Tissue, species, and environmental differences in absolute quantities of murine mRNAs coding for alpha, mu, omega, pi, and theta glutathione S-transferases

Multi-Omics Analysis of Key microRNA-mRNA Metabolic Regulatory Networks in Skeletal Muscle of Obese Rabbits

microRNAs (miRNAs), small non-coding RNA with a length of about 22 nucleotides, are involved in the energy metabolism of skeletal muscle cells. However, their molecular mechanism of metabolism in rabbit skeletal muscle is still unclear. In this study, 16 rabbits, 8 in the control group (CON-G) and 8 in the experimental group (HFD-G), were chosen to construct an obese model induced by a high-fat diet fed from 35 to 70 days of age. Subsequently, 54 differentially expressed miRNAs, 248 differentially expressed mRNAs, and 108 differentially expressed proteins related to the metabolism of skeletal muscle were detected and analyzed with three sequencing techniques (small RNA sequencing, transcriptome sequencing, and tandem mass tab (TMT) protein technology). It was found that 12 miRNAs and 12 core genes (e.g., CRYL1, VDAC3 and APIP) were significantly different in skeletal muscle from rabbits in the two groups. The network analysis showed that seven miRNA-mRNA pairs were involved in metabolism. Importantly, two miRNAs (miR-92a-3p and miR-30a/c/d-5p) regulated three transcription factors (MYBL2, STAT1 and IKZF1) that may be essential for lipid metabolism. These results enhance our understanding of molecular mechanisms associated with rabbit skeletal muscle metabolism and provide a basis for future studies in the metabolic diseases of human obesity.

Omics technologies and their applications to evaluate metal toxicity in mice M. spretus as a bioindicator

Metals are important components of living organisms since many biological functions critically depend on their interaction with some metal in the cell. However, human activities have increased toxic metal levels in the terrestrial and aquatic ecosystems affecting living organisms. The impact of metals on cellular metabolism and global homeostasis has been traditionally assessed in free-living organisms by using conventional biomarkers; however, to obtain a global vision of metal toxicity mechanisms and the responses that metals elicit in the organisms, new analytical methodologies are needed. We review the use of omics approaches to assess the response of living organisms under metal stress illustrating the possibilities of different methodologies on the basis of our previous results. Most of this research has been based on free-living mice Mus spretus, a conventional bioindicator used to monitor metal pollution in Doñana National Park (DNP) (SW Spain), which is an important European biological reserve for migrating birds affected by agricultural, mining and industrial activities. The benefits of using omic techniques such as heterologous microarrays, proteomics methodologies (2-DE, iTRAQ®), metallomics, ionomics or metabolomics has been remarked; however, the complexity of these areas requires the integration of omics to achieve a comprehensive assessment of their environmental status. This article is part of a Special Issue entitled: Environmental and structural proteomics.

BIOLOGICAL SIGNIFICANCE

This work presents new contributions in the study of environmental metal pollution in terrestrial ecosystems using Mus spretus mice as bioindicator in Doñana National Park (SW Spain) and surroundings. In addition, it has been demonstrated that the integration of omics multi-analytical approaches provides a very suitable approach for the study of the biological response and metal interactions in exposed and free-living mice (Mus musculus and Mus spretus, respectively) under metal pollution.

Adaptive and specialised transcriptional responses to xenobiotic stress in Caenorhabditis elegans are regulated by nuclear hormone receptors

Characterisation of the pathways by which xenobiotics are metabolised and excreted in both target and non-target organisms is crucial for the rational design of effective and specific novel bioactive molecules. Consequently, we have investigated the induced responses of the model nematode Caenorhabditis elegans to a variety of xenobiotics which represent a range of putative modes of action. The majority of genes that were specifically induced in preliminary microarray analyses encoded enzymes from Phase I and II metabolism, including cytochrome P450s, short chain dehydrogenases, UDP-glucuronosyl transferases and glutathione transferases. Changes in gene expression were confirmed by quantitative PCR and GFP induction in reporter strains driven by promoters for transcription of twelve induced enzymes was investigated. The particular complement of metabolic genes induced was found to be highly contingent on the xenobiotic applied. The known regulators of responses to applied chemicals ahr-1, hif-1, mdt-15 and nhr-8 were not required for any of these inducible responses and skn-1 regulated GFP expression from only two of the promoters. Reporter strains were used in conjunction with systematic RNAi screens to identify transcription factors which drive expression of these genes under xenobiotic exposure. These transcription factors appeared to regulate specific xenobiotic responses and have no reported phenotypes under standard conditions. Focussing on nhr-176 we demonstrate the role of this transcription factor in mediating the resistance to thiabendazole.

Biochemical and molecular mechanisms of N-acetyl cysteine and silymarin-mediated protection against maneb- and paraquat-induced hepatotoxicity in rats

Oxidative stress is one of the major players in the pathogenesis of maneb (MB) and paraquat (PQ)-induced disorders. N-acetyl cysteine (NAC), a glutathione (GSH) precursor and silymarin (SIL), a naturally occurring antioxidant, encounter oxidative stress-mediated cellular damage. The present study was aimed to investigate the effects of NAC and SIL against MB and/or PQ-induced hepatotoxicity in rats. The levels of hepatotoxicity markers - alanine aminotransaminase (ALT), aspartate aminotransaminase (AST) and total bilirubin, histological changes, oxidative stress indices, phase I and phase II xenobiotic metabolizing enzymes - cytochrome P450 (CYP) and glutathione S-transferase (GST) and pro-inflammatory molecules - inducible nitric oxide synthase (iNOS), tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) were measured in animals treated with MB and/or PQ in the presence or absence of NAC and SIL. MB and/or PQ augmented ALT, AST, total bilirubin, lipid peroxidation and nitrite contents and catalytic activities of superoxide dismutase and glutathione peroxidase however, the GSH content was attenuated. NAC and SIL restored the above-mentioned alterations towards basal levels but the restorations were more pronounced in SIL treated groups. Similarly, MB and/or PQ-mediated histopathological symptoms and changes in the catalytic activities/expressions of CYP1A2, CYP2E1, iNOS, TNF-α, and IL-1β were alleviated by NAC and SIL. Conversely, MB and/or PQ-induced GSTA4-4 expression/activity was further increased by NAC/SIL and glutathione reductase activity was also increased. The results obtained thus suggest that NAC and SIL protect MB and/or PQ-induced hepatotoxicity by reducing oxidative stress, inflammation and by modulating xenobitic metabolizing machinery and SIL seems to be more effective.

Oxidative stress contributes to liver damage in a murine model of alpha-1-antitrypsin deficiency

Alpha-1-antitrypsin deficiency is a genetic disorder resulting in the expression of misfolded mutant protein that can polymerize and accumulate in hepatocytes, leading to liver disease in some individuals. Transgenic PiZ mice are a well-characterized model, which express human alpha-1-antitrypsin mutant Z protein (ATZ protein) and faithfully recapitulate the human liver disease. Liver tissue expressing alpha-1-antitrypsin mutant Z protein exhibits inflammation, injury and replacement of damaged cells. Fibrosis and hepatocellular carcinoma (HCC) develop in aging PiZ mice. In this study, microarray analysis was performed comparing young PiZ (ZY) mice to wild-type (WY), and indicated that there were alterations in gene expression levels that could influence a number of pathways leading to liver disease. Redox-regulating genes were up-regulated in ZY tissue, including carbonyl reductase 3 (CBR3), glutathione S-transferase alpha 1 + 2 (GSTA(1 + 2)) and glutathione S-transferase mu 3 (GSTM3). We hypothesized that oxidative stress could develop in Z mouse liver, contributing to tissue damage and disease progression with age. The results of biochemical analysis of PiZ mouse liver revealed that higher levels of reactive oxygen species (ROS) and a more oxidized, cellular redox state occurred in liver tissue from ZY mice than WY. ZY mice showed little evidence of oxidative cellular damage as assessed by protein carbonylation levels, malondialdehyde levels and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8oxodG) staining. Aging liver tissue from PiZ older mice (ZO) had elevated ROS, generally lower levels of antioxidant enzymes than younger mice and evidence of cellular damage. These data indicate that oxidative stress is a contributing factor in the development of liver disease in this model of alpha-1-antitrypsin deficiency.

Omic approaches in environmental issues

Biomonitoring requires the application of batteries of different biomarkers, as environmental contaminants induce multiple responses in organisms that are not necessarily correlated. Omic technologies were proposed as an alternative to conventional biomarkers since these techniques quantitatively monitor many biological molecules in a high-throughput manner and thus provide a general appraisal of biological responses altered by exposure to contaminants. As the studies using omic technologies increase, it is becoming clear that any single omic approach may not be sufficient to characterize the complexity of ecosystems. This work aims to provide a preliminary working scheme for the use of combined transcriptomic and proteomic methodologies in environmental biomonitoring. There are difficulties in working with nonmodel organisms as bioindicators when combining several omic approaches. As a whole, our results with heterologous microarrays in M. spretus and suppressive subtractive hybridization (SSH) in P. clarkii indicated that animals sustaining a heavy pollution burden exhibited an enhanced immune response and/or cell apoptosis. The proteomic studies, although preliminary, provide a holistic insight regarding the manner by which pollution shifts protein intensity in two-dimensional gel electrophoresis (2-DE), completing the transcriptomic approach. In our study, the sediment element concentration was in agreement with the intensity of protein expression changes in C. maenas crabs. In conclusion, omics are useful technologies in addressing environmental issues and the determination of contamination threats.

Increased oxidative stress and antioxidant expression in mouse keratinocytes following exposure to paraquat

Paraquat (1,1'-dimethyl-4,4'-bipyridinium) is a widely used herbicide known to induce skin toxicity. This is thought to be due to oxidative stress resulting from the generation of cytotoxic reactive oxygen intermediates (ROI) during paraquat redox cycling. The skin contains a diverse array of antioxidant enzymes which protect against oxidative stress including superoxide dismutase (SOD), catalase, glutathione peroxidase-1 (GPx-1), heme oxygenase-1 (HO-1), metallothionein-2 (MT-2), and glutathione-S-transferases (GST). In the present studies we compared paraquat redox cycling in primary cultures of undifferentiated and differentiated mouse keratinocytes and determined if this was associated with oxidative stress and altered expression of antioxidant enzymes. We found that paraquat readily undergoes redox cycling in both undifferentiated and differentiated keratinocytes, generating superoxide anion and hydrogen peroxide as well as increased protein oxidation which was greater in differentiated cells. Paraquat treatment also resulted in increased expression of HO-1, Cu,Zn-SOD, catalase, GSTP1, GSTA3 and GSTA4. However, no major differences in expression of these enzymes were evident between undifferentiated and differentiated cells. In contrast, expression of GSTA1-2 was significantly greater in differentiated relative to undifferentiated cells after paraquat treatment. No changes in expression of MT-2, Mn-SOD, GPx-1, GSTM1 or the microsomal GST's mGST1, mGST2 and mGST3, were observed in response to paraquat. These data demonstrate that paraquat induces oxidative stress in keratinocytes leading to increased expression of antioxidant genes. These intracellular proteins may be important in protecting the skin from paraquat-mediated cytotoxicity.

Integrated application of transcriptomics, proteomics, and metallomics in environmental studies

Here we report a preliminary working scheme for the integrative application of transcriptomic, proteomic, and metallomic methodologies in environmental monitoring, by using as sentinel the wildlife species Mus spretus and as reference the gene/protein sequence databases from the key model species Mus musculus. We have demonstrated that the absolute transcript expression signatures quantified by reverse transcription (RT) and real-time polymerase chain reaction (PCR) of selected key genes (e.g., those coding for biotransformation enzymes) in M. spretus is a useful and reliable novel biomonitoring end-point. The suitability of commercial M. musculus oligonucleotide arrays for genome-wide transcriptional profiling in M. spretus has been also shown. Transcriptomic studies indicate considerable gene sequence similarities between both mouse species. Based on these similarities, we have demonstrated the applicability in free-living M. spretus of high-throughput proteomic methods, based on matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry (MALDI-TOFMS) analysis of tryptic 2D electrophoresis (2-DE) spot digest and peptide matching with M. musculus database. A metallomic approach based on size exclusion chromatography inductively coupled plasma-mass spectrometry (SEC-ICP-MS) was applied to trace metal-biomolecule profiles. A preliminary integration of these three -omics has been addressed to M. musculus/M. spretus couple, two rodent species that separated 3 million years ago. The integrated application of transcriptomic and proteomic data and the bidirectional use of metallomics and proteomics for selective isolation of metal-biomolecules are covered in the working scheme MEPROTRANS-triple-OMIC reported in this study.

Tissue and species distribution of the glutathione pathway transcriptome

The goal of this study was to compare and contrast the basal gene expression levels of the various enzymes involved in glutathione metabolism among tissues and genders of the rat, mouse and canine. The approach taken was to use Affymetrix GeneChip microarray data for rat, mouse and canine tissues, comparing intensity levels for individual probes between tissues and genders. As was hypothesized, the relative expression in liver, lung, heart, kidney and testis varied from gene to gene, with differences of expression between tissues sometimes greater than a 1000-fold. The pattern of differential expression was usually similar between male and female animals, but varied greatly between the three species. Gstp1 appears to be expressed at high levels in male mouse liver, reasonable levels in canine liver, but very low levels in male rat liver. In all species examined, Gstp1 expression was below detectable levels in testis. Gsta3/Yc2 expression appeared high in rodent liver and female canine liver, but not male canine liver. Finally, Mgst1 and Gpx3 expression appeared to be lower in canine heart and testis than seen in rodents. Given the critical role of the glutathione pathway in the detoxification of many drugs and xenobiotics, the observed differences in basal tissue distribution among mouse, rat and canine has far-reaching implications in comparing responses of these species in safety testing.

Absolute transcript expression signatures of Cyp and Gst genes in Mus spretus to detect environmental contamination

We evaluated whether quantitation of mRNA molecules of key genes is a reliable biomonitoring end-point. We examined the Mus spretus expression levels of 19 transcripts encoding different cytochrome-P450s and glutathione transferases. Mice dwelling at the Doñana Biological Reserve were compared to those from an industrial settlement (PS). Metal biomonitoring indicated that PS animals sustained a heavier pollutant burden than those from the reference site. Transcript quantitations showed the following: (i) gender-related differences in the expression of most Cyp and Gst genes; (ii) one PS female displaying much smaller/larger transcript amounts than the remaining females; (iii) the concomitant up-regulation of Cyp1a2, Cyp2a5, Cyp2e1, Cyp4a10, Gsta1, Gsta2, Gstm1, and Gstm2 mRNAs in liver of PS males; and (iv) outstanding qualitative and quantitative differences between the hepatic expression signature of PS males and that promoted by paraquat. We conclude that (i) absolute amounts of transcripts encoding biotransformation enzymes are more potent biomarkers in males than in females, and in liver than in kidney; (ii) individual quantitations prevent biased interpretations by specimens with abnormal expression levels; and (iii)transcript expression signature of PS males is consistent with exposure to a complex profile of organic pollutants, other than oxidative stressors.