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Anunciado-Koza RVP, Yin H, Bilodeau CL, Cooke D, Ables GP, Ryzhov S, Koza RA. Interindividual differences of dietary fat-inducible Mest in white adipose tissue of C57BL/6J mice are not heritable. Obesity (Silver Spring) 2024; 32:1144-1155. [PMID: 38616328 PMCID: PMC11132930 DOI: 10.1002/oby.24020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/20/2024] [Indexed: 04/16/2024]
Abstract
OBJECTIVE Differences in white adipose tissue (WAT) expression of mesoderm-specific transcript (Mest) in C57BL6/J mice fed a high-fat diet (HFD) are concomitant with and predictive for the development of obesity. However, the basis for differences in WAT Mest among mice is unknown. This study investigated whether HFD-inducible WAT Mest, as well as susceptibility to obesity, is transmissible from parents to offspring. METHODS WAT biopsies of mice fed an HFD for 2 weeks identified parents with low and high WAT Mest for breeding. Obesity phenotypes, WAT Mest, hepatic gene expression, and serum metabolites were determined in offspring fed an HFD for 2 weeks. RESULTS Offspring showed no heritability of obesity or WAT Mest phenotypes from parents but did show hepatic and serum metabolite changes consistent with their WAT Mest. Importantly, retired male breeders showed WAT Mest expression congruent with initial WAT biopsies even though HFD exposure occurred early in life. CONCLUSIONS Disparity of HFD-induced Mest in mice is not heritable but, rather, is reestablished during each generation and remains fixed from an early age to adulthood. Short-term HFD feeding reveals variation of WAT Mest expression within isogenic mice that is positively associated with the development of obesity.
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Affiliation(s)
| | - Haifeng Yin
- MaineHealth Institute for Research, Scarborough, Maine, USA
| | | | - Diana Cooke
- Orentreich Foundation for the Advancement of Science, Inc., Cold Spring, New York, USA
| | - Gene P. Ables
- Orentreich Foundation for the Advancement of Science, Inc., Cold Spring, New York, USA
| | - Sergey Ryzhov
- MaineHealth Institute for Research, Scarborough, Maine, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
- Department of Medicine, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Robert A. Koza
- MaineHealth Institute for Research, Scarborough, Maine, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA
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2
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Hwang S, Koo I, Patterson AD, Lambert JD. Comparative urine metabolomics of mice treated with non-toxic and toxic oral doses of (-)-epigallocatechin-3-gallate. Food Funct 2023; 14:9434-9445. [PMID: 37796030 DOI: 10.1039/d3fo02710d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
The green tea polyphenol, (-)-epigallocatechin-3-gallate (EGCG), has been studied for its potential positive health effects, but human and animal model studies have reported potential toxicity at high oral bolus doses. This study used liquid chromatography-mass spectrometry-based metabolomics to compare the urinary EGCG metabolite profile after administration of a single non-toxic (100 mg kg-1) or toxic (750 mg kg-1) oral bolus dose to male C57BL6/J mice to better understand how EGCG metabolism varies with dose. EGCG metabolites, including methyl, glucuronide, sulfate, and glucoside conjugates, were tentatively identified based on their mass to charge (m/z) ratio and fragment ion patterns. Partial least squares discriminant analysis (PLS-DA) results showed clear separation of the urine metabolite profiles between treatment groups. The most differentiating metabolites in the negative and positive ion modes were provisionally identified as di-glucuronidated EGCG quinone and di-glucuronidated EGCG, respectively. The presence of EGCG oxidation products at toxic dose is consistent with studies showing that EGCG toxicity is associated with oxidative stress. Relative amounts of methylated metabolites increased with dose to a lesser extent than glucuronide and sulfate metabolites, indicating that methylation is more prominent at low doses, whereas glucuronidation and sulfation may be more important at higher doses. One limitation of the current work is that the lack of commercially-available EGCG metabolite standards prevented absolute metabolite quantification and identification. Despite this limitation, these findings provide a basis for better understanding the dose-dependent changes in EGCG metabolism and advance studies on how these differences may contribute to the toxicity of high doses of EGCG.
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Affiliation(s)
- Soomee Hwang
- Department of Food Science, The Pennsylvania State University, 332 Food Science Building, University Park, PA 16802, USA.
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joshua D Lambert
- Department of Food Science, The Pennsylvania State University, 332 Food Science Building, University Park, PA 16802, USA.
- Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA 16802, USA
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3
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Costello HM, Johnston JG, Juffre A, Crislip GR, Gumz ML. Circadian clocks of the kidney: function, mechanism, and regulation. Physiol Rev 2022; 102:1669-1701. [PMID: 35575250 PMCID: PMC9273266 DOI: 10.1152/physrev.00045.2021] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/03/2022] [Accepted: 05/07/2022] [Indexed: 11/22/2022] Open
Abstract
An intrinsic cellular circadian clock is located in nearly every cell of the body. The peripheral circadian clocks within the cells of the kidney contribute to the regulation of a variety of renal processes. In this review, we summarize what is currently known regarding the function, mechanism, and regulation of kidney clocks. Additionally, the effect of extrarenal physiological processes, such as endocrine and neuronal signals, on kidney function is also reviewed. Circadian rhythms in renal function are an integral part of kidney physiology, underscoring the importance of considering time of day as a key biological variable. The field of circadian renal physiology is of tremendous relevance, but with limited physiological and mechanistic information on the kidney clocks this is an area in need of extensive investigation.
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Affiliation(s)
- Hannah M Costello
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
| | - Jermaine G Johnston
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
- North Florida/South Georgia Malcom Randall Department of Veterans Affairs Medical Center, Gainesville, Florida
| | - Alexandria Juffre
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida
| | - G Ryan Crislip
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
| | - Michelle L Gumz
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
- North Florida/South Georgia Malcom Randall Department of Veterans Affairs Medical Center, Gainesville, Florida
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida
- Center for Integrative Cardiovascular and Metabolic Diseases, University of Florida, Gainesville, Florida
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4
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MicroRNAs in Learning and Memory and Their Impact on Alzheimer’s Disease. Biomedicines 2022; 10:biomedicines10081856. [PMID: 36009403 PMCID: PMC9405363 DOI: 10.3390/biomedicines10081856] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022] Open
Abstract
Learning and memory formation rely on the precise spatiotemporal regulation of gene expression, such as microRNA (miRNA)-associated silencing, to fine-tune gene expression for the induction and maintenance of synaptic plasticity. Much progress has been made in presenting direct evidence of miRNA regulation in learning and memory. Here, we summarize studies that have manipulated miRNA expression using various approaches in rodents, with changes in cognitive performance. Some of these are involved in well-known mechanisms, such as the CREB-dependent signaling pathway, and some of their roles are in fear- and stress-related disorders, particularly cognitive impairment. We also summarize extensive studies on miRNAs correlated with pathogenic tau and amyloid-β that drive the processes of Alzheimer’s disease (AD). Although altered miRNA profiles in human patients with AD and in mouse models have been well studied, little is known about their clinical applications and therapeutics. Studies on miRNAs as biomarkers still show inconsistencies, and more challenges need to be confronted in standardizing blood-based biomarkers for use in AD.
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5
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Wang IF, Wang Y, Yang YH, Huang GJ, Tsai KJ, Shen CKJ. Activation of a hippocampal CREB-pCREB-miRNA-MEF2 axis modulates individual variation of spatial learning and memory capability. Cell Rep 2021; 36:109477. [PMID: 34348143 DOI: 10.1016/j.celrep.2021.109477] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022] Open
Abstract
Phenotypic variation is a fundamental prerequisite for cell and organism evolution by natural selection. Whereas the role of stochastic gene expression in phenotypic diversity of genetically identical cells is well studied, not much is known regarding the relationship between stochastic gene expression and individual behavioral variation in animals. We demonstrate that a specific miRNA (miR-466f-3p) is upregulated in the hippocampus of a portion of individual inbred mice upon a Morris water maze task. Significantly, miR-466f-3p positively regulates the neuron morphology, function and spatial learning, and memory capability of mice. Mechanistically, miR-466f-3p represses translation of MEF2A, a negative regulator of learning/memory. Finally, we show that varied upregulation of hippocampal miR-466f-3p results from randomized phosphorylation of hippocampal cyclic AMP (cAMP)-response element binding (CREB) in individuals. This finding of modulation of spatial learning and memory via a randomized hippocampal signaling axis upon neuronal stimulation represents a demonstration of how variation in tissue gene expression lead to varied animal behavior.
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Affiliation(s)
- I-Fang Wang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yihan Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hua Yang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan; Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Guo-Jen Huang
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou 33302, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan; Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan.
| | - Che-Kun James Shen
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.
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Bashkeel N, Perkins TJ, Kærn M, Lee JM. Human gene expression variability and its dependence on methylation and aging. BMC Genomics 2019; 20:941. [PMID: 31810449 PMCID: PMC6898959 DOI: 10.1186/s12864-019-6308-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 11/18/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Phenotypic variability of human populations is partly the result of gene polymorphism and differential gene expression. As such, understanding the molecular basis for diversity requires identifying genes with both high and low population expression variance and identifying the mechanisms underlying their expression control. Key issues remain unanswered with respect to expression variability in human populations. The role of gene methylation as well as the contribution that age, sex and tissue-specific factors have on expression variability are not well understood. RESULTS Here we used a novel method that accounts for sampling error to classify human genes based on their expression variability in normal human breast and brain tissues. We find that high expression variability is almost exclusively unimodal, indicating that variance is not the result of segregation into distinct expression states. Genes with high expression variability differ markedly between tissues and we find that genes with high population expression variability are likely to have age-, but not sex-dependent expression. Lastly, we find that methylation likely has a key role in controlling expression variability insofar as genes with low expression variability are likely to be non-methylated. CONCLUSIONS We conclude that gene expression variability in the human population is likely to be important in tissue development and identity, methylation, and in natural biological aging. The expression variability of a gene is an important functional characteristic of the gene itself and the classification of a gene as one with Hyper-Variability or Hypo-Variability in a human population or in a specific tissue should be useful in the identification of important genes that functionally regulate development or disease.
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Affiliation(s)
- Nasser Bashkeel
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H 8M5 Canada
| | - Theodore J. Perkins
- Ottawa Hospital Research Institute, 501 Smyth Rd, Ottawa, Ontario K1H 8L6 Canada
| | - Mads Kærn
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H 8M5 Canada
| | - Jonathan M. Lee
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H 8M5 Canada
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7
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Abstract
The identification of genes that are differentially expressed provides a molecular foothold onto biological questions of interest. Whether some genes are more likely to be differentially expressed than others, and to what degree, has never been assessed on a global scale. Here, we reanalyze more than 600 studies and find that knowledge of a gene’s prior probability of differential expression (DE) allows for accurate prediction of DE hit lists, regardless of the biological question. This result suggests redundancy in transcriptomics experiments that both informs gene set interpretation and highlights room for growth within the field. Differential expression (DE) is commonly used to explore molecular mechanisms of biological conditions. While many studies report significant results between their groups of interest, the degree to which results are specific to the question at hand is not generally assessed, potentially leading to inaccurate interpretation. This could be particularly problematic for metaanalysis where replicability across datasets is taken as strong evidence for the existence of a specific, biologically relevant signal, but which instead may arise from recurrence of generic processes. To address this, we developed an approach to predict DE based on an analysis of over 600 studies. A predictor based on empirical prior probability of DE performs very well at this task (mean area under the receiver operating characteristic curve, ∼0.8), indicating that a large fraction of DE hit lists are nonspecific. In contrast, predictors based on attributes such as gene function, mutation rates, or network features perform poorly. Genes associated with sex, the extracellular matrix, the immune system, and stress responses are prominent within the “DE prior.” In a series of control studies, we show that these patterns reflect shared biology rather than technical artifacts or ascertainment biases. Finally, we demonstrate the application of the DE prior to data interpretation in three use cases: (i) breast cancer subtyping, (ii) single-cell genomics of pancreatic islet cells, and (iii) metaanalysis of lung adenocarcinoma and renal transplant rejection transcriptomics. In all cases, we find hallmarks of generic DE, highlighting the need for nuanced interpretation of gene phenotypic associations.
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8
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Nguyen L, Sandoval J, De Dios R, Yihdego E, Zarate M, Castro O, McKenna S, Wright CJ. The hepatic innate immune response is lobe-specific in a murine model endotoxemia. Innate Immun 2019; 25:144-154. [PMID: 30774009 PMCID: PMC6784545 DOI: 10.1177/1753425918823900] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The liver plays a central role in the innate immune response to endotoxemia.
While previous studies have demonstrated lobe-specific transcriptional responses
to various insults, whether this is true in response to endotoxemia is unknown.
We sought to assess whether there were significant intra- and inter-lobe
differences in the murine hepatic innate immune transcriptional response to
endotoxemia. Adult male ICR mice were exposed to i.p. LPS (5 mg/kg, 30 min,
60 min, 5 h) and primary (Tnf, Cxcl1, Nfkbia, Tnfiap3) and
secondary (Il6, Nos2) innate immune response gene expression
was assessed in the left medial, right medial, left lateral, and right lateral
lobes, and the papillary and caudate processes. The expression of all innate
immune response genes increased following i.p. LPS challenge. When tested at the
early time points (30 and 60 min), the left medial lobe and caudate process
consistently demonstrated the highest induction of gene expression. Most
inter-lobe differences were attenuated at later time points (5 h). To improve
reproducibility of the study of endotoxemia induced by i.p. LPS challenge,
inclusion of appropriate methodological details regarding collection of hepatic
tissue should be included when reporting scientific results in published
manuscripts.
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Affiliation(s)
- Leanna Nguyen
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Jeryl Sandoval
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Robyn De Dios
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Elesa Yihdego
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Miguel Zarate
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Odalis Castro
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Sarah McKenna
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Clyde J Wright
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
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Berghout J, Li Q, Pouladi N, Li J, Lussier YA. Single subject transcriptome analysis to identify functionally signed gene set or pathway activity. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018; 23:400-411. [PMID: 29218900 PMCID: PMC5730358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Analysis of single-subject transcriptome response data is an unmet need of precision medicine, made challenging by the high dimension, dynamic nature and difficulty in extracting meaningful signals from biological or stochastic noise. We have proposed a method for single subject analysis that uses a mixture model for transcript fold-change clustering from isogenically paired samples, followed by integration of these distributions with Gene Ontology Biological Processes (GO-BP) to reduce dimension and identify functional attributes. We then extended these methods to develop functional signing metrics for gene set process regulation by incorporating biological repressor relationships encoded in GO-BP as negatively_regulates edges. Results revealed reproducible and biologically meaningful signals from analysis of a single subject's response, opening the door to future transcriptomic studies where subject and resource availability are currently limiting. We used inbred mouse strains fed different diets to provide isogenic biological replicates, permitting rigorous validation of our method. We compared significant genotype-specific GO-BP term results for overlap and rank order across three replicate pairs per genotype, and cross-methods to reference standards (limma+FET, SAM+FET, and GSEA). All single-subject analytics findings were robust and highly reproducible (median area under the ROC curve=0.96, n=24 genotypes × 3 replicates), providing confidence and validation of this approach for analyses in single subjects. R code is available online at http://www.lussiergroup.org/publications/PathwayActivity.
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Affiliation(s)
- Joanne Berghout
- Center for Biomedical Informatics and Biostatistics (CB2) & The Center for Applied Genetics and Genomic Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85721, USA,
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Die JV, Roman B, Flores F, Rowland LJ. Design and Sampling Plan Optimization for RT-qPCR Experiments in Plants: A Case Study in Blueberry. FRONTIERS IN PLANT SCIENCE 2016; 7:271. [PMID: 27014296 PMCID: PMC4779984 DOI: 10.3389/fpls.2016.00271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
The qPCR assay has become a routine technology in plant biotechnology and agricultural research. It is unlikely to be technically improved, but there are still challenges which center around minimizing the variability in results and transparency when reporting technical data in support of the conclusions of a study. There are a number of aspects of the pre- and post-assay workflow that contribute to variability of results. Here, through the study of the introduction of error in qPCR measurements at different stages of the workflow, we describe the most important causes of technical variability in a case study using blueberry. In this study, we found that the stage for which increasing the number of replicates would be the most beneficial depends on the tissue used. For example, we would recommend the use of more RT replicates when working with leaf tissue, while the use of more sampling (RNA extraction) replicates would be recommended when working with stems or fruits to obtain the most optimal results. The use of more qPCR replicates provides the least benefit as it is the most reproducible step. By knowing the distribution of error over an entire experiment and the costs at each step, we have developed a script to identify the optimal sampling plan within the limits of a given budget. These findings should help plant scientists improve the design of qPCR experiments and refine their laboratory practices in order to conduct qPCR assays in a more reliable-manner to produce more consistent and reproducible data.
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Affiliation(s)
- Jose V. Die
- U.S. Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Belen Roman
- Area Mejora y Biotecnologia, IFAPA Centro Alameda del ObispoCordoba, Spain
| | - Fernando Flores
- Departamento Ciencias Agroforestales, Universidad de HuelvaHuelva, Spain
| | - Lisa J. Rowland
- U.S. Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
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Santos EADS, Marques TEBS, Matos HDC, Leite JP, Garcia-Cairasco N, Paçó-Larson ML, Gitaí DLG. Diurnal Variation Has Effect on Differential Gene Expression Analysis in the Hippocampus of the Pilocarpine-Induced Model of Mesial Temporal Lobe Epilepsy. PLoS One 2015; 10:e0141121. [PMID: 26473354 PMCID: PMC4608695 DOI: 10.1371/journal.pone.0141121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022] Open
Abstract
The molecular mechanisms underlying epileptogenesis have been widely investigated by differential gene expression approach, especially RT-qPCR methodology. However, controversial findings highlight the occurrence of unpredictable sources of variance in the experimental designs. Here, we investigated if diurnal rhythms of transcript's levels may impact on differential gene expression analysis in hippocampus of rats with experimental epilepsy. For this, we have selected six core clock genes (Per1, Per3, Bmal1, Clock, Cry1 and Cry2), whose rhythmic expression pattern in hippocampus had been previously reported. Initially, we identified Tubb2a/Rplp1 and Tubb2a/Ppia as suitable normalizers for circadian studies in hippocampus of rats maintained to 12:12 hour light:dark (LD) cycle. Next, we confirmed the temporal profiling of Per1, Per3, Bmal1, Cry1 and Cry2 mRNA levels in the hippocampus of naive rats by both Acrophase and CircWave statistical tests for circadian analysis. Finally, we showed that temporal differences of sampling can change experimental results for Per1, Per3, Bmal1, Cry1 and Cry2, but not for Clock, which was consistently decreased in rats with epilepsy in all comparison to the naive group. In conclusion, our study demonstrates it is mandatory to consider diurnal oscillations, in order to avoid erroneous conclusions in gene expression analysis in hippocampus of rats with epilepsy. Investigators, therefore, should be aware that genes with circadian expression could be out of phase in different animals of experimental and control groups. Moreover, our results indicate that a sub-expression of Clock may be involved in epileptogenicity, although the functional significance of this remains to be investigated.
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Affiliation(s)
- Evelin Antonieli da Silva Santos
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | | | - Heloísa de Carvalho Matos
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | - João Pereira Leite
- Department of Neurology, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Norberto Garcia-Cairasco
- Department of Physiology, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Maria Luisa Paçó-Larson
- Department of Cellular and Molecular Biology, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Leite Góes Gitaí
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
- * E-mail:
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12
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Kappen C, Salbaum JM. Gene expression in teratogenic exposures: a new approach to understanding individual risk. Reprod Toxicol 2014; 45:94-104. [PMID: 24491834 DOI: 10.1016/j.reprotox.2013.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/21/2013] [Accepted: 12/18/2013] [Indexed: 12/29/2022]
Abstract
The phenomenon of partial or incomplete penetrance is common to many paradigms of exposure to teratogens, where only some of the exposed individuals exhibit developmental defects. We here argue that the most widely used experimental approaches in reproductive toxicology do not take partial penetrance into account, and are thus likely to miss differences between affected and unaffected individuals that contribute to susceptibility for teratogenesis. We propose that focus on the variation between exposed individuals could help to discover factors that may play a causative role for abnormal developmental processes that occur with incomplete penetrance.
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Affiliation(s)
- Claudia Kappen
- Department of Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, 6400 Perkins Road, Baton Rouge, LA 70808, United States.
| | - J Michael Salbaum
- Laboratory of Regulation of Gene Expression, Pennington Biomedical Research Center, Louisiana State University System, 6400 Perkins Road, Baton Rouge, LA 70808, United States
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13
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Gabás-Rivera C, Martínez-Beamonte R, Ríos JL, Navarro MA, Surra JC, Arnal C, Rodríguez-Yoldi MJ, Osada J. Dietary oleanolic acid mediates circadian clock gene expression in liver independently of diet and animal model but requires apolipoprotein A1. J Nutr Biochem 2013; 24:2100-9. [PMID: 24231102 DOI: 10.1016/j.jnutbio.2013.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 07/22/2013] [Accepted: 07/31/2013] [Indexed: 12/13/2022]
Abstract
Oleanolic acid is a triterpene widely distributed throughout the plant kingdom and present in virgin olive oil at a concentration of 57 mg/kg. To test the hypotheses that its long-term administration could modify hepatic gene expression in several animal models and that this could be influenced by the presence of APOA1-containing high-density lipoproteins (HDLs), diets including 0.01% oleanolic acid were provided to Apoe- and Apoa1-deficient mice and F344 rats. Hepatic transcriptome was analyzed in Apoe-deficient mice fed long-term semipurified Western diets differing in the oleanolic acid content. Gene expression changes, confirmed by reverse transcriptase quantitative polymerase chain reaction, were sought for their implication in hepatic steatosis. To establish the effect of oleanolic acid independently of diet and animal model, male rats were fed chow diet with or without oleanolic acid, and to test the influence of HDL, Apoa1-deficient mice consuming the latter diet were used. In Apoe-deficient mice, oleanolic acid intake increased hepatic area occupied by lipid droplets with no change in oxidative stress. Bmal1 and the other core component of the circadian clock, Clock, together with Elovl3, Tubb2a and Cldn1 expressions, were significantly increased, while Amy2a5, Usp2, Per3 and Thrsp were significantly decreased in mice receiving the compound. Bmal1 and Cldn1 expressions were positively associated with lipid droplets. Increased Clock and Bmal1 expressions were also observed in rats, but not in Apoa1-deficient mice. The core liver clock components Clock-Bmal1 are a target of oleanolic acid in two animal models independently of the diets provided, and this compound requires APOA1-HDL for its hepatic action.
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Affiliation(s)
- Clara Gabás-Rivera
- Departamento Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón (IIS), Universidad de Zaragoza, Spain; CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Spain
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Osada J. The use of transcriptomics to unveil the role of nutrients in Mammalian liver. ISRN NUTRITION 2013; 2013:403792. [PMID: 24967258 PMCID: PMC4045299 DOI: 10.5402/2013/403792] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 08/04/2013] [Indexed: 01/03/2023]
Abstract
Liver is the organ primarily responding to diet, and it is crucial in determining plasma carbohydrate, protein, and lipid levels. In addition, it is mainly responsible for transformation of xenobiotics. For these reasons, it has been a target of transcriptomic analyses. In this review, we have covered the works dealing with the response of mammalian liver to different nutritional stimuli such as fasting/feeding, caloric restriction, dietary carbohydrate, cholesterol, fat, protein, bile acid, salt, vitamin, and oligoelement contents. Quality of fats or proteins has been equally addressed, and has the influence of minor dietary components. Other compounds, not purely nutritional as those represented by alcohol and food additives, have been included due to their relevance in processed food. The influence has been studied not only on mRNA but also on miRNA. The wide scope of the technology clearly reflects that any simple intervention has profound changes in many metabolic parameters and that there is a synergy in response when more compounds are included in the intervention. Standardized arrays to systematically test the same genes in all studies and analyzing data to establish patterns of response are required, particularly for RNA sequencing. Moreover, RNA is a valuable, easy-screening ally but always requires further confirmation.
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Affiliation(s)
- Jesús Osada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50013 Zaragoza, Spain ; CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
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15
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Predicting the outcome of infectious diseases: variability among inbred mice as a new and powerful tool for biomarker discovery. mBio 2012; 3:e00199-12. [PMID: 23073762 PMCID: PMC3470649 DOI: 10.1128/mbio.00199-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Individuals respond differently to infectious diseases. Even among inbred mice that are presumed to be genetically identical, the response to a microbial pathogen is variable, which is generally thought to reflect experimental inconsistencies, technical errors, and stochastic processes. Here we describe the remarkable observation that the variability of Helicobacter pylori colonization density in the stomachs of experimentally infected C57BL/6J mice is tightly correlated with weight loss and viral load after a challenge with influenza virus, though H. pylori infection per se does not affect influenza and vice versa. Since these two infectious agents are found in different tissue compartments and are detected using unrelated methods, the correlation in microbial burden must represent a biological measure of disease susceptibility among genetically nearly identical individuals and not technical or stochastic factors. We hypothesize that inbred mice represent a powerful new tool for the identification of biomarkers to predict the outcome of infectious diseases.
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16
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Robledo RF, Seburn KL, Nicholson A, Peters LL. Strain-specific hyperkyphosis and megaesophagus in Add1 null mice. Genesis 2012; 50:882-91. [PMID: 22926980 DOI: 10.1002/dvg.22342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 08/02/2012] [Accepted: 08/16/2012] [Indexed: 11/08/2022]
Abstract
The three adducin proteins (α, β, and γ) share extensive sequence, structural, and functional homology. Heterodimers of α- and β-adducin are vital components of the red cell membrane skeleton, which is required to maintain red cell elasticity and structural integrity. In addition to anemia, targeted deletion of the α-adducin gene (Add1) reveals unexpected, strain-dependent non-erythroid phenotypes. On an inbred 129 genetic background, Add1 null mice show abnormal inward curvature of the cervicothoracic spine with complete penetrance. More surprisingly, a subset of 129-Add1 null mice develop severe megaesophagus, while examination of peripheral nerves reveals a reduced number of axons in 129-Add1 null mice at four months of age. These unforeseen phenotypes, described here, reveal new functions for adducin and provide new models of mammalian disease.
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Malavolta M, Basso A, Piacenza F, Giacconi R, Costarelli L, Pierpaoli S, Mocchegiani E. Survival study of metallothionein-1 transgenic mice and respective controls (C57BL/6J): influence of a zinc-enriched environment. Rejuvenation Res 2012; 15:140-3. [PMID: 22533418 DOI: 10.1089/rej.2011.1261] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The role of metallothioneins (MTs) in aging is not completely understood. Several studies have shown evidence that these proteins could represent a defense system against oxidative damage, but survival studies on mice overexpressing MTs are poor. Here we describe a survival study performed on old MT-1-overexpressing mice (MT-TG) and their respective controls (C57BL/6J) fed a standard or zinc (Zn)-supplemented diet. MT-TG mice had significantly increased survival compared with control. Zn supplementation affects the survival curves of MT-TG and C57BL/6J mice differently. This study poses the basis for intervention based on gene therapy with MTs to enhance the health span of laboratory mice.
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Affiliation(s)
- Marco Malavolta
- Nutrition and Aging Centre, Scientific and Technological Pole INRCA, Ancona, Italy.
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18
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Alonso LC, Watanabe Y, Stefanovski D, Lee EJ, Singamsetty S, Romano LC, Zou B, Garcia-Ocaña A, Bergman RN, O'Donnell CP. Simultaneous measurement of insulin sensitivity, insulin secretion, and the disposition index in conscious unhandled mice. Obesity (Silver Spring) 2012; 20:1403-12. [PMID: 22331130 PMCID: PMC3378770 DOI: 10.1038/oby.2012.36] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Of the parameters that determine glucose disposal and progression to diabetes in humans: first-phase insulin secretion, glucose effectiveness (Sg), insulin sensitivity (Si), and the disposition index (DI), only Si can be reliably measured in conscious mice. To determine the importance of the other parameters in murine glucose homeostasis in lean and obese states, we developed the frequently sampled intravenous glucose tolerance test (FSIVGTT) for use in unhandled mice. We validated the conscious FSIVGTT against the euglycemic clamp for measuring Si in lean and obese mice. Insulin-resistant mice had increased first-phase insulin secretion, decreased Sg, and a reduced DI, qualitatively similar to humans. Intriguingly, although insulin secretion explained most of the variation in glucose disposal in lean mice, Sg and the DI more strongly predicted glucose disposal in obese mice. DI curves identified individual diet-induced obese (DIO) mice as having compensated or decompensated insulin secretion. Conscious FSIVGTT opens the door to apply mouse genetics to the determinants of in vivo insulin secretion, Sg, and DI, and further validates the mouse as a model of metabolic disease.
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Affiliation(s)
- Laura C Alonso
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA, USA.
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Corton JC, Bushel PR, Fostel J, O'Lone RB. Sources of variance in baseline gene expression in the rodent liver. Mutat Res 2012; 746:104-12. [PMID: 22230429 DOI: 10.1016/j.mrgentox.2011.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 12/13/2011] [Indexed: 12/18/2022]
Abstract
The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization of variation due to individual, environmental, and technical factors. Analysis of microarray data from untreated or vehicle-treated animals within the control arm of toxicogenomics studies has yielded useful information on baseline fluctuations in liver gene expression in the rodent. Here, studies which highlight contributions of different factors to gene expression variability in the rodent liver are discussed including a large meta-analysis of rat liver, which identified genes that vary in control animals in the absence of chemical treatment. Genes and their pathways that are the most and least variable were identified in a number of these studies. Life stage, fasting, sex, diet, circadian rhythm and liver lobe source can profoundly influence gene expression in the liver. Recognition of biological and technical factors that contribute to variability of background gene expression can help the investigator in the design of an experiment that maximizes sensitivity and reduces the influence of confounders that may lead to misinterpretation of genomic changes. The factors that contribute to variability in liver gene expression in rodents are likely analogous to those contributing to human interindividual variability in drug response and chemical toxicity. Identification of batteries of genes that are altered in a variety of background conditions could be used to predict responses to drugs and chemicals in appropriate models of the human liver.
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Affiliation(s)
- J Christopher Corton
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Lab, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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Zhang H, Good DJ. Comparison of hypothalamic mRNA levels in mice euthanized by CO₂ inhalation and focused-beam microwave irradiation. Lab Anim (NY) 2011; 40:313-8. [PMID: 22358208 DOI: 10.1038/laban1011-313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 08/17/2011] [Indexed: 11/09/2022]
Abstract
Focused-beam microwave irradiation (FBMI) is a relatively new method for euthanasia of small mammals and is available to most researchers. Compared with CO₂ inhalation, this method of euthanasia has the advantage of preserving fast-degrading metabolites. But differences in brain RNA quantity and quality, gene expression and histology in mice euthanized by CO₂ inhalation versus FBMI have not been investigated. Here the authors report that a smaller quantity of RNA was isolated from brains of mice euthanized by FBMI compared with those of mice euthanized by CO₂ inhalation. They also found relative differences in the levels of the expression of some genes. These studies suggest that either method can be used for histological analysis or RNA isolation, but the authors caution against combining the techniques within a single study on gene expression.
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Affiliation(s)
- Haiyan Zhang
- Human Nutrition, Foods and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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