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Gaspar RS, Katashima CK, Crisol BM, Carneiro FS, Sampaio I, Silveira LDR, Silva ASRD, Cintra DE, Pauli JR, Ropelle ER. Physical exercise elicits UPR mt in the skeletal muscle: The role of c-Jun N-terminal kinase. Mol Metab 2023; 78:101816. [PMID: 37821006 PMCID: PMC10590869 DOI: 10.1016/j.molmet.2023.101816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/10/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
OBJECTIVE The mitochondrial unfolded protein response (UPRmt) is an adaptive cellular response to stress to ensure mitochondrial proteostasis and function. Here we explore the capacity of physical exercise to induce UPRmt in the skeletal muscle. METHODS Therefore, we combined mouse models of exercise (swimming and treadmill running), pharmacological intervention, and bioinformatics analyses. RESULTS Firstly, RNA sequencing and Western blotting analysis revealed that an acute aerobic session stimulated several mitostress-related genes and protein content in muscle, including the UPRmt markers. Conversely, using a large panel of isogenic strains of BXD mice, we identified that BXD73a and 73b strains displayed low levels of several UPRmt-related genes in the skeletal muscle, and this genotypic feature was accompanied by body weight gain, lower locomotor activity, and aerobic capacity. Finally, we identified that c-Jun N-terminal kinase (JNK) activation was critical in exercise-induced UPRmt in the skeletal muscle since pharmacological JNK pathway inhibition blunted exercise-induced UPRmt markers in mice muscle. CONCLUSION Our findings provide new insights into how exercise triggers mitostress signals toward the oxidative capacity in the skeletal muscle.
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Affiliation(s)
- Rodrigo Stellzer Gaspar
- Laboratory of Molecular Biology of Exercise (LaBMEx), School of Applied Sciences (FCA), University of Campinas (Unicamp), Limeira, Brazil; Laboratory of Cell Signaling, Obesity and Comorbidities Research Center (OCRC), University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Carlos Kiyoshi Katashima
- Laboratory of Molecular Biology of Exercise (LaBMEx), School of Applied Sciences (FCA), University of Campinas (Unicamp), Limeira, Brazil
| | - Barbara Moreira Crisol
- Laboratory of Molecular Biology of Exercise (LaBMEx), School of Applied Sciences (FCA), University of Campinas (Unicamp), Limeira, Brazil
| | - Fernanda Silva Carneiro
- Laboratory of Molecular Biology of Exercise (LaBMEx), School of Applied Sciences (FCA), University of Campinas (Unicamp), Limeira, Brazil
| | - Igor Sampaio
- Department of Structural and Functional Biology, Biology Institute, University of Campinas (Unicamp), Campinas, Brazil
| | - Leonardo Dos Reis Silveira
- Department of Structural and Functional Biology, Biology Institute, University of Campinas (Unicamp), Campinas, Brazil
| | - Adelino Sanchez Ramos da Silva
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Dennys Esper Cintra
- Laboratory of Nutritional Genomics (Labgen), School of Applied Sciences (FCA), University of Campinas (Unicamp), Limeira, Brazil
| | - José Rodrigo Pauli
- Laboratory of Molecular Biology of Exercise (LaBMEx), School of Applied Sciences (FCA), University of Campinas (Unicamp), Limeira, Brazil
| | - Eduardo Rochete Ropelle
- Laboratory of Molecular Biology of Exercise (LaBMEx), School of Applied Sciences (FCA), University of Campinas (Unicamp), Limeira, Brazil; Faculty of Medical Sciences, Department of Internal Medicine. University of Campinas (Unicamp), Campinas, São Paulo, Brazil.
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English J, Orofino J, Cederquist CT, Paul I, Li H, Auwerx J, Emili A, Belkina A, Cardamone D, Perissi V. GPS2-mediated regulation of the adipocyte secretome modulates adipose tissue remodeling at the onset of diet-induced obesity. Mol Metab 2023; 69:101682. [PMID: 36731652 PMCID: PMC9922684 DOI: 10.1016/j.molmet.2023.101682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/22/2023] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVE Dysfunctional, unhealthy expansion of white adipose tissue due to excess dietary intake is a process at the root of obesity and Type 2 Diabetes development. The objective of this study is to contribute to a better understanding of the underlying mechanism(s) regulating the early stages of adipose tissue expansion and adaptation to dietary stress due to an acute, high-fat diet (HFD) challenge, with a focus on the communication between adipocytes and other stromal cells. METHODS We profiled the early response to high-fat diet exposure in wildtype and adipocyte-specific GPS2-KO (GPS2-AKO) mice at the cellular, tissue and organismal level. A multi-pronged approach was employed to disentangle the complex cellular interactions dictating tissue remodeling, via single-cell RNA sequencing and FACS profiling of the stromal fraction, and semi-quantitative proteomics of the adipocyte-derived exosomal cargo after 5 weeks of HFD feeding. RESULTS Our results indicate that loss of GPS2 in mature adipocytes leads to impaired adaptation to the metabolic stress imposed by HFD feeding. GPS2-AKO mice are significantly more inflamed, insulin resistant, and obese, compared to the WT counterparts. At the cellular level, lack of GPS2 in adipocytes impacts upon other stromal populations, with both the eWAT and scWAT depots exhibiting changes in the immune and non-immune compartments that contribute to an increase in inflammatory and anti-adipogenic cell types. Our studies also revealed that adipocyte to stromal cell communication is facilitated by exosomes, and that transcriptional rewiring of the exosomal cargo is crucial for tissue remodeling. Loss of GPS2 results in increased expression of secreted factors promoting a TGFβ-driven fibrotic microenvironment favoring unhealthy tissue remodeling and expansion. CONCLUSIONS Adipocytes serve as an intercellular signaling hub, communicating with the stromal compartment via paracrine signaling. Our study highlights the importance of proper regulation of the 'secretome' released by energetically stressed adipocytes at the onset of obesity. Altered transcriptional regulation of factors secreted via adipocyte-derived exosomes (AdExos), in the absence of GPS2, contributes to the establishment of an anti-adipogenic, pro-fibrotic adipose tissue environment, and to hastened progression towards a metabolically dysfunctional phenotype.
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Affiliation(s)
- Justin English
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.
| | - Joseph Orofino
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
| | - Carly T. Cederquist
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Indranil Paul
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Center for Network Systems Biology, Boston University, Boston, MA, USA.
| | - Hao Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Center for Network Systems Biology, Boston University, Boston, MA, USA.
| | - Anna Belkina
- Flow Cytometry Core Facility, Boston University School of Medicine, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Dafne Cardamone
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
| | - Valentina Perissi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; School of Life Science, Northwestern Polytechnical University, Xi'an 710072, China.
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Nam Y, Lee DG, Bang S, Kim JH, Kim JH, Shin H. The translational network for metabolic disease - from protein interaction to disease co-occurrence. BMC Bioinformatics 2019; 20:576. [PMID: 31722666 PMCID: PMC6854734 DOI: 10.1186/s12859-019-3106-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/20/2019] [Indexed: 02/08/2023] Open
Abstract
Background The recent advances in human disease network have provided insights into establishing the relationships between the genotypes and phenotypes of diseases. In spite of the great progress, it yet remains as only a map of topologies between diseases, but not being able to be a pragmatic diagnostic/prognostic tool in medicine. It can further evolve from a map to a translational tool if it equips with a function of scoring that measures the likelihoods of the association between diseases. Then, a physician, when practicing on a patient, can suggest several diseases that are highly likely to co-occur with a primary disease according to the scores. In this study, we propose a method of implementing ‘n-of-1 utility’ (n potential diseases of one patient) to human disease network—the translational disease network. Results We first construct a disease network by introducing the notion of walk in graph theory to protein-protein interaction network, and then provide a scoring algorithm quantifying the likelihoods of disease co-occurrence given a primary disease. Metabolic diseases, that are highly prevalent but have found only a few associations in previous studies, are chosen as entries of the network. Conclusions The proposed method substantially increased connectivity between metabolic diseases and provided scores of co-occurring diseases. The increase in connectivity turned the disease network info-richer. The result lifted the AUC of random guessing up to 0.72 and appeared to be concordant with the existing literatures on disease comorbidity.
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Affiliation(s)
- Yonghyun Nam
- Department of Industrial Engineering, Ajou University, 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Dong-Gi Lee
- Department of Industrial Engineering, Ajou University, 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Sunjoo Bang
- Department of Industrial Engineering, Ajou University, 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jae-Hoon Kim
- Department of Industrial Engineering, Ajou University, 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea.
| | - Hyunjung Shin
- Department of Industrial Engineering, Ajou University, 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea.
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Leandro J, Violante S, Argmann CA, Hagen J, Dodatko T, Bender A, Zhang W, Williams EG, Bachmann AM, Auwerx J, Yu C, Houten SM. Mild inborn errors of metabolism in commonly used inbred mouse strains. Mol Genet Metab 2019; 126:388-396. [PMID: 30709776 PMCID: PMC6535113 DOI: 10.1016/j.ymgme.2019.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
Inbred mouse strains are a cornerstone of translational research but paradoxically many strains carry mild inborn errors of metabolism. For example, α-aminoadipic acidemia and branched-chain ketoacid dehydrogenase deficiency are known in C57BL/6J mice. Using RNA sequencing, we now reveal the causal variants in Dhtkd1 and Bckdhb, and the molecular mechanism underlying these metabolic defects. C57BL/6J mice have decreased Dhtkd1 mRNA expression due to a solitary long terminal repeat (LTR) in intron 4 of Dhtkd1. This LTR harbors an alternate splice donor site leading to a partial splicing defect and as a consequence decreased total and functional Dhtkd1 mRNA, decreased DHTKD1 protein and α-aminoadipic acidemia. Similarly, C57BL/6J mice have decreased Bckdhb mRNA expression due to an LTR retrotransposon in intron 1 of Bckdhb. This transposable element encodes an alternative exon 1 causing aberrant splicing, decreased total and functional Bckdhb mRNA and decreased BCKDHB protein. Using a targeted metabolomics screen, we also reveal elevated plasma C5-carnitine in 129 substrains. This biochemical phenotype resembles isovaleric acidemia and is caused by an exonic splice mutation in Ivd leading to partial skipping of exon 10 and IVD protein deficiency. In summary, this study identifies three causal variants underlying mild inborn errors of metabolism in commonly used inbred mouse strains.
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Affiliation(s)
- João Leandro
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Sara Violante
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA; Mount Sinai Genomics, Inc, One Gustave L Levy Place #1497, New York, NY 10029, USA
| | - Carmen A Argmann
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Jacob Hagen
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Aaron Bender
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Wei Zhang
- Mount Sinai Genomics, Inc, One Gustave L Levy Place #1497, New York, NY 10029, USA
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich CH-8093, Switzerland
| | - Alexis M Bachmann
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Chunli Yu
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA; Mount Sinai Genomics, Inc, One Gustave L Levy Place #1497, New York, NY 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA.
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Salinas-Rubio D, Tovar AR, Torre-Villalvazo I, Granados-Portillo O, Torres N, Pedraza-Chaverri J, Noriega LG. Interaction between leucine and palmitate catabolism in 3T3-L1 adipocytes and primary adipocytes from control and obese rats. J Nutr Biochem 2018; 59:29-36. [DOI: 10.1016/j.jnutbio.2018.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/14/2018] [Accepted: 05/31/2018] [Indexed: 12/19/2022]
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Smith RL, Soeters MR, Wüst RCI, Houtkooper RH. Metabolic Flexibility as an Adaptation to Energy Resources and Requirements in Health and Disease. Endocr Rev 2018; 39:489-517. [PMID: 29697773 PMCID: PMC6093334 DOI: 10.1210/er.2017-00211] [Citation(s) in RCA: 413] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 04/19/2018] [Indexed: 12/15/2022]
Abstract
The ability to efficiently adapt metabolism by substrate sensing, trafficking, storage, and utilization, dependent on availability and requirement, is known as metabolic flexibility. In this review, we discuss the breadth and depth of metabolic flexibility and its impact on health and disease. Metabolic flexibility is essential to maintain energy homeostasis in times of either caloric excess or caloric restriction, and in times of either low or high energy demand, such as during exercise. The liver, adipose tissue, and muscle govern systemic metabolic flexibility and manage nutrient sensing, uptake, transport, storage, and expenditure by communication via endocrine cues. At a molecular level, metabolic flexibility relies on the configuration of metabolic pathways, which are regulated by key metabolic enzymes and transcription factors, many of which interact closely with the mitochondria. Disrupted metabolic flexibility, or metabolic inflexibility, however, is associated with many pathological conditions including metabolic syndrome, type 2 diabetes mellitus, and cancer. Multiple factors such as dietary composition and feeding frequency, exercise training, and use of pharmacological compounds, influence metabolic flexibility and will be discussed here. Last, we outline important advances in metabolic flexibility research and discuss medical horizons and translational aspects.
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Affiliation(s)
- Reuben L Smith
- Laboratory of Genetic Metabolic Diseases, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Gastroenterology and Metabolism, Academic Medical Center, AZ Amsterdam, Netherlands
| | - Maarten R Soeters
- Amsterdam Gastroenterology and Metabolism, Academic Medical Center, AZ Amsterdam, Netherlands.,Department of Endocrinology and Metabolism, Internal Medicine, Academic Medical Center, AZ Amsterdam, Netherlands
| | - Rob C I Wüst
- Laboratory of Genetic Metabolic Diseases, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Cardiovascular Sciences, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Movement Sciences, Academic Medical Center, AZ Amsterdam, Netherlands
| | - Riekelt H Houtkooper
- Laboratory of Genetic Metabolic Diseases, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Gastroenterology and Metabolism, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Cardiovascular Sciences, Academic Medical Center, AZ Amsterdam, Netherlands
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Senapati VA, Gupta GS, Pandey AK, Shanker R, Dhawan A, Kumar A. Zinc oxide nanoparticle induced age dependent immunotoxicity in BALB/c mice. Toxicol Res (Camb) 2017; 6:342-352. [PMID: 30090503 DOI: 10.1039/c6tx00439c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/13/2017] [Indexed: 11/21/2022] Open
Abstract
Zinc oxide (ZnO) nanoparticles (NPs) have potential applications in cosmetics, food packaging and biomedicine but concerns regarding their safety need to be addressed. In the present study, the immunotoxic potential of ZnO NPs was evaluated in different ages of BALB/c mice after sub-acute exposure. The cytokine release, immunophenotyping, distribution of ZnO NPs and ultrastructural changes were assessed. A significant (p < 0.05) change in the CD4- and CD8-cells, levels of IL-6, IFN-γ and TNF-α and reactive oxygen species were observed in aged mice. In juvenile mice, increase in reactive oxygen species and IL-6 and TNF-α levels was observed with no significant changes in adult mice. A significant (p < 0.05) increase in the expression levels of mitogen activated protein kinase (MAPK) cascade proteins such as phospho-ERK1/2, phospho-JNK and phospho-p38 were also induced in aged mice. Collectively, our results indicate that the aged mice are more susceptible to ZnO NP induced immunotoxicity.
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Affiliation(s)
- Violet Aileen Senapati
- Division of Biological & Life Sciences , School of Arts & Sciences , Ahmedabad University , University Road , Ahmedabad 380009 , Gujarat , India . ; ; Tel: +91-79-26302414
| | - Govind Sharan Gupta
- Division of Biological & Life Sciences , School of Arts & Sciences , Ahmedabad University , University Road , Ahmedabad 380009 , Gujarat , India . ; ; Tel: +91-79-26302414
| | - Alok Kumar Pandey
- CSIR-Indian Institute of Toxicology Research , Vishvigyan Bhavan , 31 , Mahatma Gandhi Marg , P.O. Box 80 , Lucknow 226001 , Uttar Pradesh , India .
| | - Rishi Shanker
- Division of Biological & Life Sciences , School of Arts & Sciences , Ahmedabad University , University Road , Ahmedabad 380009 , Gujarat , India . ; ; Tel: +91-79-26302414
| | - Alok Dhawan
- CSIR-Indian Institute of Toxicology Research , Vishvigyan Bhavan , 31 , Mahatma Gandhi Marg , P.O. Box 80 , Lucknow 226001 , Uttar Pradesh , India .
| | - Ashutosh Kumar
- Division of Biological & Life Sciences , School of Arts & Sciences , Ahmedabad University , University Road , Ahmedabad 380009 , Gujarat , India . ; ; Tel: +91-79-26302414
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Nano zinc, an alternative to conventional zinc as animal feed supplement: A review. ACTA ACUST UNITED AC 2016; 2:134-141. [PMID: 29767083 PMCID: PMC5941028 DOI: 10.1016/j.aninu.2016.06.003] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/17/2016] [Indexed: 11/22/2022]
Abstract
The uniqueness of Zn is that, it is the second most abundant trace element in the animal body but can't be stored in the body, thus regular dietary intake is required. Zinc oxide (ZnO) nanoparticles (NP) particles are being extensively used in paints, skin lotions pigments, food, electronics appliances, biological and pharmaceutical applications and many more. Zinc oxide nanoparticles are the specially prepared mineral salt having particle size of 1 to 100 nm. It promotes growth can act as antibacterial agent, modulates the immunity and reproduction of the animals. Both in lower and higher doses of specifications it has exhibited a variety of effects on animal performances. Apart from being highly bio-available, reports have already pointed out the growth promoting, antibacterial, immuno-modulatory and many more effects of nano zinc (nZn). These can be used at lower doses and can provide better result than the conventional Zn sources and indirectly prevents environmental contamination also. The toxicological studies provide mixed results in animal models. Studies been undertaken in diversified animal species and encouraging effects have been reported with nZn supplementation. However, there is a need to optimize the dose and duration of ZnO NP supplementation for human and livestock, depending on its biological effects. Actual bioavailability of ZnO NP in livestock is still to be worked out. In this review we have attempted to summarize, conclude the beneficial effects of nZnO and its possible usage as mineral supplement to different categories of human and livestock.
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Rabhi N, Denechaud PD, Gromada X, Hannou SA, Zhang H, Rashid T, Salas E, Durand E, Sand O, Bonnefond A, Yengo L, Chavey C, Bonner C, Kerr-Conte J, Abderrahmani A, Auwerx J, Fajas L, Froguel P, Annicotte JS. KAT2B Is Required for Pancreatic Beta Cell Adaptation to Metabolic Stress by Controlling the Unfolded Protein Response. Cell Rep 2016; 15:1051-1061. [DOI: 10.1016/j.celrep.2016.03.079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 02/02/2016] [Accepted: 03/22/2016] [Indexed: 01/01/2023] Open
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Abstract
Inborn errors of metabolism (IEM) are not unlike common diseases. They often present as a spectrum of disease phenotypes that correlates poorly with the severity of the disease-causing mutations. This greatly impacts patient care and reveals fundamental gaps in our knowledge of disease modifying biology. Systems biology approaches that integrate multi-omics data into molecular networks have significantly improved our understanding of complex diseases. Similar approaches to study IEM are rare despite their complex nature. We highlight that existing common disease-derived datasets and networks can be repurposed to generate novel mechanistic insight in IEM and potentially identify candidate modifiers. While understanding disease pathophysiology will advance the IEM field, the ultimate goal should be to understand per individual how their phenotype emerges given their primary mutation on the background of their whole genome, not unlike personalized medicine. We foresee that panomics and network strategies combined with recent experimental innovations will facilitate this.
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Affiliation(s)
- Carmen A Argmann
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA.
| | - Sander M Houten
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA.
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Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research. Cell Rep 2015; 10:1681-1691. [PMID: 25772356 DOI: 10.1016/j.celrep.2015.02.034] [Citation(s) in RCA: 348] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 02/03/2015] [Accepted: 02/13/2015] [Indexed: 11/22/2022] Open
Abstract
In recent years, tetracyclines, such as doxycycline, have become broadly used to control gene expression by virtue of the Tet-on/Tet-off systems. However, the wide range of direct effects of tetracycline use has not been fully appreciated. We show here that these antibiotics induce a mitonuclear protein imbalance through their effects on mitochondrial translation, an effect that likely reflects the evolutionary relationship between mitochondria and proteobacteria. Even at low concentrations, tetracyclines induce mitochondrial proteotoxic stress, leading to changes in nuclear gene expression and altered mitochondrial dynamics and function in commonly used cell types, as well as worms, flies, mice, and plants. Given that tetracyclines are so widely applied in research, scientists should be aware of their potentially confounding effects on experimental results. Furthermore, these results caution against extensive use of tetracyclines in livestock due to potential downstream impacts on the environment and human health.
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A method to identify and validate mitochondrial modulators using mammalian cells and the worm C. elegans. Sci Rep 2014; 4:5285. [PMID: 24923838 PMCID: PMC4055904 DOI: 10.1038/srep05285] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/21/2014] [Indexed: 12/21/2022] Open
Abstract
Mitochondria are semi-autonomous organelles regulated by a complex network of proteins that are vital for many cellular functions. Because mitochondrial modulators can impact many aspects of cellular homeostasis, their identification and validation has proven challenging. It requires the measurement of multiple parameters in parallel to understand the exact nature of the changes induced by such compounds. We developed a platform of assays scoring for mitochondrial function in two complementary models systems, mammalian cells and C. elegans. We first optimized cell culture conditions and established the mitochondrial signature of 1,200 FDA-approved drugs in liver cells. Using cell-based and C. elegans assays, we further defined the metabolic effects of two pharmacological classes that emerged from our hit list, i.e. imidazoles and statins. We found that these two drug classes affect respiration through different and cholesterol-independent mechanisms in both models. Our screening strategy enabled us to unequivocally identify compounds that have toxic or beneficial effects on mitochondrial activity. Furthermore, the cross-species approach provided novel mechanistic insight and allowed early validation of hits that act on mitochondrial function.
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Mottis A, Jovaisaite V, Auwerx J. The mitochondrial unfolded protein response in mammalian physiology. Mamm Genome 2014; 25:424-33. [PMID: 24898297 DOI: 10.1007/s00335-014-9525-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/06/2014] [Indexed: 12/27/2022]
Abstract
Mitochondria, the main site of cellular energy harvesting, are derived from proteobacteria that evolved within our cells in endosymbiosis. Mitochondria retained vestiges of their proteobacterial genome, the circular mitochondrial DNA, which encodes 13 subunits of the oxidative phosphorylation multiprotein complexes in the electron transport chain (ETC), while the remaining ~80 ETC components are encoded in the nuclear DNA (nDNA). A further ~1,400 proteins, which are essential for mitochondrial function are also encoded in nDNA. Thus, a majority of mitochondrial proteins are translated in the cytoplasm, then imported, processed, and assembled in the mitochondria. An intricate protein quality control (PQC) network, constituted of chaperones and proteases that refold or degrade defective proteins, maintains mitochondrial proteostasis and ensures the cell and organism health. The mitochondrial unfolded protein response is a relatively recently discovered PQC pathway, which senses the proteostatic disturbances specifically in the mitochondria and resolves the stress by retrograde signaling to the nucleus and consequent transcriptional activation of protective genes. This PQC system does not only transiently resolve the local stress but also can have long-lasting effects on whole body metabolism, fitness, and longevity. A delicate tuning of its activation levels might constitute a treatment of various diseases, such as metabolic diseases, cancer, and neurodegenerative disorders.
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Affiliation(s)
- Adrienne Mottis
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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14
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Metabolic characterization of a Sirt5 deficient mouse model. Sci Rep 2013; 3:2806. [PMID: 24076663 PMCID: PMC3786297 DOI: 10.1038/srep02806] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 09/12/2013] [Indexed: 12/14/2022] Open
Abstract
Sirt5, localized in the mitochondria, is a member of sirtuin family of NAD+-dependent deacetylases. Sirt5 was shown to deacetylate and activate carbamoyl phosphate synthase 1. Most recently, Sirt5 was reported to be the predominant protein desuccinylase and demalonylase in the mitochondria because the ablation of Sirt5 enhanced the global succinylation and malonylation of mitochondrial proteins, including many metabolic enzymes. In order to determine the physiological role of Sirt5 in metabolic homeostasis, we generated a germline Sirt5 deficient (Sirt5−/−) mouse model and performed a thorough metabolic characterization of this mouse line. Although a global protein hypersuccinylation and elevated serum ammonia during fasting were observed in our Sirt5−/− mouse model, Sirt5 deficiency did not lead to any overt metabolic abnormalities under either chow or high fat diet conditions. These observations suggest that Sirt5 is likely to be dispensable for the metabolic homeostasis under the basal conditions.
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15
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Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW, Auwerx J. Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 2013; 497:451-7. [PMID: 23698443 PMCID: PMC3663447 DOI: 10.1038/nature12188] [Citation(s) in RCA: 808] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 04/15/2013] [Indexed: 11/09/2022]
Abstract
Longevity is regulated by a network of intimately linked metabolic systems. We used a combination of mouse population genetics and RNAi in C. elegans to identify mitochondrial ribosomal protein S5 (Mrps5) and other mitochondrial ribosomal proteins (MRPs) as metabolic and longevity regulators. MRP knockdown triggers mitonuclear protein imbalance, reducing mitochondrial respiration and activating the mitochondrial unfolded protein response (UPRmt). Specific antibiotics targeting mitochondrial translation and ethidium bromide, which impairs mitochondrial DNA transcription, pharmacologically mimic mrp knockdown and extend lifespan by inducing mitonuclear protein imbalance, also in mammalian cells. In addition, resveratrol and rapamycin, longevity compounds acting on different molecular targets, similarly induced mitonuclear protein imbalance, UPRmt and lifespan extention in C. elegans. Collectively these data demonstrate that MRPs represent an evolutionary conserved protein family that ties the mitochondrial ribosome and mitonuclear protein imbalance to UPRmt, an overarching longevity pathway across multiple species.
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Affiliation(s)
- Riekelt H Houtkooper
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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16
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Sokolović A, Montenegro-Miranda PS, de Waart DR, Cappai RMN, Duijst S, Sokolović M, Bosma PJ. Overexpression of insulin like growth factor binding protein 5 reduces liver fibrosis in chronic cholangiopathy. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1822:996-1003. [PMID: 22434064 DOI: 10.1016/j.bbadis.2012.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/12/2012] [Accepted: 02/26/2012] [Indexed: 01/01/2023]
Abstract
The ATP-binding cassette, sub-family B member 4 knock-out mouse (Abcb4(-/-)) is a relevant model for chronic cholangiopathy in man. Due to the lack of this P-glycoprotein in the canalicular membrane of hepatocytes, the secretion of phospholipids into bile is absent, resulting in increased bile toxicity. Expression of insulin like growth factor binding protein 5 (Igfbp5) increases in time in the livers of these mice. It is unclear whether this induction is a consequence of or plays a role in the progression of liver pathology. The aim of this study was therefore to investigate the effect of IGFBP5 induction on the progression of liver fibrosis caused by chronic cholangiopathy. IGFBP5 and, as a control, green fluorescent protein were overexpressed in the hepatocytes of Abcb4(-/-) mice, using an adeno-associated viral vector (AAV). Progression of liver fibrosis was studied 3, 6, and 12 weeks after vector injection by analyzing serum parameters, collagen deposition, expression of pro-fibrotic genes, inflammation and oxidative stress. A single administration of the AAV vectors provided prolonged expression of IGFBP5 and GFP in the livers of Abcb4(-/-) mice. Compared to GFP control, fractional liver weight, extracellular matrix deposition and amount of activated hepatic stellate cells significantly decreased in IGFBP5 overexpressing mice even 12 weeks after treatment. This effect was not due to a change in bile composition, but driven by reduced inflammation, oxidative stress, and proliferation. Overexpression of IGFBP5 seems to have a protective effect on liver pathology in this model for chronic cholangiopathy.
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Affiliation(s)
- Aleksandar Sokolović
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, The Netherlands.
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17
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Muscle or liver-specific Sirt3 deficiency induces hyperacetylation of mitochondrial proteins without affecting global metabolic homeostasis. Sci Rep 2012; 2:425. [PMID: 22645641 PMCID: PMC3361023 DOI: 10.1038/srep00425] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/14/2012] [Indexed: 01/07/2023] Open
Abstract
Sirt3 is a mitochondrial sirtuin, predominantly expressed in highly metabolic tissues. Germline ablation of Sirt3 has major metabolic consequences, including increased susceptibility to metabolic damage and oxidative stress after high fat feeding. In order to determine the contribution of liver and skeletal muscle to these phenotypes, we generated muscle-specific Sirt3 (Sirt3skm−/−) and liver-specific Sirt3 (Sirt3hep−/−) knock-out mice. Despite a marked global hyperacetylation of mitochondrial proteins, Sirt3skm−/− and Sirt3hep−/− mice did not manifest any overt metabolic phenotype under either chow or high fat diet conditions. Similarly, there was no evidence for increased oxidative stress in muscle or liver when Sirt3 was ablated in a tissue-specific manner. These observations suggest that the mitochondrial hyperacetylation induced by Sirt3-deletion in a tissue specific manner is not necessarily linked to mitochondrial dysfunction and does not recapitulate the metabolic abnormalities observed in the germline Sirt3 knock-out mice.
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18
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NCoR1 is a conserved physiological modulator of muscle mass and oxidative function. Cell 2012; 147:827-39. [PMID: 22078881 DOI: 10.1016/j.cell.2011.10.017] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 08/09/2011] [Accepted: 10/06/2011] [Indexed: 02/08/2023]
Abstract
Transcriptional coregulators control the activity of many transcription factors and are thought to have wide-ranging effects on gene expression patterns. We show here that muscle-specific loss of nuclear receptor corepressor 1 (NCoR1) in mice leads to enhanced exercise endurance due to an increase of both muscle mass and of mitochondrial number and activity. The activation of selected transcription factors that control muscle function, such as MEF2, PPARβ/δ, and ERRs, underpins these phenotypic alterations. NCoR1 levels are decreased in conditions that require fat oxidation, resetting transcriptional programs to boost oxidative metabolism. Knockdown of gei-8, the sole C. elegans NCoR homolog, also robustly increased muscle mitochondria and respiration, suggesting conservation of NCoR1 function. Collectively, our data suggest that NCoR1 plays an adaptive role in muscle physiology and that interference with NCoR1 action could be used to improve muscle function.
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Induction of oxidative stress, DNA damage and apoptosis in mouse liver after sub-acute oral exposure to zinc oxide nanoparticles. Mutat Res 2011; 745:84-91. [PMID: 22198329 DOI: 10.1016/j.mrgentox.2011.12.009] [Citation(s) in RCA: 285] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 12/17/2022]
Abstract
Zinc oxide (ZnO) nanoparticles are finding applications in a wide range of products including cosmetics, food packaging, imaging, etc. This increases the likelihood of human exposure to these nanoparticles through dermal, inhalation and oral routes. Presently, the majority of the studies concerning ZnO nanoparticle toxicity have been conducted using in vitro systems which lack the complex cell-cell, cell-matrix interactions and hormonal effects found in the in vivo scenario. The present in vivo study in mice was aimed at investigating the oral toxicity of ZnO nanoparticles. Our results showed a significant accumulation of nanoparticles in the liver leading to cellular injury after sub-acute oral exposure of ZnO nanoparticles (300 mg/kg) for 14 consecutive days. This was evident by the elevated alanine aminotransferase (ALT) and alkaline phosphatase (ALP) serum levels and pathological lesions in the liver. ZnO nanoparticles were also found to induce oxidative stress indicated by an increase in lipid peroxidation. The DNA damage in the liver and kidney cells of mice was evaluated by the Fpg-modified Comet assay which revealed a significant (p<0.05) increase in the Fpg-specific DNA lesions in liver indicating oxidative stress as the cause of DNA damage. The TUNEL assay revealed an induction of apoptosis in the liver of mice exposed to ZnO nanoparticles compared to the control. Our results conclusively demonstrate that sub-acute oral exposure to ZnO nanoparticles in mice leads to an accumulation of nanoparticles in the liver causing oxidative stress mediated DNA damage and apoptosis. These results also suggest the need for a complete risk assessment of any new engineered nanoparticle before its arrival into the consumer market.
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Jiang M, Strand DW, Franco OE, Clark PE, Hayward SW. PPARγ: a molecular link between systemic metabolic disease and benign prostate hyperplasia. Differentiation 2011; 82:220-36. [PMID: 21645960 PMCID: PMC3174339 DOI: 10.1016/j.diff.2011.05.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/02/2011] [Accepted: 05/04/2011] [Indexed: 11/26/2022]
Abstract
The emergent epidemic of metabolic syndrome and its complex list of sequelae mandate a more thorough understanding of benign prostatic hyperplasia and lower urinary tract symptoms (BPH/LUTS) in the context of systemic metabolic disease. Here we discuss the nature and origins of BPH, examine its role as a component of LUTS and review retrospective clinical studies that have drawn associations between BPH/LUTS and type II diabetes, inflammation and dyslipidemia. PPARγ signaling, which sits at the nexus of systemic metabolic disease and BPH/LUTS through its regulation of inflammation and insulin resistance, is proposed as a candidate for molecular manipulation in regard to BPH/LUTS. Finally, we introduce new cell and animal models that are being used to study the consequences of obesity, diabetes and inflammation on benign prostatic growth.
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Affiliation(s)
- Ming Jiang
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Douglas W. Strand
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Omar E. Franco
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Peter E. Clark
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Simon W. Hayward
- Department of Urologic Surgery, Vanderbilt University Medical Center, Nashville, TN
- Department of Cancer Biology, Vanderbilt-Ingram Cancer Center, Nashville, TN
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21
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Disease embryo development network reveals the relationship between disease genes and embryo development genes. J Theor Biol 2011; 287:100-8. [PMID: 21824480 PMCID: PMC7094120 DOI: 10.1016/j.jtbi.2011.07.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 06/15/2011] [Accepted: 07/22/2011] [Indexed: 11/20/2022]
Abstract
A basic problem for contemporary biology and medicine is exploring the correlation between human disease and underlying cellular mechanisms. For a long time, several efforts were made to reveal the similarity between embryo development and disease process, but few from the system level. In this article, we used the human protein-protein interactions (PPIs), disease genes with their classifications and embryo development genes and reconstructed a human disease-embryo development network to investigate the relationship between disease genes and embryo development genes. We found that disease genes and embryo development genes are prone to connect with each other. Furthermore, diseases can be categorized into three groups according to the closeness with embryo development in gene overlapping, interacting pattern in PPI network and co-regulated by microRNAs or transcription factors. Embryo development high-related disease genes show their closeness with embryo development at least in three biological levels. But it is not for embryo development medium-related disease genes and embryo development low-related disease genes. We also found that embryo development high-related disease genes are more central than other disease genes in the human PPI network. In addition, the results show that embryo development high-related disease genes tend to be essential genes compared with other diseases' genes. This network-based approach could provide evidence for the intricate correlation between disease process and embryo development, and help to uncover potential mechanisms of human complex diseases.
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22
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Assessment of subclinical, toxicant-induced hepatic gene expression profiles after low-dose, short-term exposures in mice. Regul Toxicol Pharmacol 2011; 60:54-72. [DOI: 10.1016/j.yrtph.2011.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 02/09/2011] [Accepted: 02/09/2011] [Indexed: 12/19/2022]
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23
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Gofflot F, Wendling O, Chartoire N, Birling MC, Warot X, Auwerx J. Characterization and Validation of Cre-Driver Mouse Lines. CURRENT PROTOCOLS IN MOUSE BIOLOGY 2011; 1:1-15. [PMID: 26068985 DOI: 10.1002/9780470942390.mo100103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Conditional gene manipulations in mice are increasingly popular strategies in biomedical research. These approaches rely on the production of conditional genetically engineered mutant mouse (GEMM) lines with mutations in protein-encoding genes. These conditional GEMMs are then bred with one or several transgenic mouse lines expressing a site-specific recombinase, most often the Cre recombinase, in a tissue-specific manner. Conditional GEMMs can only be exploited if Cre transgenic mouse lines are available to generate somatic mutations, and thus the number of Cre transgenic lines has significantly increased over the last 15 years. Once produced, these transgenic lines must be validated for reliable, efficient, and specific Cre expression and Cre-mediated recombination. In this overview, the minimum level of information that is ideally required to validate a Cre-driver transgenic line is first discussed. The vagaries associated with validation procedures are considered next, and some solutions are proposed to assess the expression and activity of constitutive or inducible Cre recombinase before undertaking extensive breeding experiments and exhaustive phenotyping. Curr. Protoc. Mouse Biol. 1:1-15. © 2011 by John Wiley & Sons, Inc.
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Affiliation(s)
- Françoise Gofflot
- Institut Clinique de la Souris (ICS), Illkirch, France.,Université Catholique de Louvain, Life Science Institute, Louvain-la-Neuve, Belgium
| | - Olivia Wendling
- Institut Clinique de la Souris (ICS), Illkirch, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université Louis Pasteur, Illkirch, France
| | | | | | - Xavier Warot
- Institut Clinique de la Souris (ICS), Illkirch, France.,Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Institut Clinique de la Souris (ICS), Illkirch, France.,Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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24
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Likić VA, McConville MJ, Lithgow T, Bacic A. Systems biology: the next frontier for bioinformatics. Adv Bioinformatics 2011; 2010:268925. [PMID: 21331364 PMCID: PMC3038413 DOI: 10.1155/2010/268925] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 11/01/2010] [Indexed: 01/01/2023] Open
Abstract
Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i) mathematical and computational modeling; (ii) the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii) the use of near-comprehensive data sets derived from 'omics platform technologies, in particular "downstream" technologies relative to genome sequencing, including transcriptomics, proteomics and metabolomics. The future progress in understanding biological principles will increasingly depend on the development of temporal and spatial analytical techniques that will provide high-resolution data for systems analyses. To date, particularly successful were strategies involving (a) quantitative measurements of cellular components at the mRNA, protein and metabolite levels, as well as in vivo metabolic reaction rates, (b) development of mathematical models that integrate biochemical knowledge with the information generated by high-throughput experiments, and (c) applications to microbial organisms. The inevitable role bioinformatics plays in modern systems biology puts mathematical and computational sciences as an equal partner to analytical and experimental biology. Furthermore, mathematical and computational models are expected to become increasingly prevalent representations of our knowledge about specific biochemical systems.
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Affiliation(s)
- Vladimir A. Likić
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Malcolm J. McConville
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Trevor Lithgow
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Antony Bacic
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Australian Centre for Plant Functional Genomics, School of Botany, The University of Melbourne, Parkville, VIC, 3010, Australia
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25
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Mutagenicity and genotoxicity of isatin in mammalian cells in vivo. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2011; 719:47-51. [DOI: 10.1016/j.mrgentox.2010.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 11/09/2010] [Accepted: 11/18/2010] [Indexed: 11/22/2022]
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Abstract
Genetic tests can help clinicians to diagnose rare monogenic liver diseases. For most common liver diseases, however, multiple gene variants that have small to moderate individual phenotypic effects contribute to the overall risk of disease. An individual's level of risk depends on interactions between environmental factors and a wide range of modifier genes, which are yet to be identified systematically. The latest genome-wide association studies in large cohorts of patients with gallstones, fatty liver disease, viral hepatitis, chronic cholestatic liver diseases or drug-induced liver injury have provided new insights into the pathophysiology of these illnesses and have suggested the contribution of previously unsuspected pathogenic pathways. Studies in mouse models have identified further susceptibility genes for several complex liver diseases. As a result, in the future polygenic risk scores might help to define subgroups of patients at risk of developing liver diseases who would benefit from preventative measures and/or personalized therapy. Now that whole-genome sequencing is possible, comprehensive strategies for integrating genomic data and counseling of patients need to be developed.
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27
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Kim IY, Shin JH, Seong JK. Mouse phenogenomics, toolbox for functional annotation of human genome. BMB Rep 2010; 43:79-90. [PMID: 20193125 DOI: 10.5483/bmbrep.2010.43.2.079] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mouse models are crucial for the functional annotation of human genome. Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of human diseases. Several international consortium and programs are under way to deliver mutations in every gene in mouse genome. The information from studying these GEM can be shared through international collaboration. However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing and evaluating data from GEM. The recent improvement in mouse genetics has now moved the bottleneck in mouse functional genomics from the production of GEM to the systematic mouse phenotype analysis of GEM. Enhanced, reproducible and comprehensive mouse phenotype analysis has thus emerged as a prerequisite for effectively engaging the phenotyping bottleneck. In this review, current information on systematic mouse phenotype analysis and an issue-oriented perspective will be provided.
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Affiliation(s)
- Il Yong Kim
- Laboratory of Developmental Biology and Genomics, BK21 Program for Veterinary Science, Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
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28
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Chrispell JD, Feathers KL, Kane MA, Kim CY, Brooks M, Khanna R, Kurth I, Hübner CA, Gal A, Mears AJ, Swaroop A, Napoli JL, Sparrow JR, Thompson DA. Rdh12 activity and effects on retinoid processing in the murine retina. J Biol Chem 2009; 284:21468-77. [PMID: 19506076 PMCID: PMC2755871 DOI: 10.1074/jbc.m109.020966] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 06/04/2009] [Indexed: 11/06/2022] Open
Abstract
RDH12 mutations are responsible for early-onset autosomal recessive retinal dystrophy, which results in profound retinal pathology and severe visual handicap in patients. To investigate the function of RDH12 within the network of retinoid dehydrogenases/reductases (RDHs) present in retina, we studied the retinal phenotype of Rdh12-deficient mice. In vivo rates of all-trans-retinal reduction and 11-cis-retinal formation during recovery from bleaching were similar in Rdh12-deficient and wild-type mice matched for an Rpe65 polymorphism that impacts visual cycle efficiency. However, retinal homogenates from Rdh12-deficient mice exhibited markedly decreased capacity to reduce exogenous retinaldehydes in vitro. Furthermore, in vivo levels of the bisretinoid compound diretinoid-pyridinium-ethanolamine (A2E) were increased in Rdh12-deficient mice of various genetic backgrounds. Conversely, in vivo levels of retinoic acid and total retinol were significantly decreased. Rdh12 transcript levels in wild-type mice homozygous for the Rpe65-Leu(450) polymorphism were greater than in Rpe65-Met(450) mice and increased during postnatal development in wild-type mice and Nrl-deficient mice having an all-cone retina. Rdh12-deficient mice did not exhibit increased retinal degeneration relative to wild-type mice at advanced ages, when bred on the light-sensitive BALB/c background, or when heterozygous for a null allele of superoxide dismutase 2 (Sod2(+/-)). Our findings suggest that a critical function of RDH12 is the reduction of all-trans-retinal that exceeds the reductive capacity of the photoreceptor outer segments.
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Affiliation(s)
| | - Kecia L. Feathers
- Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Maureen A. Kane
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
| | - Chul Y. Kim
- Departments of Ophthalmology and Pathology and Cell Biology, Columbia University, New York, New York 10032
| | - Matthew Brooks
- Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan 48105
- Neurobiology-Neurodegeneration and Repair Laboratory, NEI, National Institutes of Health, Bethesda, Maryland 20892
| | - Ritu Khanna
- Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Ingo Kurth
- Institute of Human Genetics, University of Hamburg-Eppendorf, D-20251 Hamburg, Germany
| | - Christian A. Hübner
- Department of Clinical Chemistry, Friedrich-Schiller-Universität, D-07747 Jena, Germany
| | - Andreas Gal
- Institute of Human Genetics, University of Hamburg-Eppendorf, D-20251 Hamburg, Germany
| | - Alan J. Mears
- Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan 48105
- University of Ottawa Eye Institute and Ottawa Health Research Institute, Ottawa, Ontario K1Y 4E9, Canada, and
| | - Anand Swaroop
- Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan 48105
- Neurobiology-Neurodegeneration and Repair Laboratory, NEI, National Institutes of Health, Bethesda, Maryland 20892
| | - Joseph L. Napoli
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
| | - Janet R. Sparrow
- Departments of Ophthalmology and Pathology and Cell Biology, Columbia University, New York, New York 10032
| | - Debra A. Thompson
- From the Departments of Biological Chemistry and
- Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan 48105
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29
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The implications of human metabolic network topology for disease comorbidity. Proc Natl Acad Sci U S A 2008; 105:9880-5. [PMID: 18599447 DOI: 10.1073/pnas.0802208105] [Citation(s) in RCA: 335] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most diseases are the consequence of the breakdown of cellular processes, but the relationships among genetic/epigenetic defects, the molecular interaction networks underlying them, and the disease phenotypes remain poorly understood. To gain insights into such relationships, here we constructed a bipartite human disease association network in which nodes are diseases and two diseases are linked if mutated enzymes associated with them catalyze adjacent metabolic reactions. We find that connected disease pairs display higher correlated reaction flux rate, corresponding enzyme-encoding gene coexpression, and higher comorbidity than those that have no metabolic link between them. Furthermore, the more connected a disease is to other diseases, the higher is its prevalence and associated mortality rate. The network topology-based approach also helps to uncover potential mechanisms that contribute to their shared pathophysiology. Thus, the structure and modeled function of the human metabolic network can provide insights into disease comorbidity, with potentially important consequences for disease diagnosis and prevention.
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30
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van Ommen B, Keijer J, Kleemann R, Elliott R, Drevon CA, McArdle H, Gibney M, Müller M. The challenges for molecular nutrition research 2: quantification of the nutritional phenotype. GENES AND NUTRITION 2008; 3:51-9. [PMID: 18850187 DOI: 10.1007/s12263-008-0084-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2008] [Accepted: 05/26/2008] [Indexed: 12/20/2022]
Abstract
In quantifying the beneficial effect of dietary interventions in healthy subjects, nutrition research meets a number of new challenges. Inter individual variation in biomarker values often is larger than the effect related to the intervention. Healthy subjects have a remarkable capacity to maintain homeostasis, both through direct metabolic regulation, metabolic compensation of altered diets, and effective defence and repair mechanisms in oxidative and inflammatory stress. Processes involved in these regulatory activities essentially different from processes involved in early onset of diet related diseases. So, new concepts and approaches are needed to better quantify the subtle effects possibly achieved by dietary interventions in healthy subjects. Apart from quantification of the genotype and food intake (these are discussed in separate reviews in this series), four major areas of innovation are discussed: the biomarker profile concept, perturbation of homeostasis combined with omics analysis, imaging, modelling and fluxes. All of these areas contribute to a better understanding and quantification of the nutritional phenotype.
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Affiliation(s)
- Ben van Ommen
- Department of BioSciences, TNO-Quality of Life, Zeist, The Netherlands,
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Champy MF, Selloum M, Zeitler V, Caradec C, Jung B, Rousseau S, Pouilly L, Sorg T, Auwerx J. Genetic background determines metabolic phenotypes in the mouse. Mamm Genome 2008; 19:318-31. [PMID: 18392653 DOI: 10.1007/s00335-008-9107-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 03/06/2008] [Indexed: 11/30/2022]
Abstract
To evaluate the contribution of genetic background to phenotypic variation, we compared a large range of biochemical and metabolic parameters at different ages of four inbred mice strains, C57BL/6J, 129SvPas, C3HeB/FeJ, and Balb/cByJ. Our results demonstrate that important metabolic, hematologic, and biochemical differences exist between these different inbred strains. Most of these differences are gender independent and are maintained or accentuated throughout life. It is therefore imperative that the genetic background is carefully defined in phenotypic studies. Our results also argue that certain backgrounds are more suited to study a given physiologic phenomenon, as distinct mouse strains have a different propensity to develop particular biochemical, hematologic, and metabolic abnormalities. These genetic differences can furthermore be exploited to identify new genes/proteins that contribute to phenotypic abnormalities. The choice of the genetic background in which to generate and analyze genetically engineered mutant mice is important as it is, together with environmental factors, one of the most important contributors to the variability of phenotypic results.
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Argmann CA, Dierich A, Auwerx J. Uses of forward and reverse genetics in mice to study gene function. ACTA ACUST UNITED AC 2008; Chapter 29:Unit 29A.1. [PMID: 18265381 DOI: 10.1002/0471142727.mb29a01s73] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
As the focus of human genetics shifts from Mendelian traits to complex diseases, a sophisticated genetic tool kit-with space for genetics (classical, molecular, statistical, and quantitative), metabolics, proteomics, bioinformatics, and mathematics-is required to elucidate their multifactorial traits and regulatory processes. Importantly, mouse resources optimized to study the actions of isolated genetic loci on a fixed background are insufficient on their own for studying intact polygenic networks and genetic interactions, and researchers must work in the context of experimental model systems that optimally mimic the genetic structure of human populations. The success of such phenogenomic approaches depend on the efficacy by which specific mutations (gene targeting) and variability (recombinant inbreeding) can be introduced into the mouse genome, and on the optimization of phenotyping analyses of the mutant mouse lines. This unit describes the basic genetic approaches used to in the study of mouse model systems.
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Affiliation(s)
- Carmen A Argmann
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
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Fearnside JF, Dumas ME, Rothwell AR, Wilder SP, Cloarec O, Toye A, Blancher C, Holmes E, Tatoud R, Barton RH, Scott J, Nicholson JK, Gauguier D. Phylometabonomic patterns of adaptation to high fat diet feeding in inbred mice. PLoS One 2008; 3:e1668. [PMID: 18301746 PMCID: PMC2244706 DOI: 10.1371/journal.pone.0001668] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 01/25/2008] [Indexed: 11/18/2022] Open
Abstract
Insulin resistance plays a central role in type 2 diabetes and obesity, which develop as a consequence of genetic and environmental factors. Dietary changes including high fat diet (HFD) feeding promotes insulin resistance in rodent models which present useful systems for studying interactions between genetic background and environmental influences contributing to disease susceptibility and progression. We applied a combination of classical physiological, biochemical and hormonal studies and plasma 1H NMR spectroscopy-based metabonomics to characterize the phenotypic and metabotypic consequences of HFD (40%) feeding in inbred mouse strains (C57BL/6, 129S6, BALB/c, DBA/2, C3H) frequently used in genetic studies. We showed the wide range of phenotypic and metabonomic adaptations to HFD across the five strains and the increased nutrigenomic predisposition of 129S6 and C57BL/6 to insulin resistance and obesity relative to the other strains. In contrast mice of the BALB/c and DBA/2 strains showed relative resistance to HFD-induced glucose intolerance and obesity. Hierarchical metabonomic clustering derived from 1H NMR spectral data of the strains provided a phylometabonomic classification of strain-specific metabolic features and differential responses to HFD which closely match SNP-based phylogenetic relationships between strains. Our results support the concept of genomic clustering of functionally related genes and provide important information for defining biological markers predicting spontaneous susceptibility to insulin resistance and pathological adaptations to fat feeding.
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Affiliation(s)
- Jane F. Fearnside
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Marc-Emmanuel Dumas
- Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Department of Biomolecular Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
- Centre Européen de Résonance Magnétique Nucléaire à Très Hauts Champs à Lyon (CRMN Lyon) (FRE 3008), Laboratory of Chemistry (UMR 5185), Ecole Normale Supérieure de Lyon, Lyon, France
| | - Alice R. Rothwell
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Steven P. Wilder
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Olivier Cloarec
- Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Department of Biomolecular Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ayo Toye
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Christine Blancher
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elaine Holmes
- Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Department of Biomolecular Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Roger Tatoud
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Richard H. Barton
- Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Department of Biomolecular Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - James Scott
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jeremy K. Nicholson
- Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Department of Biomolecular Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dominique Gauguier
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- *E-mail:
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Masson R, Sorg T, Warot X. Génomique fonctionnelle de la souris : la dynamique européenne. Med Sci (Paris) 2007; 23:877-9. [DOI: 10.1051/medsci/20072310877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Volle DH, Duggavathi R, Magnier BC, Houten SM, Cummins CL, Lobaccaro JMA, Verhoeven G, Schoonjans K, Auwerx J. The small heterodimer partner is a gonadal gatekeeper of sexual maturation in male mice. Genes Dev 2007; 21:303-15. [PMID: 17289919 PMCID: PMC1785120 DOI: 10.1101/gad.409307] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The small heterodimer partner (SHP) is an atypical nuclear receptor known mainly for its role in bile acid homeostasis in the enterohepatic tract. We explore here the role of SHP in the testis. SHP is expressed in the interstitial compartment of the adult testes, which contain the Leydig cells. SHP there inhibits the expression of steroidogenic genes, on the one hand by inhibiting the expression of the nuclear receptors steroidogenic factor-1 and liver receptor homolog-1 (lrh-1), and on the other hand by directly repressing the transcriptional activity of LRH-1. Consequently, in SHP knockout mice, testicular testosterone synthesis is increased independently of the hypothalamus-pituitary axis. Independent of its action on androgen synthesis, SHP also determines the timing of germ cell differentiation by controlling testicular retinoic acid metabolism. Through the inhibition of the transcriptional activity of retinoic acid receptors, SHP controls the expression of stimulated by retinoic acid gene 8 (stra8) - a gene that is indispensable for germ cell meiosis and differentiation. Together, our data demonstrate new roles for SHP in testicular androgen and retinoic acid metabolism, making SHP a testicular gatekeeper of the timing of male sexual maturation.
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Affiliation(s)
- David H. Volle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)/Institut National de la Santé et de la Recherche Médicale (INSERM)/Université Louis Pasteur (ULP), 67404 Illkirch, France
| | - Rajesha Duggavathi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)/Institut National de la Santé et de la Recherche Médicale (INSERM)/Université Louis Pasteur (ULP), 67404 Illkirch, France
| | - Benjamin C. Magnier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)/Institut National de la Santé et de la Recherche Médicale (INSERM)/Université Louis Pasteur (ULP), 67404 Illkirch, France
| | - Sander M. Houten
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)/Institut National de la Santé et de la Recherche Médicale (INSERM)/Université Louis Pasteur (ULP), 67404 Illkirch, France
| | - Carolyn L. Cummins
- Department of Pharmacology and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jean-Marc A. Lobaccaro
- Laboratoire de Physiologie Comparée et Endocrinologie Moléculaire, UMR CNRS 6547, 63177 Aubière, France
| | - Guido Verhoeven
- Laboratory for Experimental Medecine and Endocrinology, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Kristina Schoonjans
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)/Institut National de la Santé et de la Recherche Médicale (INSERM)/Université Louis Pasteur (ULP), 67404 Illkirch, France
| | - Johan Auwerx
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)/Institut National de la Santé et de la Recherche Médicale (INSERM)/Université Louis Pasteur (ULP), 67404 Illkirch, France
- Institut Clinique de la Souris (ICS), 67404 Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Laboratoire de Biochimie Générale et Spécialisée, 67000 Strasbourg, France
- Corresponding author.E-MAIL ; FAX 33-3-88653201
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Kurth I, Thompson DA, Rüther K, Feathers KL, Chrispell JD, Schroth J, McHenry CL, Schweizer M, Skosyrski S, Gal A, Hübner CA. Targeted disruption of the murine retinal dehydrogenase gene Rdh12 does not limit visual cycle function. Mol Cell Biol 2007; 27:1370-9. [PMID: 17130236 PMCID: PMC1800705 DOI: 10.1128/mcb.01486-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 09/22/2006] [Accepted: 11/16/2006] [Indexed: 11/20/2022] Open
Abstract
RDH12 codes for a member of the family of short-chain alcohol dehydrogenases/reductases proposed to function in the visual cycle that supplies the chromophore 11-cis retinal to photoreceptor cells. Mutations in RDH12 cause severe and progressive childhood onset autosomal-recessive retinal dystrophy, including Leber congenital amaurosis. We generated Rdh12 knockout mice, which exhibited grossly normal retinal histology at 10 months of age. Levels of all-trans and 11-cis retinoids in dark- and light-adapted animals and scotopic and photopic electroretinogram (ERG) responses were similar to those for the wild type, as was recovery of the ERG response following bleaching, for animals matched for an Rpe65 polymorphism (p.L450M). Lipid peroxidation products and other measures of oxidative stress did not appear to be elevated in Rdh12(-/-) animals. RDH12 was localized to photoreceptor inner segments and the outer nuclear layer in both mouse and human retinas by immunohistochemistry. The present findings, together with those of earlier studies showing only minor functional deficits in mice deficient for Rdh5, Rdh8, or Rdh11, suggest that the activity of any one isoform is not rate limiting in the visual response.
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Affiliation(s)
- Ingo Kurth
- Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Butenfeld 42, 22529 Hamburg, Germany
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Davey RA, MacLean HE. Current and future approaches using genetically modified mice in endocrine research. Am J Physiol Endocrinol Metab 2006; 291:E429-38. [PMID: 16684850 DOI: 10.1152/ajpendo.00124.2006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetically modified mouse models have been used widely to advance our knowledge in the field of endocrinology and metabolism. A number of different approaches to generate genetically modified mice are now available, which provide the power to analyze the role of individual proteins in vivo. However, there are a number of points to be considered in the use and interpretation of these models. This review discusses the advantages and disadvantages involved in the generation and use of different genetically modified mouse models in endocrine research, including conventional techniques (e.g., overexpression, knockout, and knock-in models), tissue- and/or time-specific deletion of target genes [e.g., Cre-loxP and short interfering (si)RNA transgenic approaches], and gene-trap approaches to undertake functional genomics. This review also highlights the many factors that should be considered when assessing the phenotype of these mouse models, many of which are relevant to all murine physiological studies. These approaches are a powerful means by which to dissect the function of genes and are revolutionizing our understanding of endocrine physiology and metabolism.
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Affiliation(s)
- Rachel A Davey
- Dept. of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
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Mutch DM, Crespy V, Clough J, Henderson CJ, Lariani S, Mansourian R, Moulin J, Wolf CR, Williamson G. Hepatic cytochrome P-450 reductase-null mice show reduced transcriptional response to quercetin and reveal physiological homeostasis between jejunum and liver. Am J Physiol Gastrointest Liver Physiol 2006; 291:G63-72. [PMID: 16455785 DOI: 10.1152/ajpgi.00565.2005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Using mice deficient in hepatic cytochrome P-450 oxidoreductase (POR), which disables the liver cytochrome P-450 system, we examined the metabolism and biological response of the anticarcinogenic flavonoid, quercetin. Profiling circulating metabolites revealed similar profiles over 72 h in wild-type (WT) and POR-null (KO) mice, showing that hepatic P450 and reduced biliary secretion do not affect quercetin metabolism. Transcriptional profiling at 24 h revealed that two- to threefold more genes responded significantly to quercetin in WT compared with KO in the jejunum, ileum, colon, and liver, suggesting that hepatic P450s mediate many of the biological effects of quercetin, such as immune function, estrogen receptor signaling, and lipid, glutathione, purine, and amino acid metabolism, even though quercetin metabolism is not modified. The functional interpretation of expression data in response to quercetin (single dose of 7 mg/animal) revealed a molecular relationship between the liver and jejunum. In WT animals, amino acid and sterol metabolism was predominantly modulated in the liver, fatty acid metabolism response was shared between the liver and jejunum, and glutathione metabolism was modulated in the small intestine. In contrast, KO animals do not regulate amino acid metabolism in the liver or small intestine, they share the control of fatty acid metabolism between the liver and jejunum, and regulation of sterol metabolism is shifted from the liver to the jejunum and that of glutathione metabolism from the jejunum to the liver. This demonstrates that the quercetin-mediated regulation of these biological functions in extrahepatic tissues is dependent on the functionality of the liver POR. In conclusion, using a systems biology approach to explore the contribution of hepatic phase 1 detoxification on quercetin metabolism demonstrated the resiliency and adaptive capacity of a biological organism in dealing with a bioactive nutrient when faced with a tissue-specific molecular dysfunction.
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Affiliation(s)
- David M Mutch
- Nutrient Bioavailability, Nestlé Research Center Vers-Chez-Les-Blanc, Lausanne 26, Switzerland
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