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Kruse CJ, Dieu M, Renaud B, François AC, Stern D, Demazy C, Burteau S, Boemer F, Art T, Renard P, Votion DM. New Pathophysiological Insights from Serum Proteome Profiling in Equine Atypical Myopathy. ACS OMEGA 2024; 9:6505-6526. [PMID: 38371826 PMCID: PMC10870397 DOI: 10.1021/acsomega.3c06647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/15/2023] [Accepted: 12/29/2023] [Indexed: 02/20/2024]
Abstract
Equine atypical myopathy (AM) is a severe environmental intoxication linked to the ingestion of protoxins contained in seeds and seedlings of the sycamore maple (Acer pseudoplatanus) in Europe. The toxic metabolites cause a frequently fatal rhabdomyolysis syndrome in grazing horses. Since these toxic metabolites can also be present in cograzing horses, it is still unclear as to why, in a similar environmental context, some horses show signs of AM, whereas others remain clinically healthy. Label-free proteomic analyses on the serum of 26 diseased AM, 23 cograzers, and 11 control horses were performed to provide insights into biological processes and pathways. A total of 43 and 44 differentially abundant proteins between "AM vs cograzing horses" and "AM vs control horses" were found. Disease-linked changes in the proteome of different groups were found to correlate with detected amounts of toxins, and principal component analyses were performed to identify the 29 proteins representing a robust AM signature. Among the pathway-specific changes, the glycolysis/gluconeogenesis pathway, the coagulation/complement cascade, and the biosynthesis of amino acids were affected. Sycamore maple poisoning results in a combination of inflammation, oxidative stress, and impaired lipid metabolism, which is trying to be counteracted by enhanced glycolysis.
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Affiliation(s)
- Caroline-J. Kruse
- Department
of Functional Sciences, Faculty of Veterinary Medicine, Physiology
and Sport Medicine, Fundamental and Applied
Research for Animals & Health (FARAH), University of Liège, Sart Tilman, 4000 Liège 1, Belgium
| | - Marc Dieu
- Namur
Research Institute for Life Sciences (Narilis), University of Namur (UNamur), Namur 5000, Belgium
- MaSUN,
Mass Spectrometry Facility, University of
Namur (UNamur), Namur 5000, Belgium
| | - Benoît Renaud
- Department
of Functional Sciences, Faculty of Veterinary Medicine, Pharmacology
and Toxicology, Fundamental and Applied
Research for Animals & Health (FARAH), University of Liège, Sart Tilman, 4000 Liège 1, Belgium
| | - Anne-Christine François
- Department
of Functional Sciences, Faculty of Veterinary Medicine, Pharmacology
and Toxicology, Fundamental and Applied
Research for Animals & Health (FARAH), University of Liège, Sart Tilman, 4000 Liège 1, Belgium
| | - David Stern
- GIGA
Bioinformatics Platform, GIGA Institute, University of Liège, Sart Tilman, 4000 Liège, Belgium
| | - Catherine Demazy
- Namur
Research Institute for Life Sciences (Narilis), University of Namur (UNamur), Namur 5000, Belgium
- MaSUN,
Mass Spectrometry Facility, University of
Namur (UNamur), Namur 5000, Belgium
| | - Sophie Burteau
- Namur
Research Institute for Life Sciences (Narilis), University of Namur (UNamur), Namur 5000, Belgium
- MaSUN,
Mass Spectrometry Facility, University of
Namur (UNamur), Namur 5000, Belgium
| | - François Boemer
- Biochemical
Genetics Lab, Department of Human Genetics, CHU of Liège, University of Liège, Sart Tilman, 4000 Liège, Belgium
| | - Tatiana Art
- Department
of Functional Sciences, Faculty of Veterinary Medicine, Physiology
and Sport Medicine, Fundamental and Applied
Research for Animals & Health (FARAH), University of Liège, Sart Tilman, 4000 Liège 1, Belgium
| | - Patricia Renard
- Namur
Research Institute for Life Sciences (Narilis), University of Namur (UNamur), Namur 5000, Belgium
- MaSUN,
Mass Spectrometry Facility, University of
Namur (UNamur), Namur 5000, Belgium
| | - Dominique-M. Votion
- Department
of Functional Sciences, Faculty of Veterinary Medicine, Pharmacology
and Toxicology, Fundamental and Applied
Research for Animals & Health (FARAH), University of Liège, Sart Tilman, 4000 Liège 1, Belgium
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Valberg SJ, Velez-Irizarry D, Williams ZJ, Henry ML, Iglewski H, Herrick K, Fenger C. Enriched Pathways of Calcium Regulation, Cellular/Oxidative Stress, Inflammation, and Cell Proliferation Characterize Gluteal Muscle of Standardbred Horses between Episodes of Recurrent Exertional Rhabdomyolysis. Genes (Basel) 2022; 13:1853. [PMID: 36292738 PMCID: PMC9601720 DOI: 10.3390/genes13101853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/04/2022] Open
Abstract
Certain Standardbred racehorses develop recurrent exertional rhabdomyolysis (RER-STD) for unknown reasons. We compared gluteal muscle histopathology and gene/protein expression between Standardbreds with a history of, but not currently experiencing rhabdomyolysis (N = 9), and race-trained controls (N = 7). Eight RER-STD had a few mature fibers with small internalized myonuclei, one out of nine had histologic evidence of regeneration and zero out of nine degeneration. However, RER-STD versus controls had 791/13,531 differentially expressed genes (DEG). The top three gene ontology (GO) enriched pathways for upregulated DEG (N = 433) were inflammation/immune response (62 GO terms), cell proliferation (31 GO terms), and hypoxia/oxidative stress (31 GO terms). Calcium ion regulation (39 GO terms), purine nucleotide metabolism (32 GO terms), and electron transport (29 GO terms) were the top three enriched GO pathways for down-regulated DEG (N = 305). DEG regulated RYR1 and sarcoplasmic reticulum calcium stores. Differentially expressed proteins (DEP ↑N = 50, ↓N = 12) involved the sarcomere (24% of DEP), electron transport (23%), metabolism (20%), inflammation (6%), cell/oxidative stress (7%), and other (17%). DEP included ↑superoxide dismutase, ↑catalase, and DEP/DEG included several cysteine-based antioxidants. In conclusion, gluteal muscle of RER-susceptible Standardbreds is characterized by perturbation of pathways for calcium regulation, cellular/oxidative stress, inflammation, and cellular regeneration weeks after an episode of rhabdomyolysis that could represent therapeutic targets.
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Affiliation(s)
- Stephanie J. Valberg
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Deborah Velez-Irizarry
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Zoë J. Williams
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Marisa L. Henry
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Hailey Iglewski
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Keely Herrick
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Clara Fenger
- Equine Integrated Medicine, PLC, Lexington, KY 40324, USA
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Pathways of calcium regulation, electron transport, and mitochondrial protein translation are molecular signatures of susceptibility to recurrent exertional rhabdomyolysis in Thoroughbred racehorses. PLoS One 2021; 16:e0244556. [PMID: 33566847 PMCID: PMC7875397 DOI: 10.1371/journal.pone.0244556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/13/2020] [Indexed: 12/13/2022] Open
Abstract
Recurrent exertional rhabdomyolysis (RER) is a chronic muscle disorder of unknown etiology in racehorses. A potential role of intramuscular calcium (Ca2+) dysregulation in RER has led to the use of dantrolene to prevent episodes of rhabdomyolysis. We examined differentially expressed proteins (DEP) and gene transcripts (DEG) in gluteal muscle of Thoroughbred race-trained mares after exercise among three groups of 5 horses each; 1) horses susceptible to, but not currently experiencing rhabdomyolysis, 2) healthy horses with no history of RER (control), 3) RER-susceptible horses treated with dantrolene pre-exercise (RER-D). Tandem mass tag LC/MS/MS quantitative proteomics and RNA-seq analysis (FDR <0.05) was followed by gene ontology (GO) and semantic similarity of enrichment terms. Of the 375 proteins expressed, 125 were DEP in RER-susceptible versus control, with 52 ↑DEP mainly involving Ca2+ regulation (N = 11) (e.g. RYR1, calmodulin, calsequestrin, calpain), protein degradation (N = 6), antioxidants (N = 4), plasma membranes (N = 3), glyco(geno)lysis (N = 3) and 21 DEP being blood-borne. ↓DEP (N = 73) were largely mitochondrial (N = 45) impacting the electron transport system (28), enzymes (6), heat shock proteins (4), and contractile proteins (12) including Ca2+ binding proteins. There were 812 DEG in RER-susceptible versus control involving the electron transfer system, the mitochondrial transcription/translational response and notably the pro-apoptotic Ca2+-activated mitochondrial membrane transition pore (SLC25A27, BAX, ATP5 subunits). Upregulated mitochondrial DEG frequently had downregulation of their encoded DEP with semantic similarities highlighting signaling mechanisms regulating mitochondrial protein translation. RER-susceptible horses treated with dantrolene, which slows sarcoplasmic reticulum Ca2+ release, showed no DEG compared to control horses. We conclude that RER-susceptibility is associated with alterations in proteins, genes and pathways impacting myoplasmic Ca2+ regulation, the mitochondrion and protein degradation with opposing effects on mitochondrial transcriptional/translational responses and mitochondrial protein content. RER could potentially arise from excessive sarcoplasmic reticulum Ca2+ release and subsequent mitochondrial buffering of excessive myoplasmic Ca2+.
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Dhorne-Pollet S, Barrey E, Pollet N. A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants. BMC Genomics 2020; 21:785. [PMID: 33176683 PMCID: PMC7661214 DOI: 10.1186/s12864-020-07183-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 10/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step. RESULTS We optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequenced these amplified mitochondrial DNA using nanopore sequencing technology and obtained mitochondrial DNA reads that represented up to half of the sequencing output. The sequence reads were 2.3 kb of mean length and provided an even coverage of the mitochondrial genome. Long-reads spanning half or more of the whole mtDNA provided a coverage that varied between 118X and 488X. We evaluated SNPs identified using these long-reads by Sanger sequencing as ground truth and found a precision of 100.0%; a recall of 93.1% and a F1-score of 0.964 using the Twilight horse mtDNA reference. The choice of the mtDNA reference impacted variant calling efficiency with F1-scores varying between 0.947 and 0.964. CONCLUSIONS Our method to amplify mtDNA and to sequence it using the nanopore technology is usable for mitochondrial DNA variant analysis. With minor modifications, this approach could easily be applied to other large circular DNA molecules.
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Affiliation(s)
- Sophie Dhorne-Pollet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Eric Barrey
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Nicolas Pollet
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.
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Valberg SJ, Soave K, Williams ZJ, Perumbakkam S, Schott M, Finno CJ, Petersen JL, Fenger C, Autry JM, Thomas DD. Coding sequences of sarcoplasmic reticulum calcium ATPase regulatory peptides and expression of calcium regulatory genes in recurrent exertional rhabdomyolysis. J Vet Intern Med 2019; 33:933-941. [PMID: 30720217 PMCID: PMC6430904 DOI: 10.1111/jvim.15425] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/11/2019] [Indexed: 12/12/2022] Open
Abstract
Background Sarcolipin (SLN), myoregulin (MRLN), and dwarf open reading frame (DWORF) are transmembrane regulators of the sarcoplasmic reticulum calcium transporting ATPase (SERCA) that we hypothesized played a role in recurrent exertional rhabdomyolysis (RER). Objectives Compare coding sequences of SLN, MRLN, DWORF across species and between RER and control horses. Compare expression of muscle Ca2+ regulatory genes between RER and control horses. Animals Twenty Thoroughbreds (TB), 5 Standardbreds (STD), 6 Quarter Horses (QH) with RER and 39 breed‐matched controls. Methods Sanger sequencing of SERCA regulatory genes with comparison of amino acid (AA) sequences among control, RER horses, human, mouse, and rabbit reference genomes. In RER and control gluteal muscle, quantitative real‐time polymerase chain reaction of SERCA regulatory peptides, the calcium release channel (RYR1), and its accessory proteins calsequestrin (CASQ1), and calstabin (FKBP1A). Results The SLN gene was the highest expressed horse SERCA regulatory gene with a uniquely truncated AA sequence (29 versus 31) versus other species. Coding sequences of SLN, MRLN, and DWORF were identical in RER and control horses. A sex‐by‐phenotype effect occurred with lower CASQ1 expression in RER males versus control males (P < .001) and RER females (P = .05) and higher FKBP1A (P = .01) expression in RER males versus control males. Conclusions and Clinical Importance The SLN gene encodes a uniquely truncated peptide in the horse versus other species. Variants in the coding sequence of SLN, MLRN, or DWORF were not associated with RER. Males with RER have differential gene expression that could reflect adaptations to stabilize RYR1.
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Affiliation(s)
- Stephanie J Valberg
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Kaitlin Soave
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Zoë J Williams
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Sudeep Perumbakkam
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Melissa Schott
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California-Davis, Davis, California
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Clara Fenger
- Equine Integrated Medicine, PLC, Lexington, Kentucky
| | - Joseph M Autry
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota
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Valberg SJ, Perumbakkam S, McKenzie EC, Finno CJ. Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways. Physiol Genomics 2018; 50:1036-1050. [PMID: 30289745 PMCID: PMC6337024 DOI: 10.1152/physiolgenomics.00044.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Equine myofibrillar myopathy (MFM) causes exertional muscle pain and is characterized by myofibrillar disarray and ectopic desmin aggregates of unknown origin. To investigate the pathophysiology of MFM, we compared resting and 3 h postexercise transcriptomes of gluteal muscle and the resting skeletal muscle proteome of MFM and control Arabian horses with RNA sequencing and isobaric tags for relative and absolute quantitation analyses. Three hours after exercise, 191 genes were identified as differentially expressed (DE) in MFM vs. control muscle with >1 log2 fold change (FC) in genes involved in sulfur compound/cysteine metabolism such as cystathionine-beta-synthase ( CBS, ↓4.51), a cysteine and neutral amino acid membrane transporter ( SLC7A10, ↓1.80 MFM), and a cationic transporter (SLC24A1, ↓1.11 MFM). In MFM vs. control at rest, 284 genes were DE with >1 log2 FC in pathways for structure morphogenesis, fiber organization, tissue development, and cell differentiation including > 1 log2 FC in cardiac alpha actin ( ACTC1 ↑2.5 MFM), cytoskeletal desmoplakin ( DSP ↑2.4 MFM), and basement membrane usherin ( USH2A ↓2.9 MFM). Proteome analysis revealed significantly lower antioxidant peroxiredoxin 6 content (PRDX6, ↓4.14 log2 FC MFM), higher fatty acid transport enzyme carnitine palmitoyl transferase (CPT1B, ↑3.49 MFM), and lower sarcomere protein tropomyosin (TPM2, ↓3.24 MFM) in MFM vs. control muscle at rest. We propose that in MFM horses, altered cysteine metabolism and a deficiency of cysteine-containing antioxidants combined with a high capacity to oxidize fatty acids and generate ROS during aerobic exercise causes chronic oxidation and aggregation of key proteins such as desmin.
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Affiliation(s)
- Stephanie J Valberg
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan.,Department of Population Sciences, University of Minnesota , St. Paul, Minnesota
| | - Sudeep Perumbakkam
- Department of Large Animal Clinical Sciences, Michigan State University , East Lansing, Michigan
| | - Erica C McKenzie
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University , Corvallis, Oregon
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California Davis , Davis, California
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McKenzie E. Current status of myopathies affecting athletic horses. COMPARATIVE EXERCISE PHYSIOLOGY 2017. [DOI: 10.3920/cep170005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Muscular disorders rank among the most prevalent problems of horses competing in a broad variety of athletic disciplines, including track racing, dressage, endurance racing and Western riding disciplines. As described in this review, active scientific investigation is continuing to elucidate the different mechanisms underlying specific muscular disorders in horses, and is discovering and defining new disorders, and new methods of diagnosis, treatment and management. The flourishing field of equine rehabilitation and regenerative medicine is also driving the progressive application of a variety of modalities to the treatment and management of musculoskeletal conditions in horses. However, it is essential that this be accompanied by appropriate scientific investigation to verify the efficacy of recommended modalities and treatment protocols.
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Affiliation(s)
- E. McKenzie
- Department of Clinical Sciences, College of Veterinary Medicine, Oregon State University, 227 Magruder Hall, Corvallis, OR 97331, USA
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Integrating genome and transcriptome profiling for elucidating the mechanism of muscle growth and lipid deposition in Pekin ducks. Sci Rep 2017. [PMID: 28630415 PMCID: PMC5476626 DOI: 10.1038/s41598-017-04178-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Muscle growth and lipid deposition are co-ordinately regulated processes. Cherry Valley Pekin duck is a lean-type duck breed with high growth rate, whereas the native Pekin duck of China has high lipid deposition. Phenotypic analysis showed that native Pekin ducks have smaller fibre diameter and larger density in the breast muscle at 3 weeks of age and higher intramuscular fat content at 6 weeks of age than those in Cherry Valley Pekin ducks. We detected 17 positively selected genes (PSGs) by comparing genes mainly involved with muscle organ development, muscle contraction, peroxisome proliferator activated receptor signalling pathway, and fatty acid metabolism. In all, 52 and 206 differentially expressed genes (DEGs) were identified in transcriptomic comparisons between the two breeds at 3 and 6 weeks of age, respectively, which could potentially affect muscle growth and lipid deposition. Based on the integration of PSGs and DEGs and their functional annotations, we found that 11 and 10 genes were correlated with muscle growth and lipid deposition, respectively. Identification of candidate genes controlling quantitative traits of duck muscle might aid in elucidating the mechanisms of muscle growth and lipid deposition and could help in improving duck breeding.
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Bailly-Chouriberry L, Baudoin F, Cormant F, Glavieux Y, Loup B, Garcia P, Popot MA, Bonnaire Y. RNA sample preparation applied to gene expression profiling for the horse biological passport. Drug Test Anal 2017; 9:1448-1455. [DOI: 10.1002/dta.2204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 04/03/2017] [Accepted: 04/03/2017] [Indexed: 01/28/2023]
Affiliation(s)
| | - Florent Baudoin
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Florence Cormant
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Yohan Glavieux
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Benoit Loup
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Patrice Garcia
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Marie-Agnès Popot
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Yves Bonnaire
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
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Garcia-Reyero N, Escalon L, Prats E, Faria M, Soares AMVM, Raldúa D. Targeted Gene Expression in Zebrafish Exposed to Chlorpyrifos-Oxon Confirms Phenotype-Specific Mechanisms Leading to Adverse Outcomes. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2016; 96:707-13. [PMID: 27086301 PMCID: PMC4882348 DOI: 10.1007/s00128-016-1798-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/07/2016] [Indexed: 05/15/2023]
Abstract
Zebrafish models for mild, moderate, and severe acute organophosphorus poisoning were previously developed by exposing zebrafish larvae to chlopyrifos-oxon. The phenotype of these models was characterized at several levels of biological organization. Oxidative stress and mitochondrial dysfunction were found to be involved in the development of the more severe phenotype. Here we used targeted gene expression to understand the dose-responsiveness of those two pathways and their involvement on generating the different zebrafish models. As the severe phenotype is irreversible after only 3 h of exposure, we also analyzed the response of the oxidative stress pathway at 3 and 24 h. Some of the genes related to oxidative stress were already differentially expressed at 3 h. There was an increase in differentially expressed genes related to both oxidative stress and mitochondrial function from the more mild to the more severe phenotype, suggesting the involvement of these mechanisms in increasing phenotype severity. Temporal data suggest that peroxynitrite leading to lipid peroxidation might be involved in phenotype transition and irreversibility.
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Affiliation(s)
- Natàlia Garcia-Reyero
- US Army Engineer Research and Development Center, 3909 Halls Ferry Rd, Vicksburg, MS, 39180, USA.
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, 2 Research Blvd, Starkville, MS, 39759, USA.
| | - Lynn Escalon
- US Army Engineer Research and Development Center, 3909 Halls Ferry Rd, Vicksburg, MS, 39180, USA
| | - Eva Prats
- CIC-CSIC, Jordi Girona 18, 08034, Barcelona, Spain
| | - Melissa Faria
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
- IDAEA-CSIC, Jordi Girona 18, 08034, Barcelona, Spain
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Benech PD, Patatian A. From experimental design to functional gene networks: DNA microarray contribution to skin ageing research. Int J Cosmet Sci 2014; 36:516-26. [PMID: 25066132 DOI: 10.1111/ics.12155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 06/28/2014] [Indexed: 12/21/2022]
Abstract
There is no doubt that the DNA microarray-based technology contributed to increase our knowledge of a wide range of processes. However, integrating genes into functional networks, rather than terms describing generic characteristics, remains an important challenge. The highly context-dependent function of a given gene and feedback mechanisms complexify greatly the interpretation of the data. Moreover, it is difficult to determine whether changes in gene expression are the result or the cause of pathologies or physiological events. In both cases, the difficulty relies on the involvement of processes that, at an early stage, can be protective and later on, deleterious because of their runaway. Each individual cell has its own transcription profile that determines its behaviour and its relationships with its neighbours. This is particularly true when a mechanism such as cell cycle is concerned. Another issue concerns the analyses from samples of different donors. Whereas the statistical tools lead to determine common features among groups, they tend to smooth the overall data and consequently, the selected values represent the 'tip of the iceberg'. There is a significant overlap in the set of genes identified in the different studies on skin ageing processes described in the present review. The reason of this overlap is because most of these genes belong to the basic machinery controlling cell growth and arrest. To get a more full picture of these processes, a hard work has still to be done to determine the precise mechanisms conferring the cell type specificity of ageing. Integrative biology applied to the huge amount of existing microarray data should fulfil gaps, through the characterization of additional actors accounting for the activation of specific signalling pathways at crossing points. Furthermore, computational tools have to be developed taking into account that expression values among similar groups may not vary 'by chance' but may reflect, along with other subtle changes, specific features of one given donor. Through a better stratification, these tools will allow to recover genes from the 'bottom of the iceberg'. Identifying these genes should contribute to understand how skin ages among individuals, thus paving the way for personalized skin care.
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Affiliation(s)
- P D Benech
- UMR 7259 (NICN) CNRS - Aix-Marseille Université, Faculté de Médecine Secteur Nord, CS80011, 51 Bd Pierre Dramard, Marseille CEDEX 15, 13344, France
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12
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Landel V, Baranger K, Virard I, Loriod B, Khrestchatisky M, Rivera S, Benech P, Féron F. Temporal gene profiling of the 5XFAD transgenic mouse model highlights the importance of microglial activation in Alzheimer's disease. Mol Neurodegener 2014; 9:33. [PMID: 25213090 PMCID: PMC4237952 DOI: 10.1186/1750-1326-9-33] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/27/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The 5XFAD early onset mouse model of Alzheimer's disease (AD) is gaining momentum. Behavioral, electrophysiological and anatomical studies have identified age-dependent alterations that can be reminiscent of human AD. However, transcriptional changes during disease progression have not yet been investigated. To this end, we carried out a transcriptomic analysis on RNAs from the neocortex and the hippocampus of 5XFAD female mice at the ages of one, four, six and nine months (M1, M4, M6, M9). RESULTS Our results show a clear shift in gene expression patterns between M1 and M4. At M1, 5XFAD animals exhibit region-specific variations in gene expression patterns whereas M4 to M9 mice share a larger proportion of differentially expressed genes (DEGs) that are common to both regions. Analysis of DEGs from M4 to M9 underlines the predominance of inflammatory and immune processes in this AD mouse model. The rise in inflammation, sustained by the overexpression of genes from the complement and integrin families, is accompanied by an increased expression of transcripts involved in the NADPH oxidase complex, phagocytic processes and IFN-γ related pathways. CONCLUSIONS Overall, our data suggest that, from M4 to M9, sustained microglial activation becomes the predominant feature and point out that both detrimental and neuroprotective mechanisms appear to be at play in this model. Furthermore, our study identifies a number of genes already known to be altered in human AD, thus confirming the use of the 5XFAD strain as a valid model for understanding AD pathogenesis and for screening potential therapeutic molecules.
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Affiliation(s)
- Véréna Landel
- Aix Marseille Université, CNRS, NICN UMR 7259, 13916 Marseille, France
| | - Kévin Baranger
- Aix Marseille Université, CNRS, NICN UMR 7259, 13916 Marseille, France
- APHM, Hôpitaux de la Timone, Service de Neurologie et Neuropsychologie, 13385 Marseille, France
| | - Isabelle Virard
- Aix Marseille Université, CNRS, NICN UMR 7259, 13916 Marseille, France
| | - Béatrice Loriod
- Aix Marseille Université, TAGC UMR 1090, 13288 Marseille, France
- INSERM, TAGC UMR 1090, 13288 Marseille, France
| | | | - Santiago Rivera
- Aix Marseille Université, CNRS, NICN UMR 7259, 13916 Marseille, France
| | - Philippe Benech
- Aix Marseille Université, CNRS, NICN UMR 7259, 13916 Marseille, France
| | - François Féron
- Aix Marseille Université, CNRS, NICN UMR 7259, 13916 Marseille, France
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Hur J, Liu Z, Tong W, Laaksonen R, Bai JPF. Drug-induced rhabdomyolysis: from systems pharmacology analysis to biochemical flux. Chem Res Toxicol 2014; 27:421-32. [PMID: 24422454 DOI: 10.1021/tx400409c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The goal of this study was to integrate systems pharmacology and biochemical flux to delineate drug-induced rhabdomyolysis by leveraging prior knowledge and publicly accessible data. A list of 211 rhabdomyolysis-inducing drugs (RIDs) was compiled and curated from multiple sources. Extended pharmacological network analysis revealed that the intermediators directly interacting with the pharmacological targets of RIDs were significantly enriched with functions such as regulation of cell cycle, apoptosis, and ubiquitin-mediated proteolysis. A total of 78 intermediators were shown to be significantly connected to at least five RIDs, including estrogen receptor 1 (ESR1), synuclein gamma (SNCG), and janus kinase 2 (JAK2). Transcriptomic analysis of RIDs profiled in Connectivity Map on the global scale revealed that multiple pathways are perturbed by RIDs, including ErbB signaling and lipid metabolism pathways, and that carnitine palmitoyl transferase 2 (CPT2) was in the top 1 percent of the most differentially perturbed genes. CPT2 was downregulated by nine drugs that perturbed the genes significantly enriched in oxidative phosphorylation and energy-metabolism pathways. With statins as the use case, biochemical pathway analysis on the local scale implicated a role for CPT2 in statin-induced perturbation of energy homeostasis, which is in agreement with reports of statin-CPT2 interaction. Considering the complexity of human biology, an integrative multiple-approach analysis composed of a biochemical flux network, pharmacological on- and off-target networks, and transcriptomic signature is important for understanding drug safety and for providing insight into clinical gene-drug interactions.
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Affiliation(s)
- Junguk Hur
- Department of Neurology, University of Michigan , Ann Arbor, Michigan 48109, United States
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Abstract
The mitochondrion relies on compartmentalization of certain enzymes, ions and metabolites for the sake of efficient metabolism. In order to fulfil its activities, a myriad of carriers are properly expressed, targeted and folded in the inner mitochondrial membrane. Among these carriers, the six-transmembrane-helix mitochondrial SLC25 (solute carrier family 25) proteins facilitate transport of solutes with disparate chemical identities across the inner mitochondrial membrane. Although their proper function replenishes building blocks needed for metabolic reactions, dysfunctional SLC25 proteins are involved in pathological states. It is the purpose of the present review to cover the current knowledge on the role of SLC25 transporters in health and disease.
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