MAP (2 mg/kg, ip) for 2 weeks. The gene expression and protein expression of Per2 in the hippocampus were increased by MAP treatment. In the hippocampus, Per2 gene expression was under the regulation of circadian rhythm and increases in Per2 expression were due to the phase shift induced by chronic MAP treatment. These findings suggest that unique expression changes of period protein-related proteins in the hippocampus occur in MAP abuse.

Classification of cDNA array genes that have a highly significant discriminative power due to their unique distribution in four brain regions

Novel statistical methods were used to distinguish functionally distinct brain regions using their cDNA array gene expression profiles, and it was found that one of four specific factors is often associated with the most regionally discriminative genes. The gene expression profiles for the substantia nigra (SN), striatum (STR), parietal cortex (PC), and posterolateral cortical amygdaloid nucleus (PLCo) brain regions were determined from each brain region. An F-test identified 339 genes of the 1185 array genes as having a P < or = 0.01 and applied a gene ranking and selection method based on Soft Independent Modeling of Class Analogy (SIMCA) to obtain 59 of the most discriminative genes. Their discriminative power was validated in three steps. The most convincing step showed their ability to correctly predict the brain regional classifications for 18 "test" gene expression sets obtained from the four regions. A two-way Hierarchical Cluster Analysis organized the 59 genes in six clusters according to their expression differences in the brain regions. Expression patterns in the SN and STR regions greatly differed from each other and the PC and PLCo. The closer similarity in the gene expression patterns of the PC and PLCo was probably due to their functional similarity. The important factors in determining differences in the regional gene expression profiles in six clusters were (1) regional myelin/oligodendrocyte levels, (2) resident neuron types, (3) neurotransmitter innervation profiles, and (4) Ca++-dependent signaling and second messenger systems.

Multiple-testing strategy for analyzing cDNA array data on gene expression

An objective of many functional genomics studies is to estimate treatment-induced changes in gene expression. cDNA arrays interrogate each tissue sample for the levels of mRNA for hundreds to tens of thousands of genes, and the use of this technology leads to a multitude of treatment contrasts. By-gene hypotheses tests evaluate the evidence supporting no effect, but selecting a significance level requires dealing with the multitude of comparisons. The p-values from these tests order the genes such that a p-value cutoff divides the genes into two sets. Ideally one set would contain the affected genes and the other would contain the unaffected genes. However, the set of genes selected as affected will have false positives, i.e., genes that are not affected by treatment. Likewise, the other set of genes, selected as unaffected, will contain false negatives, i.e., genes that are affected. A plot of the observed p-values (1 - p) versus their expectation under a uniform [0, 1] distribution allows one to estimate the number of true null hypotheses. With this estimate, the false positive rates and false negative rates associated with any p-value cutoff can be estimated. When computed for a range of cutoffs, these rates summarize the ability of the study to resolve effects. In our work, we are more interested in selecting most of the affected genes rather than protecting against a few false positives. An optimum cutoff, i.e., the best set given the data, depends upon the relative cost of falsely classifying a gene as affected versus the cost of falsely classifying a gene as unaffected. We select the cutoff by a decision-theoretic method analogous to methods developed for receiver operating characteristic curves. In addition, we estimate the false discovery rate and the false nondiscovery rate associated with any cutoff value. Two functional genomics studies that were designed to assess a treatment effect are used to illustrate how the methods allowed the investigators to determine a cutoff to suit their research goals.

Changes in Expression of the Mouse Homologues of KIAA Genes after Subchronic Methamphetamine Treatment

Amphetamine abuse may be associated with adaptive changes in gene expression in the brain. In the present study, a newly developed cDNA array system comprising mouse KIAA (mKIAA) cDNA clones was used to examine the gene expression affected by chronic methamphetamine treatment. Approximately 800 mKIAA clones were blotted onto a nylon membrane and hybridized with 33P-labeled cDNA derived from mRNAs isolated from the whole brains of mice that had been treated daily with saline or methamphetamine (2 mg/kg, i.p.) for 2 weeks. The arrays displayed robust hybridization for almost all transcripts. The results obtained from five experiments were averaged, each performed with triplicate samples. Several clones were chosen as positive candidates for methamphetamine-induced changes; however, only Per2 and mKIAA0099 genes showed a significantly increased expression (P < .05). Subsequently, with the focus on the period-related proteins, the expression of these proteins in various parts of the rat brain were assessed by immunoblot analysis. Chronic administration of methamphetamine (8 mg/kg, i.p., for 10 days) caused increased Per2 protein expression in the hippocampus. Interestingly, chronic methamphetamine treatment at a lower dose (4 mg/kg, i.p., for 10 days) induced an increase in SCN circadian oscillatory protein (SCOP) expression, also in the hippocampus. These data suggest that long-lasting alterations of the period-related gene expressions in the hippocampus might play an important role in methamphetamine addiction.

Selective Changes in Gene Expression in Cortical Regions Sensitive to Amphetamine During the Neurodegenerative Process

Gene expression profiles in several brain regions of adult male rats were evaluated following a d-amphetamine (AMPH) exposure paradigm previously established to produce AMPH neurotoxicity. Escalating doses of AMPH (5-30 mg/kg) were given over the course of 16 h per day in an 18 degrees C environment for 2 days. This paradigm produces neurotoxicity but eliminates or minimizes the hyperthermia and seizure activity that might influence gene expression in a manner unrelated to the neurotoxic effects of AMPH. The expression of 1185 genes was monitored in the striatum, parietal cortex, piriform cortex and posteriolateral cortical amygdaloid nucleus (PLCo) using cDNA array technology, and potentially significant changes were verified by RT-PCR. Gene expression was determined at time points after AMPH when neurodegeneration was beginning to appear (16 h) or maximal (64 h). Expression was also determined 14 days after AMPH to find long-term changes in gene expression that might be biomarkers of a neurotoxic event. In the parietal cortex there was a two-fold increase in neuropeptide Y precursor protein mRNA whereas nerve growth factor-induced receptor protein I-A and I-B mRNA decreased 50% at 16 h after the end of AMPH exposure. Although these changes in expression were not observed in the PLCo, insulin-like growth factor binding protein 1 mRNA was increased two-fold in the PLCo at 16 and 64 h after AMPH. Changes in gene expression in the cortical regions were all between 1.2- and 1.5-fold 14 days after AMPH but some of these changes, such as annexin V increases, may be relevant to neurotoxicity. Gene expression was not affected by more than 1.5-fold at the time points in the striatum, although 65% dopamine depletions occurred, but the plasma membrane-associated dopamine transporter and dopamine D2 receptor were decreased about 40% in the substantia nigra at 64 h and 14 days post-AMPH. Thus, the 2-day AMPH treatment produced a few changes in gene expression in the two-fold range at time points 16 h or more after exposure but the majority of expression changes were less than 1.5-fold of control. Nonetheless, some of these lesser fold-changes appeared to be relevant to the neurotoxic process.