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Beirow K, Schmidt C, Jürgen B, Schlüter R, Schweder T, Bednarski PJ. Investigation of TGF-α-overexpressing mouse hepatocytes (TAMH) cultured as spheroids for use in hepatotoxicity screening of drug candidates. J Appl Toxicol 2024; 44:272-286. [PMID: 37655636 DOI: 10.1002/jat.4538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
The immortalized mouse liver cell line TAMH has been described as a valuable tool for studying hepatotoxic mechanisms, but until now, it has only been reported to grow as a monolayer in culture. However, culturing hepatocytes as three-dimensional (3D) spheroids has been shown to result in improved liver-specific functions (e.g., metabolic capacity) by better mimicking the in vivo environment. This approach may lead to more reliable detection of drug-induced liver injury (DILI) in the early phase of drug discovery, preventing post-marketing drug withdrawals. Here, we investigated the cultivation of TAMH as 3D spheroids, characterizing them with optical and transmission electron microscopy as well as analyzing their gene expression at mRNA level (especially drug-metabolizing enzymes) compared to TAMH monolayer. In addition, comparisons were made with spheroids grown from the human hepatoblastoma cell line HepG2, another current spheroid model. The results indicate that TAMH spheroids express hepatic structures and show elevated levels of some of the key phase I and II drug-metabolizing enzymes, in contrast to TAMH monolayer. The in vitro hepatotoxic potencies of the drugs acetaminophen and flupirtine maleate were found to be very similar between TAMH spheroidal and the monolayer cultures. Both the advantages and disadvantages of TAMH spheroids as an in vitro hepatotoxicity model compared to monolayer model are discussed.
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Affiliation(s)
- Kristin Beirow
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Christian Schmidt
- Department of Pharmaceutical Biotechnology Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Britta Jürgen
- Department of Pharmaceutical Biotechnology Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Patrick J Bednarski
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
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2
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Simbula M, Manchinu MF, Mingoia M, Pala M, Asunis I, Caria CA, Perseu L, Shah M, Crossley M, Moi P, Ristaldi MS. miR-365-3p mediates BCL11A and SOX6 erythroid-specific coregulation: A new player in HbF activation. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102025. [PMID: 37744176 PMCID: PMC10514143 DOI: 10.1016/j.omtn.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Hemoglobin switching is a complex biological process not yet fully elucidated. The mechanism regulating the suppression of fetal hemoglobin (HbF) expression is of particular interest because of the positive impact of HbF on the course of diseases such as β-thalassemia and sickle cell disease, hereditary hemoglobin disorders that affect the health of countless individuals worldwide. Several transcription factors have been implicated in the control of HbF, of which BCL11A has emerged as a major player in HbF silencing. SOX6 has also been implicated in silencing HbF and is critical to the silencing of the mouse embryonic hemoglobins. BCL11A and SOX6 are co-expressed and physically interact in the erythroid compartment during differentiation. In this study, we observe that BCL11A knockout leads to post-transcriptional downregulation of SOX6 through activation of microRNA (miR)-365-3p. Downregulating SOX6 by transient ectopic expression of miR-365-3p or gene editing activates embryonic and fetal β-like globin gene expression in erythroid cells. The synchronized expression of BCL11A and SOX6 is crucial for hemoglobin switching. In this study, we identified a BCL11A/miR-365-3p/SOX6 evolutionarily conserved pathway, providing insights into the regulation of the embryonic and fetal globin genes suggesting new targets for treating β-hemoglobinopathies.
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Affiliation(s)
- Michela Simbula
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
| | - Maria Francesca Manchinu
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
| | - Maura Mingoia
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
- Dipartimento di Scienze Mediche e Sanità Pubblica, Università degli Studi di Cagliari, 09121 Cagliari, Italy
| | - Mauro Pala
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
| | - Isadora Asunis
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
| | - Cristian Antonio Caria
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
| | - Lucia Perseu
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
| | - Manan Shah
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | - Paolo Moi
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
- Dipartimento di Scienze Mediche e Sanità Pubblica, Università degli Studi di Cagliari, 09121 Cagliari, Italy
| | - Maria Serafina Ristaldi
- Istituto Di Ricerca Genetica e Biomedica del Consiglio Nazionale Delle Ricerche (IRGB-CNR), 09042 Monserrato, Italy
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3
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Shamaeizadeh N, Varshosaz J, Mirian M, Aliomrani M. Glutathione targeted tragacanthic acid-chitosan as a non-viral vector for brain delivery of miRNA-219a-5P: An in vitro/in vivo study. Int J Biol Macromol 2022; 200:543-556. [DOI: 10.1016/j.ijbiomac.2022.01.100] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/04/2022] [Accepted: 01/15/2022] [Indexed: 12/25/2022]
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4
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Mazloumfard F, Mirian M, Eftekhari SM, Aliomrani M. Hydroxychloroquine effects on miR-155-3p and miR-219 expression changes in animal model of multiple sclerosis. Metab Brain Dis 2020; 35:1299-1307. [PMID: 32860610 DOI: 10.1007/s11011-020-00609-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system which causes chronic demyelination. Hydroxychloroquine (HCQ) possess immunosuppressive and anti-inflammatory properties. The aim of this study was to investigate the effect of HCQ on miR-219 and miR-155-3p expression changes in MS-induced model. The animal model was induced by the administration of cuprizone containing food pellets (0.2%). Briefly, C57BL/6 mice were randomly divided into five groups. Group 1 received normal food and water during the study. Group 2 received cuprizone pellets for 5 weeks (demyelination phase) following one-week normal feeding during the remyelination phase. The remaining three groups received HCQ (2.5, 10 and 100 mg/kg) via drinking water during the demyelination phase. At the end of each phase, mice were deeply anesthetized, perfused with PBS through the heart, and their brains were removed. Brain sections stained with luxol fast blue and the images were analyzed. Also, the expression levels of miR-219 and miR-155-3p were evaluated by quantitative Real-Time PCR in all samples. HCQ decreased the expression of miR-155-3p and increased miR-219 expression in animals treated with 100 mg/kg of HCQ compared to the control group (p < 0.0001) and the cuprizone group (p < 0.0001). LFB method revealed a gradual increment of myelination in animals treated with 10 and 100 mg/kg of HCQ compared to the cuprizone group. Based on the obtained results of this study, HCQ can decrease microglial activity and increase oligodendrocye production by altering the expression of disease-associated miRNAs.
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Affiliation(s)
- Fatemeh Mazloumfard
- School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Mina Mirian
- Department of Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Seyed-Mehdi Eftekhari
- Department of Pathology, Azarmehr Clinical Pathology Laboratory, Isfahan, Islamic Republic of Iran
| | - Mehdi Aliomrani
- Department of Toxicology and Pharmacology and Isfahan Pharmaceutical Science Research center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
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Lenoir M, Martín R, Torres-Maravilla E, Chadi S, González-Dávila P, Sokol H, Langella P, Chain F, Bermúdez-Humarán LG. Butyrate mediates anti-inflammatory effects of Faecalibacterium prausnitzii in intestinal epithelial cells through Dact3. Gut Microbes 2020; 12:1-16. [PMID: 33054518 PMCID: PMC7567499 DOI: 10.1080/19490976.2020.1826748] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The commensal bacterium Faecalibacterium prausnitzii plays a key role in inflammatory bowel disease (IBD) pathogenesis and serves as a general health biomarker in humans. However, the host molecular mechanisms that underlie its anti-inflammatory effects remain unknown. In this study we performed a transcriptomic approach on human intestinal epithelial cells (HT-29) stimulated with TNF-α and exposed to F. prausnitzii culture supernatant (SN) in order to determine the impact of this commensal bacterium on intestinal epithelial cells. Moreover, modulation of the most upregulated gene after F. prausnitzii SN contact was validated both in vitro and in vivo. Our results showed that F. prausnitzii SN upregulates the expression of Dact3, a gene linked to the Wnt/JNK pathway. Interestingly, when we silenced Dact3 expression, the effect of F. prausnitzii SN was lost. Butyrate was identified as the F. prausnitzii effector responsible for Dact3 modulation. Dact3 upregulation was also validated in vivo in both healthy and inflamed mice treated with either F. prausnitzii SN or the live bacteria, respectively. Finally, we demonstrated by colon transcriptomics that gut microbiota directly influences Dact3 expression. This study provides new clues about the host molecular mechanisms involved in the anti-inflammatory effects of the beneficial commensal bacterium F. prausnitzii.
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Affiliation(s)
- Marion Lenoir
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Rebeca Martín
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Sead Chadi
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Harry Sokol
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France,Sorbonne Universités, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology department, F-75012Paris, France
| | - Philippe Langella
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Florian Chain
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Luis G. Bermúdez-Humarán
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France,CONTACT Luis G. Bermúdez-Humarán Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350Jouy-en-Josas, France
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6
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Benzi A, Sturla L, Heine M, Fischer AW, Spinelli S, Magnone M, Sociali G, Parodi A, Fenoglio D, Emionite L, Koch-Nolte F, Mittrücker HW, Guse AH, De Flora A, Zocchi E, Heeren J, Bruzzone S. CD38 downregulation modulates NAD + and NADP(H) levels in thermogenic adipose tissues. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1866:158819. [PMID: 33010451 DOI: 10.1016/j.bbalip.2020.158819] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/05/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022]
Abstract
Different strategies to boost NAD+ levels are considered promising means to promote healthy aging and ameliorate dysfunctional metabolism. CD38 is a NAD+-dependent enzyme involved in the regulation of different cell functions. In the context of systemic energy metabolism, it has been demonstrated that brown adipocytes, the parenchymal cells of brown adipose tissue (BAT) as well as beige adipocytes that emerge in white adipose tissue (WAT) depots in response to catabolic conditions, are important to maintain metabolic homeostasis. In this study we aim to understand the functional relevance of CD38 for NAD+ and energy metabolism in BAT and WAT, also using a CD38-/- mouse model. During cold exposure, an increase in NAD+ levels occurred in BAT of wild type mice, together with a marked downregulation of CD38, as detected at the mRNA and protein level. CD38 downregulation was observed also in WAT of cold-exposed mice, where it was accompanied by a strong increase in NADP(H) levels. Accordingly, NAD kinase and glucose-6-phosphate dehydrogenase activities were enhanced in WAT (but not in BAT). Increased NAD+ levels were observed in BAT/WAT from CD38-/- compared with wild type mice, in line with CD38 being a major NAD+-consumer in AT. CD38-/- mice kept at 6 °C had higher levels of Ucp1 and Pgc-1α in BAT and WAT, and increased levels of phosphorylated hormone-sensitive lipase in BAT, compared with wild type mice. These results demonstrate that CD38, by modulating cellular NAD(P)+ levels, is involved in the regulation of thermogenic responses in cold-activated BAT and WAT.
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Affiliation(s)
- Andrea Benzi
- DIMES-Section of Biochemistry, University of Genova, Italy
| | - Laura Sturla
- DIMES-Section of Biochemistry, University of Genova, Italy.
| | - Markus Heine
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander W Fischer
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sonia Spinelli
- DIMES-Section of Biochemistry, University of Genova, Italy
| | - Mirko Magnone
- DIMES-Section of Biochemistry, University of Genova, Italy
| | | | | | - Daniela Fenoglio
- IRCCS Ospedale Policlinico San Martino, Genova, Italy; Department of Internal Medicine, University of Genova, Italy
| | - Laura Emionite
- Animal Facility, IRCCS Ospedale Policlinico San Martino, Largo Benzi 10, 16132 Genova, Italy
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hans-Willi Mittrücker
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas H Guse
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Elena Zocchi
- DIMES-Section of Biochemistry, University of Genova, Italy
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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7
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Grabia S, Smyczynska U, Pagacz K, Fendler W. NormiRazor: tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies. BMC Bioinformatics 2020; 21:425. [PMID: 32993488 PMCID: PMC7523363 DOI: 10.1186/s12859-020-03743-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Multi-gene expression assays are an attractive tool in revealing complex regulatory mechanisms in living organisms. Normalization is an indispensable step of data analysis in all those studies, since it removes unwanted, non-biological variability from data. In targeted qPCR assays it is typically performed with respect to prespecified reference genes, but the lack of robust strategy of their selection is reported in literature, especially in studies concerning circulating microRNAs (miRNA). Unfortunately, this problem impedes translation of scientific discoveries on miRNA biomarkers into widely available laboratory assays. Previous studies concluded that averaged expressions of multi-miRNA combinations are more stable references than single genes. However, due to the number of such combinations the computational load is considerable and may be hindering for objective reference selection in large datasets. Existing implementations of normalization algorithms (geNorm, NormFinder and BestKeeper) have poor performance and may require days to compute stability values for all potential reference as the evaluation is performed sequentially. RESULTS We designed NormiRazor - an integrative tool which implements those methods in a parallel manner on a graphics processing unit (GPU) using CUDA platform. We tested our approach on publicly available miRNA expression datasets. As a result, the times of executions on 8 datasets containing from 50 to 400 miRNAs (subsets of GSE68314) decreased 18.7 ±0.6 (mean ±SD), 104.7 ±4.2 and 76.5 ±2.2 times for geNorm, BestKeeper and NormFinder with respect to previous Python implementation. To allow for easy access to normalization pipeline for biomedical researchers we implemented NormiRazor as an online platform where a user could normalize their datasets based on the automatically selected references. It is available at norm.btm.umed.pl, together with instruction manual and exemplary datasets. CONCLUSIONS NormiRazor allows for an easy, informed choice of reference genes for qPCR transcriptomic studies. As such it can improve comparability and repeatability of experiments and in longer perspective help translate newly discovered biomarkers into readily available assays.
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Affiliation(s)
- Szymon Grabia
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St., Lodz, 92-215 Poland
- Institute of Applied Computer Science, Lodz University of Technology, 18/22 Stefanowskiego St., Lodz, 90-537 Poland
| | - Urszula Smyczynska
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St., Lodz, 92-215 Poland
| | - Konrad Pagacz
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St., Lodz, 92-215 Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Zwirki i Wigury St., Warsaw, 02-091 Poland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St., Lodz, 92-215 Poland
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, 450 Brookline Av., Boston, MA 02215 USA
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8
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Kakan SS, Janga SR, Cooperman B, Craig DW, Edman MC, Okamoto CT, Hamm-Alvarez SF. Small RNA Deep Sequencing Identifies a Unique miRNA Signature Released in Serum Exosomes in a Mouse Model of Sjögren's Syndrome. Front Immunol 2020; 11:1475. [PMID: 32849505 PMCID: PMC7396589 DOI: 10.3389/fimmu.2020.01475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022] Open
Abstract
Sjögren's Syndrome (SS) is an autoimmune disease characterized by lymphocytic infiltration and loss of function of moisture-producing exocrine glands as well as systemic inflammation. SS diagnosis is cumbersome, subjective and complicated by manifestation of symptoms that overlap with those of other rheumatic and ocular diseases. Definitive diagnosis averages 4–5 years and this delay may lead to irreversible tissue damage. Thus, there is an urgent need for diagnostic biomarkers for earlier detection of SS. Extracellular vesicles called exosomes carry functional small non-coding RNAs which play a critical role in maintaining cellular homeostasis via transcriptional and translational regulation of mRNA. Alterations in levels of specific exosomal miRNAs may be predictive of disease status. Here, we have assessed serum exosomal RNA using next generation sequencing in a discovery cohort of the NOD mouse, a model of early-intermediate SS, to identify dysregulated miRNAs that may be indicative of SS. We found five miRNAs upregulated in serum exosomes of NOD mice with an adjusted p < 0.05—miRNA-127-3p, miRNA-409-3p, miRNA-410-3p, miRNA-541-5p, and miRNA-540-5p. miRNAs 127-3p and 541-5p were also statistically significantly upregulated in a validation cohort of NOD mice. Pathway analysis and existing literature indicates that differential expression of these miRNAs may dysregulate pathways involved in inflammation. Future studies will apply these findings in a human cohort to understand how they are correlated with manifestations of SS as well as understanding their functional role in systemic autoimmunity specific to SS.
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Affiliation(s)
- Shruti Singh Kakan
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Srikanth R Janga
- Department of Ophthalmology, Keck School of Medicine, Roski Eye Institute, University of Southern California, Los Angeles, CA, United States
| | - Benjamin Cooperman
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - David W Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Maria C Edman
- Department of Ophthalmology, Keck School of Medicine, Roski Eye Institute, University of Southern California, Los Angeles, CA, United States
| | - Curtis T Okamoto
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Sarah F Hamm-Alvarez
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States.,Department of Ophthalmology, Keck School of Medicine, Roski Eye Institute, University of Southern California, Los Angeles, CA, United States
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9
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Luo PH, Shu YM, Ni RJ, Liu YJ, Zhou JN. A Characteristic Expression Pattern of Core Circadian Genes in the Diurnal Tree Shrew. Neuroscience 2020; 437:145-160. [PMID: 32339628 DOI: 10.1016/j.neuroscience.2020.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 02/08/2023]
Abstract
The day-active tree shrew may serve as an animal model of human-like diurnal rhythms. However, the molecular basis for circadian rhythms in this species has remained unclear. In the present study, we investigated the expression patterns of core circadian genes involved in transcriptional/translational feedback loops (TTFLs) in both central and peripheral tissues of the tree shrew. The expression of 12 core circadian genes exhibited similar rhythmic patterns in the olfactory bulb, prefrontal cortex, hippocampus, and cerebellum, while the hypothalamus exhibited the weakest oscillations. The rhythms in peripheral tissues, especially the liver, were much more robust than those in brain tissues. ARNTL and NPAS2 were weakly rhythmic in brain tissues but exhibited almost the strongest rhythmicity in peripheral tissues. CLOCK and CRY2 exhibited the weakest rhythms in both central and peripheral tissues, while NR1D1 and CIART exhibited robust rhythms in both tissues. Most of these circadian genes were highly expressed at light/dark transitions in both brain and peripheral tissues, such as ARNTL and NPAS2 peaking at dusk while PERs peaking at dawn. Additionally, the peripheral clock was phase-advanced relative to the brain clock, as there was a significant advance (2-4 h) for PER3, DBP, NR1D1 and NR1D2. Furthermore, these genes exhibited an anti-phasic relationship between the diurnal tree shrew and the nocturnal mouse (i.e., 12-h phasing differential). Collectively, our findings demonstrate a characteristic expression pattern of core circadian genes in the tree shrew, which may provide a means for elucidating molecular mechanisms of diurnal rhythms.
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Affiliation(s)
- Peng-Hao Luo
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yu-Mian Shu
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China; School of Architecture and Civil Engineering, Chengdu University, Chengdu, China
| | - Rong-Jun Ni
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China; Psychiatric Laboratory and Mental Health Center, West China Hospital of Sichuan University, Chengdu, China
| | - Ya-Jing Liu
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China; Department of Obstetrics and Gynecology, Center for Reproductive Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jiang-Ning Zhou
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China.
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10
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Boubaker G, Strempel S, Hemphill A, Müller N, Wang J, Gottstein B, Spiliotis M. Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice. PLoS Negl Trop Dis 2020; 14:e0007640. [PMID: 32442168 PMCID: PMC7244097 DOI: 10.1371/journal.pntd.0007640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/05/2020] [Indexed: 12/15/2022] Open
Abstract
We present a comprehensive analysis of the hepatic miRNA transcriptome at one month post-infection of experimental primary alveolar echinococcosis (AE), a parasitic infection caused upon ingestion of E. multilocularis eggs. Liver tissues were collected from infected and non-infected C57BL/6 mice, then small RNA libraries were prepared for next-generation sequencing (NGS). We conducted a Stem-loop RT-qPCR for validation of most dysregulated miRNAs. In infected mice, the expression levels of 28 miRNAs were significantly altered. Of these, 9 were up-regulated (fold change (FC) ≥ 1.5) and 19 were down-regulated (FC ≤ 0.66) as compared to the non-infected controls. In infected livers, mmu-miR-148a-3p and mmu-miR-101b-3p were 8- and 6-fold down-regulated, respectively, and the expression of mmu-miR-22-3p was reduced by 50%, compared to non-infected liver tissue. Conversely, significantly higher hepatic levels were noted for Mus musculus (mmu)-miR-21a-5p (FC = 2.3) and mmu-miR-122-5p (FC = 1.8). In addition, the relative mRNA expression levels of five genes (vegfa, mtor, hif1-α, fasn and acsl1) that were identified as targets of down-regulated miRNAs were significantly enhanced. All the five genes exhibited a higher expression level in livers of E. multilocularis infected mice compared to non-infected mice. Finally, we studied the issue related to functionally mature arm selection preference (5p and/or 3p) from the miRNA precursor and showed that 9 pre-miRNAs exhibited different arm selection preferences in normal versus infected liver tissues. In conclusion, this study provides first evidence that miRNAs are regulated early in primary murine AE. Our findings raise intriguing questions such as (i) how E. multilocularis affects hepatic miRNA expression;(ii) what are the alterations in miRNA expression patterns in more advanced AE-stages; and (iii) which hepatic cellular, metabolic and/or immunologic processes are modulated through altered miRNAs in AE. Thus, further research on the regulation of miRNAs during AE is needed, since miRNAs constitute an attractive potential option for development of novel therapeutic approaches against AE. Various infectious diseases in humans have been associated with altered expression patterns of microRNAs (miRNAs), a class of small non-coding RNAs involved in negative regulation of gene expression. Herein, we revealed that significant alteration of miRNAs expression occurred in murine liver subsequently to experimental infection with E. multilocularis eggs when compared to non-infected controls. At the early stage of murine AE, hepatic miRNAs were mainly down-regulated. Respective target genes of the most extensively down-regulated miRNAs were involved in angiogenesis and fatty acid synthesis. Furthermore, we found higher mRNA levels of three angiogenic and two lipogenic genes in E. multilocularis infected livers compared to non-infected controls. Angiogenesis and fatty acid biosynthesis may be beneficial for development of the E. multilocularis metacestodes. In fact the formation of new blood vessels in the periparasitic area may ensure that parasites are supplied with oxygen and nutrients and get rid of waste products. Additionally, E. multilocularis is not able to undertake de novo fatty acid synthesis, thus lipids must be scavenged from its host. More research on the regulation of the hepatic miRNA transcriptome at more advanced stages of AE is needed.
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Affiliation(s)
- Ghalia Boubaker
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
- Department of Clinical Biology B, Laboratory of Parasitology and Mycology, University of Monastir, Monastir, Tunisia
- * E-mail: (GB); (BG)
| | | | - Andrew Hemphill
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Norbert Müller
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Junhua Wang
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Bruno Gottstein
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
- Institute of Infectious Diseases, Faculty of Medicine, University of Berne, Berne, Switzerland
- * E-mail: (GB); (BG)
| | - Markus Spiliotis
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
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11
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Kalpachidou T, Kummer KK, Mitrić M, Kress M. Tissue Specific Reference Genes for MicroRNA Expression Analysis in a Mouse Model of Peripheral Nerve Injury. Front Mol Neurosci 2019; 12:283. [PMID: 31824261 PMCID: PMC6883285 DOI: 10.3389/fnmol.2019.00283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/06/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as master switch regulators in many biological processes in health and disease, including neuropathy. miRNAs are commonly quantified by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), usually estimated as relative expression through reference genes normalization. Different non-coding RNAs (ncRNAs) are used for miRNA normalization; however, there is no study identifying the optimal reference genes in animal models for peripheral nerve injury. We evaluated the stability of eleven ncRNAs, commonly used for miRNA normalization, in dorsal root ganglia (DRG), dorsal horn of the spinal cord (dhSC), and medial prefrontal cortex (mPFC) in the mouse spared nerve injury (SNI) model. After RT-qPCR, the stability of each ncRNA was determined by using four different methods: BestKeeper, the comparative delta-Cq method, geNorm, and NormFinder. The candidates were rated according to their performance in each method and an overall ranking list was compiled. The most stable ncRNAs were: sno420, sno429, and sno202 in DRG; sno429, sno202, and U6 in dhSC; sno202, sno420, and sno142 in mPFC. We provide the first reference genes' evaluation for miRNA normalization in different neuronal tissues in an animal model of peripheral nerve injury. Our results underline the need for careful selection of reference genes for miRNA normalization in different tissues and experimental conditions. We further anticipate that our findings can be used in a broad range of nerve injury related studies, to ensure validity and promote reproducibility in miRNA quantification.
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12
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Zárybnický T, Matoušková P, Ambrož M, Šubrt Z, Skálová L, Boušová I. The Selection and Validation of Reference Genes for mRNA and microRNA Expression Studies in Human Liver Slices Using RT-qPCR. Genes (Basel) 2019; 10:genes10100763. [PMID: 31569378 PMCID: PMC6826422 DOI: 10.3390/genes10100763] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 01/06/2023] Open
Abstract
The selection of a suitable combination of reference genes (RGs) for data normalization is a crucial step for obtaining reliable and reproducible results from transcriptional response analysis using a reverse transcription-quantitative polymerase chain reaction. This is especially so if a three-dimensional multicellular model prepared from liver tissues originating from biologically diverse human individuals is used. The mRNA and miRNA RGs stability were studied in thirty-five human liver tissue samples and twelve precision-cut human liver slices (PCLS) treated for 24 h with dimethyl sulfoxide (controls) and PCLS treated with β-naphthoflavone (10 µM) or rifampicin (10 µM) as cytochrome P450 (CYP) inducers. Validation of RGs was performed by an expression analysis of CYP3A4 and CYP1A2 on rifampicin and β-naphthoflavone induction, respectively. Regarding mRNA, the best combination of RGs for the controls was YWHAZ and B2M, while YWHAZ and ACTB were selected for the liver samples and treated PCLS. Stability of all candidate miRNA RGs was comparable or better than that of generally used short non-coding RNA U6. The best combination for the control PCLS was miR-16-5p and miR-152-3p, in contrast to the miR-16-5b and miR-23b-3p selected for the treated PCLS. Our results showed that the candidate RGs were rather stable, especially for miRNA in human PCLS.
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Affiliation(s)
- Tomáš Zárybnický
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Petra Matoušková
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Martin Ambrož
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Zdeněk Šubrt
- Department of General Surgery, Third Faculty of Medicine and University Hospital Královské Vinohrady, Charles University, 100 34 Prague, Czech Republic.
- Department of Surgery, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Lenka Skálová
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Iva Boušová
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
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13
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Validation of Reference Genes for Gene Expression Normalization in RAW264.7 Cells under Different Conditions. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6131879. [PMID: 31223620 PMCID: PMC6541955 DOI: 10.1155/2019/6131879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/03/2019] [Accepted: 04/03/2019] [Indexed: 12/17/2022]
Abstract
RAW264.7 is a macrophage strain derived from mice tumour and shows a significant ability in antigen uptake. Real-time quantitative PCR (RT-qPCR) is one of the most commonly used methods in gene studies and requires suitable reference genes to normalize and quantitate the expression of gene of interest with sensitivity and specificity. However, suitable reference genes in RAW264.7 cells have not yet been identified for accurate gene expression quantification. In the current study, we evaluated expression levels of ten candidate reference genes in RAW264.7 cells under different conditions. RT-qPCR results indicated significant differences in the expression levels among the ten reference genes. Statistical analyses were carried out using geNorm, NormFinder, and BestKeeper software to further investigate the stability of the reference genes. Integrating the results from the three analytical methods, cytochrome c-1 and hydroxymethylbilane synthase were found to be the most stable and therefore more suitable reference genes, while ribosomal protein L4 and cyclophilin A were the least stable. This study emphasises the importance of identifying and selecting the most stable reference genes for normalization and provides a basis for future gene expression studies using RAW264.7 cells.
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14
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Goodarzi G, Maniati M, Qujeq D. The role of microRNAs in the healing of diabetic ulcers. Int Wound J 2019; 16:621-633. [PMID: 30821119 PMCID: PMC7949391 DOI: 10.1111/iwj.13070] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/28/2018] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small protected molecules with a length of 18 to 25 nucleotides. Many studies have recently been conducted on miRNAs, illustrating their role in regulating many biological, physiological, and pathological activities, such as maintaining cellular signalling and regulating cellular pathways. The main role of miRNAs is to regulate the expression of genes after translation, which can lead to the destruction or suppression of translation by binding to mRNAs. As any change in the regulation of miRNAs is associated with several physiological abnormalities, such as type 2 diabetes and its complications, these molecules can be used for therapeutic purposes or as biomarkers for the diagnosis of diseases such as diabetes and its complications. In this review article, we will discuss important findings about the miRNAs and the role of these molecules in different phases of the wound-healing process of chronic wounds, especially diabetic ulcer.
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Affiliation(s)
- Golnaz Goodarzi
- Department of Medical Biochemistry and Biotechnology, School of MedicineNorth Khorasan University of Medical SciencesBojnurdIran
| | - Mahmood Maniati
- School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Durdi Qujeq
- Cellular and Molecular Biology Research Center (CMBRC), Health Research InstituteBabol University of Medical SciencesBabolIran
- Dental Materials Research Center, Institute of HealthBabol University of Medical SciencesBabolIran
- Cancer Research Center, Health Research InstituteBabol University of Medical SciencesBabolIran
- Department of Clinical Biochemistry, School of MedicineBabol University of Medical SciencesBabolIran
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15
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Hanousková B, Neprašová B, Skálová L, Maletínská L, Zemanová K, Ambrož M, Matoušková P. High-fructose drinks affect microRNAs expression differently in lean and obese mice. J Nutr Biochem 2019; 68:42-50. [PMID: 31030166 DOI: 10.1016/j.jnutbio.2019.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 12/17/2018] [Accepted: 03/08/2019] [Indexed: 12/19/2022]
Abstract
High fructose intake from soft drinks and sweets is assumed to have a negative impact on human health. Yet in spite of intensive research, the molecular mechanisms of these effects have not been fully elucidated yet, for example, the effect of high fructose intake could be different in normal and obese individuals. Four groups of mice were used in this study: control groups of lean mice and mice with obesity induced by a high-fat diet, then both of these groups with or without fructose administration in drinks. In plasma of each group, triacylglycerol, cholesterol, free fatty acids, alanine aminotransferase, insulin and adiponectin were measured. The expression levels of selected microRNAs (miRNAs) in plasma, the liver, white adipose tissue, brown adipose tissue and subcutaneous adipose tissue were quantified. In both lean and obese mice, high fructose intake increased cholesterol amount in the liver, up-regulated hepatic miR-27a, down-regulated miR-33a in white adipose tissue and increased plasmatic level of miR-21. The effect of high fructose intake on other miRNAs in the liver, plasma and adipose tissues differed in normal and obese mice. Fructose intake led to hepatic hypercholesterolemia and aberrant expression of several miRNAs participating in lipid metabolism, adipocytes differentiation and nonalcoholic fatty liver disease promotion. The effect of fructose on miRNAs expression differed in normal and obese mice. Nevertheless, plasmatic miR-21, which was induced by fructose in both lean and obese mice, may be considered as a potential biomarker of excessive fructose intake.
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Affiliation(s)
- Barbora Hanousková
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203/8, Hradec Králové, Czech Republic.
| | - Barbora Neprašová
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 542/2, Prague, Czech Republic.
| | - Lenka Skálová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203/8, Hradec Králové, Czech Republic.
| | - Lenka Maletínská
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 542/2, Prague, Czech Republic.
| | - Kateřina Zemanová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203/8, Hradec Králové, Czech Republic.
| | - Martin Ambrož
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203/8, Hradec Králové, Czech Republic.
| | - Petra Matoušková
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203/8, Hradec Králové, Czech Republic.
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16
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Rankin CR, Treger J, Faure-Kumar E, Benhammou J, Anisman-Posner D, Bollinger AE, Pothoulakis C, Padua DM. Overexpressing Long Noncoding RNAs Using Gene-activating CRISPR. J Vis Exp 2019. [PMID: 30882798 DOI: 10.3791/59233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Long noncoding RNA (lncRNA) biology is a new and exciting field of research, with the number of publications from this field growing exponentially since 2007. These studies have confirmed that lncRNAs are altered in almost all diseases. However, studying the functional roles for lncRNAs in the context of disease remains difficult due to the lack of protein products, tissue-specific expression, low expression levels, complexities in splice forms, and lack of conservation among species. Given the species-specific expression, lncRNA studies are often restricted to human research contexts when studying disease processes. Since lncRNAs function at the molecular level, one way to dissect lncRNA biology is to either remove the lncRNA or overexpress the lncRNA and measure cellular effects. In this article, a written and visualized protocol to overexpress lncRNAs in vitro is presented. As a representative experiment, an lncRNA associated with inflammatory bowel disease, Interferon Gamma Antisense 1 (IFNG-AS1), is shown to be overexpressed in a Jurkat T-cell model. To accomplish this, the activating clustered regularly interspaced short palindromic repeats (CRISPR) technique is used to enable overexpression at the endogenous genomic loci. The activating CRISPR technique targets a set of transcription factors to the transcriptional start site of a gene, enabling a robust overexpression of multiple lncRNA splice forms. This procedure will be broken down into three steps, namely (i) guide RNA (gRNA) design and vector construction, (ii) virus generation and transduction, and (iii) colony screening for overexpression. For this representative experiment, a greater than 20-fold enhancement in IFNG-AS1 in Jurkat T cells was observed.
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Affiliation(s)
- Carl Robert Rankin
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California, Los Angeles
| | - Janet Treger
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California, Los Angeles
| | - Emmanuelle Faure-Kumar
- Vatche and Tamar Manoukian Division of Digestive Diseases, Integrated Molecular Technologies (IMT) Core, Department of Medicine, University of California, Los Angeles
| | - Jihane Benhammou
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California, Los Angeles
| | - Deborah Anisman-Posner
- Division of Hematology and Oncology, Department of Medicine, University of California, Los Angeles
| | - Alex Edward Bollinger
- Division of Hematology and Oncology, Department of Medicine, University of California, Los Angeles
| | - Charalabos Pothoulakis
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California, Los Angeles
| | - David Miguel Padua
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California, Los Angeles;
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17
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Pardo M, Kuperman Y, Levin L, Rudich A, Haim Y, Schauer JJ, Chen A, Rudich Y. Exposure to air pollution interacts with obesogenic nutrition to induce tissue-specific response patterns. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 239:532-543. [PMID: 29684880 DOI: 10.1016/j.envpol.2018.04.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/28/2018] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
Obesity and exposure to particular matter (PM) have become two leading global threats to public health. However, the exact mechanisms and tissue-specificity of their health effects are largely unknown. Here we investigate whether a metabolic challenge (early nutritional obesity) synergistically interacts with an environmental challenge (PM exposure) to alter genes representing key response pathways, in a tissue-specific manner. Mice subjected to 7 weeks obesogenic nutrition were exposed every other day during the final week and a half to aqueous extracts of PM collected in the city of London (UK). The expression of 61 selected genes representing key response pathways were investigated in lung, liver, white and brown adipose tissues. Principal component analysis (PCA) revealed distinct patterns of expression changes between the 4 tissues, particularly in the lungs and the liver. Surprisingly, the lung responded to the nutrition challenge. The response of these organs to the PM challenge displayed opposite patterns for some key genes, in particular, those related to the Nrf2 pathway. While the contribution to the variance in gene expression changes in mice exposed to the combined challenge were largely similar among the tissues in PCA1, PCA2 exhibited predominant contribution of inflammatory and oxidative stress responses to the variance in the lungs, and a greater contribution of autophagy genes and MAP kinases in adipose tissues. Possible involvement of alterations in DNA methylation was demonstrated by cell-type-specific responses to a methylation inhibitor. Correspondingly, the DNA methyltransferase Dnmt3a2 increased in the lungs but decreased in the liver, demonstrating potential tissue-differential synergism between nutritional and PM exposure. The results suggest that urban PM, containing dissolved metals, interacts with obesogenic nutrition to regulate diverse response pathways including inflammation and oxidative stress, in a tissue-specific manner. Tissue-differential effects on DNA methylation may underlie tissue-specific responses to key stress-response genes such as catalase and Nrf2.
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Affiliation(s)
- Michal Pardo
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Yael Kuperman
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Liron Levin
- Department of Life Sciences, Bioinformatics Core Facility, Ben-Gurion University of the Negev, Beer Sheva, 84103, Israel
| | - Assaf Rudich
- The Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84103, Israel; The National Institute of Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer-Sheva 84103, Israel
| | - Yulia Haim
- The Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84103, Israel; The National Institute of Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer-Sheva 84103, Israel
| | - James J Schauer
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Alon Chen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel; Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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18
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Zárybnický T, Matoušková P, Lancošová B, Šubrt Z, Skálová L, Boušová I. Inter-Individual Variability in Acute Toxicity of R-Pulegone and R-Menthofuran in Human Liver Slices and Their Influence on miRNA Expression Changes in Comparison to Acetaminophen. Int J Mol Sci 2018; 19:ijms19061805. [PMID: 29921785 PMCID: PMC6032148 DOI: 10.3390/ijms19061805] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/14/2018] [Accepted: 06/16/2018] [Indexed: 12/12/2022] Open
Abstract
Monoterpenes R-pulegone (PUL) and R-menthofuran (MF), abundant in the Lamiaceae family, are frequently used in herb and food products. Although their hepatotoxicity was shown in rodent species, information about their effects in human liver has been limited. The aim of our study was to test the effects of PUL, MF and acetaminophen (APAP, as a reference compound) on cell viability and microRNA (miRNA) expression in human precision-cut liver slices. Slices from five patients were used to follow up on the inter-individual variability. PUL was toxic in all liver samples (the half-maximal effective concentration was 4.0 µg/mg of tissue), while MF and surprisingly APAP only in two and three liver samples, respectively. PUL also changed miRNA expression more significantly than MF and APAP. The most pronounced effect was a marked decrease of miR-155-5p expression caused by PUL even in non-toxic concentrations in all five liver samples. Our results showed that PUL is much more toxic than MF and APAP in human liver and that miR-155-5p could be a good marker of PUL early hepatotoxicity. Marked inter-individual variabilities in all our results demonstrate the high probability of significant differences in the hepatotoxicity of tested compounds among people.
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Affiliation(s)
- Tomáš Zárybnický
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, 500 05 Hradec Králové, Czech Republic.
| | - Petra Matoušková
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, 500 05 Hradec Králové, Czech Republic.
| | - Bibiána Lancošová
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, 500 05 Hradec Králové, Czech Republic.
| | - Zdeněk Šubrt
- Department of Surgery, Faculty of Medicine in Hradec Králové, Charles University, 500 05 Hradec Králové, Czech Republic.
- Department of Surgery, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Lenka Skálová
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, 500 05 Hradec Králové, Czech Republic.
| | - Iva Boušová
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, 500 05 Hradec Králové, Czech Republic.
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19
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Silva TLA, Braz GRF, Silva SCDA, Pedroza AADS, Freitas CDM, Ferreira DJS, da Silva AI, Lagranha CJ. Serotonin transporter inhibition during neonatal period induces sex-dependent effects on mitochondrial bioenergetics in the rat brainstem. Eur J Neurosci 2018; 48:1620-1634. [PMID: 29802653 DOI: 10.1111/ejn.13971] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/19/2018] [Accepted: 05/14/2018] [Indexed: 12/29/2022]
Abstract
The serotonin reuptake is mainly regulated by the serotonin transporters (SERTs), which are abundantly found in the raphe nuclei, located in the brainstem. Previous studies have shown that dysfunction in the SERT has been associated with several disorders, including depression and cardiovascular diseases. In this manuscript, we aimed to investigate how gender and the treatment with a serotonin selective reuptake inhibitor (SSRI) could affect mitochondrial bioenergetics and oxidative stress in the brainstem of male and female rats. Fluoxetine, our chosen SSRI, was used during the neonatal period (i.e., from postnatal Day 1 to postnatal Day 21-PND1 to PND21) in both male and female animals. Thereafter, experiments were conducted in adult rats (60 days old). Our results demonstrate that, during lactation, fluoxetine treatment modulates the mitochondrial bioenergetics in a sex-dependent manner, such as improving male mitochondrial function and female antioxidant capacity.
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Affiliation(s)
- Tercya Lucidi Araujo Silva
- Neuropsychiatry and Behavioral Science Graduate Program, Federal University of Pernambuco, Recife, Brazil
| | - Glauber Rudá Feitoza Braz
- Neuropsychiatry and Behavioral Science Graduate Program, Federal University of Pernambuco, Recife, Brazil
| | | | | | | | | | - Aline Isabel da Silva
- Neuropsychiatry and Behavioral Science Graduate Program, Federal University of Pernambuco, Recife, Brazil
| | - Claudia Jacques Lagranha
- Neuropsychiatry and Behavioral Science Graduate Program, Federal University of Pernambuco, Recife, Brazil
- Biochemistry and Physiology Graduate Program, Federal University of Pernambuco, Recife, Brazil
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20
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Wang S, Wang J, Lv X. Selection of reference genes for expression analysis in mouse models of acute alcoholic liver injury. Int J Mol Med 2018; 41:3527-3536. [PMID: 29512759 DOI: 10.3892/ijmm.2018.3527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/08/2018] [Indexed: 11/06/2022] Open
Abstract
Investigations of hepatic gene expression are crucial for determining the molecular factors involved in acute alcoholic liver injury. The results of liver molecular investigations may reveal etiologically important genomic alterations. Therefore, it is necessary to normalize gene expression data to identify stable genes, which may be used as a reference under different experimental conditions. The aim of the present study was to apply reverse transcription‑quantitative polymerase chain reaction analysis and use analysis software to investigate the expression stability of candidate reference genes in hepatic tissues from mice with acute alcoholic liver injury. The acute alcoholic liver injury models were established by the intragastric administration of alcohol (5 mg/kg) in Imprinting Control Region mice. Total RNA was isolated from the mouse livers, following which the expression levels of seven reference genes, β-actin, glyceraldehyde 3-phosphate dehydrogenase (Gadph), glucuronidase β, hypoxanthine phosphoribosyltransferase 1 (Hprt1), 18S ribosomal RNA, TATA binding protein and β‑2 microglobulin, were examined, and gene expression stability was assessed using the geNorm, NormFinder and BestKeeper tools. The geNorm analysis revealed that the gene with the lowest variability was Hprt1. Hprt1 and Gapdh were validated as the optimal reference gene pair in all samples from all groups. The NormFinder and BestKeeper results showed that Hprt1 was the most stable gene in all samples. Alcohol induces endoplasmic reticulum (ER) stress, causing changes in the expression levels of ER stress‑associated genes. The stability of Hprt1 was verified by the expression analysis of ER stress‑associated genes, and gene expression levels in the ethanol groups were upregulated, with a significant difference in expression, compared with those in the control group. Therefore, Hprt1 was selected as the most stable gene, and Hprt1 and Gapdh were determined to be the optimum gene pair in mouse models of acute alcoholic liver injury. The reliability of the Hprt1 gene was confirmed by expression analysis of ER stress‑associated genes.
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Affiliation(s)
- Sheng Wang
- School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Jianqing Wang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Xiongwen Lv
- School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, P.R. China
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Identification of Reference Genes for Analysis of microRNA Expression Patterns in Equine Chorioallantoic Membrane and Serum. Mol Biotechnol 2017; 60:62-73. [DOI: 10.1007/s12033-017-0047-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Edvinsson M, Tallkvist J, Nyström-Rosander C, Ilbäck NG. Cholesterol uptake in the mouse aorta increases during Chlamydia pneumoniae infection. Pathog Dis 2017; 75:2966466. [PMID: 28158541 DOI: 10.1093/femspd/ftx004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 02/01/2017] [Indexed: 01/08/2023] Open
Abstract
Chlamydia pneumoniae has been suggested as a stimulator of the atherosclerotic process. Mice fed a normal diet were infected intranasally with C. pneumoniae and given one intraperitoneal injection of 14C-cholesterol tracer per day for 12 days. Bacteria were demonstrated in the aorta in the early phase of infection and in lungs and liver throughout the study period of 20 days. 14C-cholesterol was not affected in the heart but increased in the blood, liver and aorta on day 4 when the infection was clinically most severe. Furthermore, on day 20 14C-cholesterol tended to be increased in the aorta. Accordingly, copper- and zinc levels and expressions of the infection biomarkers Cxcl2 and Ifng increased in the liver on day 4 with a tendency of increased of copper, zinc and Ifng on day 20. In mice where bacteria could be cultivated from the lungs, expressions of cholesterol transporters Abca1 and Idol were both increased in the liver on day 4. The increased levels of 14C-cholesterol in blood and aorta together with increased Abca1 and Idol in the liver during C. pneumoniae infection in mice fed a normal diet suggest that this pathogen may have a role in the initiation of the atherosclerotic process.
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Affiliation(s)
- Marie Edvinsson
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, 75185 Uppsala, Sweden
| | - Jonas Tallkvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Christina Nyström-Rosander
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, 75185 Uppsala, Sweden
| | - Nils-Gunnar Ilbäck
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, 75185 Uppsala, Sweden.,Risk Benefit Assessment Department, National Food Agency, 75126 Uppsala, Sweden
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Wu X, Liu S, Lyu J, Zhou S, Yang Y, Wang C, Gu W, Zuo Q, Li B, Fan C. Endogenous controls of gene expression in N-methyl-N-nitrosourea-induced T-cell lymphoma in p53-deficient mice. BMC Cancer 2017; 17:545. [PMID: 28807016 PMCID: PMC5557555 DOI: 10.1186/s12885-017-3536-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022] Open
Abstract
Background Real-time polymerase chain reaction (PCR) has become an increasingly important technique for gene expression profiling because it can provide insights into complex biological and pathological processes and be used to predict disease or treatment outcomes. Although normalized data are necessary for an accurate estimation of mRNA expression levels, several pieces of evidence suggest that the expression of so-called housekeeping genes is not stable. This study aimed to validate reference genes for the normalization of real-time PCR in an N-methyl-N-nitrosourea (MNU)-induced T-cell lymphoma mouse model. Methods T-cell lymphomas were generated in p53-deficient mice by treatment with 37.5 mg/kg MNU. Thymus and spleen were identified as the primary target organs with the highest incidences of lymphomas. We analyzed the RNA expression levels of eight potential endogenous reference genes (Gapdh, Rn18s, Actb, Hprt, B2M, Rplp0, Gusb, Ctbp1). The expression stabilities of these reference genes were tested at different time points after MNU treatment using geNorm and NormFinder algorithms. Results A total of 65% of MNU-treated mice developed T-cell lymphomas, with the spleen and thymus as the major target organs. All candidate reference genes were amplified efficiently by quantitative reverse-transcription polymerase chain reaction (RT-qPCR). Gene stability evaluation after MNU treatment and during lymphomagenesis revealed that Ctbp1 and Rplp0 were the most stably expressed genes in the thymus and spleen, respectively. RT-PCR of thymus RNA using two additional sets of primer confirmed that Ctbp1 was the most stable of all the candidate reference genes. Conclusions We provided suitable endogenous controls for gene expression studies in the T-cell lymphoma model. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3536-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xi Wu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, No. 2 Tiantan Xili, Beijing, 100050, China
| | - Susu Liu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, No. 2 Tiantan Xili, Beijing, 100050, China
| | - Jianjun Lyu
- National Center for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, Beijing Economic-Technological Development Area, A8 Hongda Middle Street, Beijing, 100176, China
| | - Shuya Zhou
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, No. 2 Tiantan Xili, Beijing, 100050, China
| | - Yanwei Yang
- National Center for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, Beijing Economic-Technological Development Area, A8 Hongda Middle Street, Beijing, 100176, China
| | - Chenfei Wang
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, No. 2 Tiantan Xili, Beijing, 100050, China
| | - Wenda Gu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, No. 2 Tiantan Xili, Beijing, 100050, China
| | - Qin Zuo
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, No. 2 Tiantan Xili, Beijing, 100050, China
| | - Baowen Li
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, No. 2 Tiantan Xili, Beijing, 100050, China
| | - Changfa Fan
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, No. 2 Tiantan Xili, Beijing, 100050, China.
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Validation of optimal reference genes for quantitative real time PCR in muscle and adipose tissue for obesity and diabetes research. Sci Rep 2017; 7:3612. [PMID: 28620170 PMCID: PMC5472619 DOI: 10.1038/s41598-017-03730-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/02/2017] [Indexed: 12/11/2022] Open
Abstract
The global incidence of obesity has led to an increasing need for understanding the molecular mechanisms that drive this epidemic and its comorbidities. Quantitative real-time RT-PCR (RT-qPCR) is the most reliable and widely used method for gene expression analysis. The selection of suitable reference genes (RGs) is critical for obtaining accurate gene expression information. The current study aimed to identify optimal RGs to perform quantitative transcriptomic analysis based on RT-qPCR for obesity and diabetes research, employing in vitro and mouse models, and human tissue samples. Using the ReFinder program we evaluated the stability of a total of 15 RGs. The impact of choosing the most suitable RGs versus less suitable RGs on RT-qPCR results was assessed. Optimal RGs differed between tissue and cell type, species, and experimental conditions. By employing different sets of RGs to normalize the mRNA expression of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α), we show that sub-optimal RGs can markedly alter the PGC1α gene expression profile. Our study demonstrates the importance of validating RGs prior to normalizing transcriptional expression levels of target genes and identifies optimal RG pairs for reliable RT-qPCR normalization in cells and in human and murine muscle and adipose tissue for obesity/diabetes research.
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25
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Iron Homeostasis in Tissues Is Affected during Persistent Chlamydia pneumoniae Infection in Mice. BIOMED RESEARCH INTERNATIONAL 2017; 2017:3642301. [PMID: 28691023 PMCID: PMC5485268 DOI: 10.1155/2017/3642301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 05/09/2017] [Indexed: 11/18/2022]
Abstract
Chlamydia pneumoniae (C. pneumoniae) may be a mediator in the pathogenesis of atherosclerosis. For its growth C. pneumoniae depends on iron (Fe), but how Fe changes in tissues during persistent infection or affects bacterial replication in tissues is unknown. C. pneumoniae-infected C57BL/6J mice were sacrificed on days 4, 8, 20, and 40. Mice had bacteria in the lungs and liver on all days. Inflammatory markers, chemokine Cxcl2 and interferon-gamma, were not affected in the liver on day 40. The copper (Cu)/zinc (Zn) ratio in serum, another marker of infection/inflammation, increased on day 4 and tended to increase again on day 40. The Fe markers, transferrin receptor (TfR), Hepcidin (Hamp1), and ferroportin 1 (Fpn1), increased in the liver on day 4 and then normalized except for TfR that tended to decrease. TfR responses were similar to Fe in serum that increased on day 4 but tended to decrease thereafter. In the liver, Fe was increased on day 4 and also on day 40. The reappearing increases in Cu/Zn on day 40 concomitant with the increase in liver Fe on day 40, even though TfR tended to decrease, and the fact that viable C. pneumoniae was present in the lungs and liver may indicate the early phase of activation of recurrent infection.
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26
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Barroso WA, Victorino VJ, Jeremias IC, Petroni RC, Ariga SKK, Salles TA, Barbeiro DF, de Lima TM, de Souza HP. High-fat diet inhibits PGC-1α suppressive effect on NFκB signaling in hepatocytes. Eur J Nutr 2017; 57:1891-1900. [DOI: 10.1007/s00394-017-1472-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
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Etich J, Bergmeier V, Pitzler L, Brachvogel B. Identification of a reference gene for the quantification of mRNA and miRNA expression during skin wound healing. Connect Tissue Res 2017; 58:196-207. [PMID: 27386825 DOI: 10.1080/03008207.2016.1210606] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AIM Wound healing is a coordinated process to restore tissue homeostasis and reestablish the protective barrier of the skin. miRNAs may modulate the expression of target genes to contribute to repair processes, but due to the complexity of the tissue it is challenging to quantify gene expression during the distinct phases of wound repair. Here, we aimed to identify a common reference gene to quantify changes in miRNA and mRNA expression during skin wound healing. METHODS Quantitative real-time PCR and bioinformatic analysis tools were used to identify suitable reference genes during skin repair and their reliability was tested by studying the expression of mRNAs and miRNAs. RESULTS Morphological assessment of wounds showed that the injury model recapitulates the distinct phases of skin repair. Non-degraded RNA could be isolated from skin and wounds and used to study the expression of non-coding small nuclear RNAs during wound healing. Among those, RNU6B was most constantly expressed during skin repair. Using this reference gene we could confirm the transient upregulation of IL-1β and PTPRC/CD45 during the early phase as well as the increased expression of collagen type I at later stages of repair and validate the differential expression of miR-204, miR-205, and miR-31 in skin wounds. In contrast to Gapdh the normalization to multiple reference genes gave a similar outcome. CONCLUSION RNU6B is an accurate alternative normalizer to quantify mRNA and miRNA expression during the distinct phases of skin wound healing when analysis of multiple reference genes is not feasible.
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Affiliation(s)
- Julia Etich
- a Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty , University of Cologne , Cologne , Germany.,b Center for Biochemistry, Medical Faculty , University of Cologne , Cologne , Germany
| | - Vera Bergmeier
- a Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty , University of Cologne , Cologne , Germany.,b Center for Biochemistry, Medical Faculty , University of Cologne , Cologne , Germany
| | - Lena Pitzler
- a Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty , University of Cologne , Cologne , Germany.,b Center for Biochemistry, Medical Faculty , University of Cologne , Cologne , Germany
| | - Bent Brachvogel
- a Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty , University of Cologne , Cologne , Germany.,b Center for Biochemistry, Medical Faculty , University of Cologne , Cologne , Germany
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28
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Massart J, Katayama M, Krook A. microManaging glucose and lipid metabolism in skeletal muscle: Role of microRNAs. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:2130-2138. [DOI: 10.1016/j.bbalip.2016.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/03/2016] [Accepted: 05/10/2016] [Indexed: 01/28/2023]
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Jacobsen KS, Nielsen KO, Winther TN, Glebe D, Pociot F, Hogh B. Identification of valid reference genes for microRNA expression studies in a hepatitis B virus replicating liver cell line. BMC Res Notes 2016; 9:38. [PMID: 26801621 PMCID: PMC4724106 DOI: 10.1186/s13104-016-1848-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/08/2016] [Indexed: 12/22/2022] Open
Abstract
Background MicroRNAs are regulatory molecules and suggested as non-invasive biomarkers for molecular diagnostics and prognostics. Altered expression levels of specific microRNAs are associated with hepatitis B virus infection and hepatocellular carcinoma. We previously identified differentially expressed microRNAs with liver-specific target genes in plasma from children with chronic hepatitis B. To further understand the biological role of these microRNAs in the pathogenesis of chronic hepatitis B, we have used the human liver cell line HepG2, with and without HBV replication, after transfection of hepatitis B virus expression vectors. RT-qPCR is the preferred method for microRNA studies, and a careful normalisation strategy, verifying the optimal set of reference genes, is decisive for correctly evaluating microRNA expression levels. The aim of this study was to provide valid reference genes for the human HCC-derived cell line HepG2. Results A panel of 739 microRNAs was screened to identify the most stably expressed microRNAs, followed by a PubMed search identifying microRNAs previously used as reference genes. Sixteen candidate reference genes were validated by RT-qPCR. Reference gene stabilities were calculated first by standard deviations of ΔCt values and then by geNorm and NormFinder analyses, taking into account the amplification efficiency of each microRNA primer set. The optimal set of reference genes was verified by a target analysis using RT-qPCR on miR-215-5p. Conclusion We identified miR-24-3p, miR-151a-5p, and miR-425-5p as the most valid combination of reference genes for microRNA RT-qPCR studies in our hepatitis B virus replicating HepG2 cell model. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-1848-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kari Stougaard Jacobsen
- Department of Paediatrics, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark. .,Department of Paediatrics and Center for Non-Coding RNA in Technology and Health, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark.
| | - Kirstine Overgaard Nielsen
- Department of Paediatrics, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark. .,Department of Paediatrics and Center for Non-Coding RNA in Technology and Health, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark.
| | - Thilde Nordmann Winther
- Department of Paediatrics, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark.
| | - Dieter Glebe
- Institute of Medical Virology, National Reference Center for Hepatitis B and D Viruses, German Center for Infection Research, Biomedical Research Center Seltersberg, Justus-Liebig University Giessen, Giessen, Germany.
| | - Flemming Pociot
- Department of Paediatrics and Center for Non-Coding RNA in Technology and Health, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark.
| | - Birthe Hogh
- Department of Paediatrics, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark.
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White HM, Carvalho ER, Koser SL, Schmelz-Roberts NS, Pezzanite LM, Slabaugh AC, Doane PH, Donkin SS. Short communication: Regulation of hepatic gluconeogenic enzymes by dietary glycerol in transition dairy cows. J Dairy Sci 2015; 99:812-7. [PMID: 26547649 DOI: 10.3168/jds.2015-9953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/21/2015] [Indexed: 11/19/2022]
Abstract
Nutritional status and glucose precursors are known regulators of gluconeogenic gene expression. Glycerol can replace corn in diets fed to dairy cows and use of glycerol is linked to increased rumen propionate production. The effect of dietary glycerol on the regulation of gluconeogenic enzymes is unknown. The objective of this study was to examine the effect of glycerol on expression of pyruvate carboxylase (PC), cytosolic and mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-C and PEPCK-M), and glucose-6-phosphatase. Twenty-six multiparous Holstein cows were fed either a control diet or a diet where high-moisture corn was replaced by glycerol from -28 through +56 d relative to calving (DRTC). Liver tissue was collected via percutaneous liver biopsy at -28, -14, +1, +14, +28, and +56 DRTC for RNA analysis. Expression of PC mRNA increased 6-fold at +1 and 4-fold at +14 DRTC relative to precalving levels. Dietary glycerol did not alter expression of PC mRNA expression. Expression of PEPCK-C increased 2.5-fold at +14 and 3-fold at +28 DRTC compared with +1 DRTC. Overall, dietary glycerol increased PEPCK-C expression compared with that of cows fed control diets. The ratio of PC to PEPCK-C was increased 6.3-fold at +1 DRTC compared with precalving and tended to be decreased in cows fed glycerol. We detected no effect of diet or DRTC on PEPCK-M or glucose-6-phosphatase mRNA, and there were no interactions of dietary treatment and DRTC for any transcript measured. Substituting corn with glycerol increased the expression of PEPCK-C mRNA during transition to lactation and suggests that dietary energy source alters hepatic expression. The observed increase in PEPCK-C expression with glycerol feeding may indicate regulation of hepatic gene expression by changes in rumen propionate production.
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Affiliation(s)
- H M White
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - E R Carvalho
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - S L Koser
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | | | - L M Pezzanite
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - A C Slabaugh
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - P H Doane
- Archer Daniels Midland Company, Decatur, IL 62521
| | - S S Donkin
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Cranberry extract–enriched diets increase NAD(P)H:quinone oxidoreductase and catalase activities in obese but not in nonobese mice. Nutr Res 2015; 35:901-909. [DOI: 10.1016/j.nutres.2015.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/30/2015] [Accepted: 08/05/2015] [Indexed: 11/17/2022]
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32
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Lecová L, Růžičková M, Laing R, Vogel H, Szotáková B, Prchal L, Lamka J, Vokřál I, Skálová L, Matoušková P. Reliable reference gene selection for quantitative real time PCR in Haemonchus contortus. Mol Biochem Parasitol 2015; 201:123-7. [PMID: 26255779 DOI: 10.1016/j.molbiopara.2015.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 11/27/2022]
Abstract
The aim of this work was to identify reliable reference genes for expression studies in adult Haemonchus contortus. Eleven candidate genes were identified and the stability of their expression was assessed in adult males and females of two genetically divergent H. contortus isolates: drug-susceptible (ISE) and multi-drug-resistant (WR). Five genes with the most stable expression patterns were further assessed for suitability as reference genes in anthelmintic-treated H. contortus adults versus non-treated controls. We identified important differences in the expression of a number of candidate genes in anthelmintic-treated samples, confirming the need for careful validation of control genes for such experiments. We propose the use of multiple reference genes for expression studies in this species and found gpd, ama and far most suitable for adult H. contortus.
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Affiliation(s)
- Lenka Lecová
- Department of Biochemical Sciences, Charles University in Prague, Faculty of Pharmacy, Hradec Králové, Czech Republic
| | - Michaela Růžičková
- Department of Biochemical Sciences, Charles University in Prague, Faculty of Pharmacy, Hradec Králové, Czech Republic
| | - Roz Laing
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, Scotland, UK
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Department of Entomology, Jena D-07745, Germany
| | - Barbora Szotáková
- Department of Biochemical Sciences, Charles University in Prague, Faculty of Pharmacy, Hradec Králové, Czech Republic
| | - Lukáš Prchal
- Department of Biochemical Sciences, Charles University in Prague, Faculty of Pharmacy, Hradec Králové, Czech Republic
| | - Jiří Lamka
- Department of Pharmacology and Toxicology, Charles University in Prague, Faculty of Pharmacy, Hradec Králové, Czech Republic
| | - Ivan Vokřál
- Department of Pharmacology and Toxicology, Charles University in Prague, Faculty of Pharmacy, Hradec Králové, Czech Republic
| | - Lenka Skálová
- Department of Biochemical Sciences, Charles University in Prague, Faculty of Pharmacy, Hradec Králové, Czech Republic
| | - Petra Matoušková
- Department of Biochemical Sciences, Charles University in Prague, Faculty of Pharmacy, Hradec Králové, Czech Republic.
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Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z. Amplification-based method for microRNA detection. Biosens Bioelectron 2015; 71:322-331. [PMID: 25930002 DOI: 10.1016/j.bios.2015.04.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/20/2022]
Abstract
Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zuhong Lu
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
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Kamran F, Andrade AC, Nella AA, Clokie SJ, Rezvani G, Nilsson O, Baron J, Lui JC. Evidence That Up-Regulation of MicroRNA-29 Contributes to Postnatal Body Growth Deceleration. Mol Endocrinol 2015; 29:921-32. [PMID: 25866874 DOI: 10.1210/me.2015-1047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Body growth is rapid in infancy but subsequently slows and eventually ceases due to a progressive decline in cell proliferation that occurs simultaneously in multiple organs. We previously showed that this decline in proliferation is driven in part by postnatal down-regulation of a large set of growth-promoting genes in multiple organs. We hypothesized that this growth-limiting genetic program is orchestrated by microRNAs (miRNAs). Bioinformatic analysis identified target sequences of the miR-29 family of miRNAs to be overrepresented in age-down-regulated genes. Concomitantly, expression microarray analysis in mouse kidney and lung showed that all members of the miR-29 family, miR-29a, -b, and -c, were strongly up-regulated from 1 to 6 weeks of age. Real-time PCR confirmed that miR-29a, -b, and -c were up-regulated with age in liver, kidney, lung, and heart, and their expression levels were higher in hepatocytes isolated from 5-week-old mice than in hepatocytes from embryonic mouse liver at embryonic day 16.5. We next focused on 3 predicted miR-29 target genes (Igf1, Imp1, and Mest), all of which are growth-promoting. A 3'-untranslated region containing the predicted target sequences from each gene was placed individually in a luciferase reporter construct. Transfection of miR-29 mimics suppressed luciferase gene activity for all 3 genes, and this suppression was diminished by mutating the target sequences, suggesting that these genes are indeed regulated by miR-29. Taken together, the findings suggest that up-regulation of miR-29 during juvenile life drives the down-regulation of multiple growth-promoting genes, thus contributing to physiological slowing and eventual cessation of body growth.
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Affiliation(s)
- Fariha Kamran
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Anenisia C Andrade
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Aikaterini A Nella
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Samuel J Clokie
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Geoffrey Rezvani
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Ola Nilsson
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Jeffrey Baron
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Julian C Lui
- Section on Growth and Development (F.K., A.A.N., G.R., J.B., J.C.L.) and Section on Neuroendocrinology (S.J.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; and Center for Molecular Medicine and Pediatric Endocrinology Unit (A.C.A., O.N.), Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, SE-171 76 Stockholm, Sweden
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Ferdous J, Li Y, Reid N, Langridge P, Shi BJ, Tricker PJ. Identification of reference genes for quantitative expression analysis of microRNAs and mRNAs in barley under various stress conditions. PLoS One 2015; 10:e0118503. [PMID: 25793505 PMCID: PMC4368757 DOI: 10.1371/journal.pone.0118503] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 01/19/2015] [Indexed: 01/22/2023] Open
Abstract
For accurate and reliable gene expression analysis using quantitative real-time reverse transcription PCR (qPCR), the selection of appropriate reference genes as an internal control for normalization is crucial. We hypothesized that non-coding, small nucleolar RNAs (snoRNAs) would be stably expressed in different barley varieties and under different experimental treatments, in different tissues and at different developmental stages of plant growth and therefore might prove to be suitable reference genes for expression analysis of both microRNAs (miRNAs) and mRNAs. In this study, we examined the expression stability of ten candidate reference genes in six barley genotypes under five experimental stresses, drought, fungal infection, boron toxicity, nutrient deficiency and salinity. We compared four commonly used housekeeping genes; Actin (ACT), alpha-Tubulin (α-TUB), Glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ADP-ribosylation factor 1-like protein (ADP), four snoRNAs; (U18, U61, snoR14 and snoR23) and two microRNAs (miR168, miR159) as candidate reference genes. We found that ADP, snoR14 and snoR23 were ranked as the best of these candidates across diverse samples. For accurate and reliable gene expression analysis using quantitative real-time reverse transcription PCR (qPCR), the selection of appropriate reference genes as an internal control for normalization is crucial. We hypothesized that non-coding, small nucleolar RNAs (snoRNAs) would be stably expressed in different barley varieties and under different experimental treatments, in different tissues and at different developmental stages of plant growth and therefore might prove to be suitable reference genes for expression analysis of both microRNAs (miRNAs) and mRNAs. In this study, we examined the expression stability of ten candidate reference genes in six barley genotypes under five experimental stresses, drought, fungal infection, boron toxicity, nutrient deficiency and salinity. We compared four commonly used housekeeping genes; Actin (ACT), alpha-Tubulin (α-TUB), Glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ADP-ribosylation factor 1-like protein (ADP), four snoRNAs; (U18, U61, snoR14 and snoR23) and two microRNAs (miR168, miR159) as candidate reference genes. We found that ADP, snoR14 and snoR23 were ranked as the best of these candidates across diverse samples. Additionally, we found that miR168 was a suitable reference gene for expression analysis in barley. Finally, we validated the performance of our stable and unstable candidate reference genes for both mRNA and miRNA qPCR data normalization under different stress conditions and demonstrated the superiority of the stable candidates. Our data demonstrate the suitability of barley snoRNAs and miRNAs as potential reference genes for miRNA and mRNA qPCR data normalization under different stress treatments.
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Affiliation(s)
- Jannatul Ferdous
- Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Yuan Li
- Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Nicolas Reid
- Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Peter Langridge
- Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Bu-Jun Shi
- Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae, South Australia 5064, Australia
- * E-mail:
| | - Penny J. Tricker
- Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae, South Australia 5064, Australia
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Stefanon B, Pomari E, Colitti M. Effects of Rosmarinus officinalis extract on human primary omental preadipocytes and adipocytes. Exp Biol Med (Maywood) 2015; 240:884-95. [PMID: 25710930 DOI: 10.1177/1535370214562341] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/12/2014] [Indexed: 12/13/2022] Open
Abstract
The prevalence of obesity is increasing all over the world. Although it has been shown that natural substances influence fat metabolism, little is known about the effect on cellular and molecular mechanisms in human. In this in vitro study, the activity of Rosmarinus officinalis (RO) standardized extract in modulating human primary visceral preadipocytes differentiation, lipolysis, and apoptosis was investigated. Moreover, gene expression of key adipogenesis modulators and microRNAs-seq were evaluated. Preadipocytes treated with RO extract significantly reduced triglyceride incorporation during maturation in a dose-dependent manner without affecting cell viability. In addition, RO extract stimulated lipolytic activity in differentiating preadipocytes and mature adipocytes in treated cells compared to controls. Differentiating preadipocytes incubated in the presence of RO extract showed a decreased expression of cell cycle genes such as cyclin D1, cyclin-dependent kinase 4, cyclin-dependent kinase inhibitor 1A (p21, Cip1) and an increased expression of GATA binding protein 3, wingless-type MMTV integration site family, member 3A mRNA levels. Recent studies have demonstrated that some phytochemicals alter the expression of specific genes and microRNAs that play a fundamental role in the pathogenesis of obesity and related diseases. Interestingly, genes modulated in RO-treated cells were found to be validated miRNAs targets, such as let-7f-1, miR-17, and miR-143. The results indicated that RO extract modulates human adipocyte differentiation and significantly interferes with adipogenesis and lipid metabolism, supporting its interest as dietary supplement.
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Affiliation(s)
- Bruno Stefanon
- Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy
| | - Elena Pomari
- Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy
| | - Monica Colitti
- Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy
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Boušová I, Matoušková P, Bártíková H, Szotáková B, Hanušová V, Tománková V, Anzenbacherová E, Lišková B, Anzenbacher P, Skálová L. Influence of diet supplementation with green tea extract on drug-metabolizing enzymes in a mouse model of monosodium glutamate-induced obesity. Eur J Nutr 2015; 55:361-71. [PMID: 25663641 DOI: 10.1007/s00394-015-0856-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/31/2015] [Indexed: 12/22/2022]
Abstract
PURPOSE Consumption of dietary supplements with green tea extract (GTE) is popular for weight management, but it may be accompanied by various side effects, including interactions with drugs. The aim of the present in vivo study was to evaluate the effect of defined GTE (Polyphenon 60) in three dosage schemes on insulin, leptin and drug-metabolizing enzymes in obese mice. METHODS Experimental obesity was induced by repeated s.c. application of monosodium glutamate to newborn mice. Green tea extract was administered in three dosage schemes in chow diet. The plasmatic levels of insulin and leptin were assayed using enzyme-linked immunosorbent assay. Enzyme activities and mRNA expressions of drug-metabolizing enzymes (totally 13) were analyzed in liver and small intestine using spectrophotometric and HPLC assays and RT-PCR, respectively. RESULTS GTE-treatment decreased insulin and leptin levels. Eleven enzymes were significantly affected by GTE-treatment. Long-term administration of 0.01% GTE caused increase in the activity and mRNA level of cytochrome P450 3A4 (CYP3A4) ortholog in the liver as well as in the small intestine. Interestingly, short-term overdose by GTE (0.1%) had more pronounced effects on enzyme activities and mRNA expressions than long-term overdose. CONCLUSIONS GTE-mediated induction of CYP3A4 ortholog, the main drug-metabolizing enzyme, could result in decreased efficacy of simultaneously or subsequently administered drug in obese individuals.
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Affiliation(s)
- Iva Boušová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic.
| | - Petra Matoušková
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Hana Bártíková
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Barbora Szotáková
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Veronika Hanušová
- Faculty of Medicine in Hradec Králové, Charles University in Prague, Šimkova 870, 500 38, Hradec Králové, Czech Republic
| | - Veronika Tománková
- Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 775 15, Olomouc, Czech Republic
| | - Eva Anzenbacherová
- Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 775 15, Olomouc, Czech Republic
| | - Barbora Lišková
- Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 775 15, Olomouc, Czech Republic
| | - Pavel Anzenbacher
- Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 775 15, Olomouc, Czech Republic
| | - Lenka Skálová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
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Stixová L, Sehnalová P, Legartová S, Suchánková J, Hrušková T, Kozubek S, Sorokin DV, Matula P, Raška I, Kovařík A, Fulneček J, Bártová E. HP1β-dependent recruitment of UBF1 to irradiated chromatin occurs simultaneously with CPDs. Epigenetics Chromatin 2014; 7:39. [PMID: 25587355 PMCID: PMC4293114 DOI: 10.1186/1756-8935-7-39] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 12/12/2014] [Indexed: 11/24/2022] Open
Abstract
Background The repair of spontaneous and induced DNA lesions is a multistep process. Depending on the type of injury, damaged DNA is recognized by many proteins specifically involved in distinct DNA repair pathways. Results We analyzed the DNA-damage response after ultraviolet A (UVA) and γ irradiation of mouse embryonic fibroblasts and focused on upstream binding factor 1 (UBF1), a key protein in the regulation of ribosomal gene transcription. We found that UBF1, but not nucleolar proteins RPA194, TCOF, or fibrillarin, was recruited to UVA-irradiated chromatin concurrently with an increase in heterochromatin protein 1β (HP1β) level. Moreover, Förster Resonance Energy Transfer (FRET) confirmed interaction between UBF1 and HP1β that was dependent on a functional chromo shadow domain of HP1β. Thus, overexpression of HP1β with a deleted chromo shadow domain had a dominant-negative effect on UBF1 recruitment to UVA-damaged chromatin. Transcription factor UBF1 also interacted directly with DNA inside the nucleolus but no interaction of UBF1 and DNA was confirmed outside the nucleolus, where UBF1 recruitment to DNA lesions appeared simultaneously with cyclobutane pyrimidine dimers; this occurrence was cell-cycle-independent. Conclusions We propose that the simultaneous presence and interaction of UBF1 and HP1β at DNA lesions is activated by the presence of cyclobutane pyrimidine dimers and mediated by the chromo shadow domain of HP1β. This might have functional significance for nucleotide excision repair. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-7-39) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lenka Stixová
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Sehnalová
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Soňa Legartová
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Jana Suchánková
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Tereza Hrušková
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Stanislav Kozubek
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Dmitry V Sorokin
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic ; Faculty of Informatics, Masaryk University, Botanická 68a, 602 00 Brno, Czech Republic
| | - Pavel Matula
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic ; Faculty of Informatics, Masaryk University, Botanická 68a, 602 00 Brno, Czech Republic
| | - Ivan Raška
- Institute of Cellular Biology and Pathology, the First Faculty of Medicine, Charles University in Prague, Albertov 4, 128 01 Prague, Czech Republic
| | - Aleš Kovařík
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Jaroslav Fulneček
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Eva Bártová
- Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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Matoušková P, Bártíková H, Boušová I, Levorová L, Szotáková B, Skálová L. Drug-Metabolizing and Antioxidant Enzymes in Monosodium L-Glutamate Obese Mice. Drug Metab Dispos 2014; 43:258-65. [DOI: 10.1124/dmd.114.061176] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Sparks ME, Shelby KS, Kuhar D, Gundersen-Rindal DE. Transcriptome of the invasive brown marmorated stink bug, Halyomorpha halys (Stål) (Heteroptera: Pentatomidae). PLoS One 2014; 9:e111646. [PMID: 25386688 PMCID: PMC4227672 DOI: 10.1371/journal.pone.0111646] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/03/2014] [Indexed: 01/29/2023] Open
Abstract
Halyomorpha halys (Stål) (Heteroptera: Pentatomidae), the brown marmorated stink bug, is an invasive agricultural and nuisance pest rapidly expanding its incidence in North America. This voracious pest poses a significant threat to rural and urban agriculture, especially to specialty crops such as apples, grapes and ornamentals, as well as staple crops including soybean and corn. The object of this study was to generate transcript sequence resources for H. halys. RNA-seq libraries derived from distinct developmental stages and sexes were sequenced and assembled into 248,569 putatively unique transcripts (PUTs). PUTs were segmented into three disjoint tiers of varying reliability, with 4,794 classified as gold tier (highest quality), 16,878 as silver, and 14,357 as bronze. The gold-tier PUTs associated with 2,580 distinct non-redundant protein sequences from the NCBI NR database--1,785 of these (69%) mapped to annotated UniProtKB database proteins, from which 1,273 unique Pfam families and 459 unique Molecular Function GO terms were encountered. Of the silver tier's 6,527 PUTs associated with unique proteins, 4,193 mapped to UniProtKB (64%), from which 1,941 and 640 unique Pfam and Molecular Function GO terms were extracted. H. halys PUTs related to important life processes like immunity, endocrinology, reproduction, development, behavior, neurotransmission, neurotoxicity, olfaction, and small RNA pathways were validated through quantitative Real-Time PCR (qRT-PCR) for differential expression during distinct life stages (eggs, 2nd instar nymphs, 4th instar nymphs, female adults, male adults). PUTs similar to hypothetical proteins identified in symbiont microbes, including Pantoea and Nosema species, were more abundantly expressed in adults versus nymphs. These comprehensive H. halys transcriptomic resources can be utilized to aid development of novel control methodologies to disrupt life processes; to conduct reverse genetic screens to determine host gene function; and to design environmentally unobtrusive means to control host populations or target specific H. halys life stages, such as molecular biopesticides.
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Affiliation(s)
- Michael E. Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Kent S. Shelby
- USDA-ARS Biological Control of Insects Research Laboratory, Columbia, Missouri, United States of America
| | - Daniel Kuhar
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Dawn E. Gundersen-Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
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Bouhaddioui W, Provost PR, Tremblay Y. Identification of most stable endogenous control genes for microRNA quantification in the developing mouse lung. PLoS One 2014; 9:e111855. [PMID: 25368994 PMCID: PMC4219792 DOI: 10.1371/journal.pone.0111855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/07/2014] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous small non coding RNAs acting as negative regulators. miRNA are involved in lung development and pulmonary diseases. Measurement of their levels by qPCR is directly influenced by the stability of normalization gene(s), which can be affected by the experimental conditions. The developing lung is a changing tissue and one normalization gene showing stability on one developmental day may be modulated over time. Moreover, some developmental events are affected by sex, which also has to be considered. In this study, we compared stability of five putative control genes in the lung between sexes from the pseudoglandular to the alveolar stages and in adult lungs. Expression of sno135, sno142, sno202, sno234, and sno251 was studied by qPCR in male and female lung samples collected at seven time points from GD 15.5 to PN 30. Cq values of sno251 showed the highest variation across the different developmental stages, while sno234 was the most stable gene. Gene expression stability was studied by geNorm, NormFinder and BestKeeper. Our data showed that ranking of genes based on expression stability changed according to developmental time and sex. sno135/sno234 and sno142/sno234 were proposed as best combinations of normalization genes when both sexes and all the studied developmental stages are considered. Normalization of let7-a RNA levels with different pairs of control genes proposed by geNorm and NormFinder gave similar data, while the use of less stable genes introduced a statistically significant difference on PN 0. In conclusion, variations in stability of normalization gene expression are observed over time and according to sex during lung development. Best pairs of normalization genes are presented for specific developmental stages, and for the period extending from the pseudoglandular to the alveolar stages. The use of normalization genes selected for their expression stability is essential in lung development studies.
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Affiliation(s)
- Wafae Bouhaddioui
- Reproduction, Mother and Youth Health, Centre de recherche CHU de Québec, Québec, QC, Canada
- Centre de Recherche en Biologie de la Reproduction (CRBR), Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Pierre R. Provost
- Reproduction, Mother and Youth Health, Centre de recherche CHU de Québec, Québec, QC, Canada
- Department of Obstetrics/Gynecology & Reproduction, Faculty of Medicine, Université Laval, Québec, QC, Canada
- Centre de Recherche en Biologie de la Reproduction (CRBR), Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Yves Tremblay
- Reproduction, Mother and Youth Health, Centre de recherche CHU de Québec, Québec, QC, Canada
- Department of Obstetrics/Gynecology & Reproduction, Faculty of Medicine, Université Laval, Québec, QC, Canada
- Centre de Recherche en Biologie de la Reproduction (CRBR), Faculté de Médecine, Université Laval, Québec, QC, Canada
- * E-mail:
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Moura J, Børsheim E, Carvalho E. The Role of MicroRNAs in Diabetic Complications-Special Emphasis on Wound Healing. Genes (Basel) 2014; 5:926-56. [PMID: 25268390 PMCID: PMC4276920 DOI: 10.3390/genes5040926] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/05/2014] [Accepted: 09/10/2014] [Indexed: 12/19/2022] Open
Abstract
Overweight and obesity are major problems in today’s society, driving the prevalence of diabetes and its related complications. It is important to understand the molecular mechanisms underlying the chronic complications in diabetes in order to develop better therapeutic approaches for these conditions. Some of the most important complications include macrovascular abnormalities, e.g., heart disease and atherosclerosis, and microvascular abnormalities, e.g., retinopathy, nephropathy and neuropathy, in particular diabetic foot ulceration. The highly conserved endogenous small non-coding RNA molecules, the micro RNAs (miRNAs) have in recent years been found to be involved in a number of biological processes, including the pathogenesis of disease. Their main function is to regulate post-transcriptional gene expression by binding to their target messenger RNAs (mRNAs), leading to mRNA degradation, suppression of translation or even gene activation. These molecules are promising therapeutic targets and demonstrate great potential as diagnostic biomarkers for disease. This review aims to describe the most recent findings regarding the important roles of miRNAs in diabetes and its complications, with special attention given to the different phases of diabetic wound healing.
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Affiliation(s)
- João Moura
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-517, Portugal.
| | - Elisabet Børsheim
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, AR 72202, USA.
| | - Eugenia Carvalho
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-517, Portugal.
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Matoušková P, Bártíková H, Boušová I, Szotáková B, Martin J, Skorkovská J, Hanušová V, Tománková V, Anzenbacherová E, Lišková B, Anzenbacher P, Skálová L. Effect of defined green tea extract in various dosage schemes on drug-metabolizing enzymes in mice in vivo. J Funct Foods 2014. [DOI: 10.1016/j.jff.2014.06.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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McCann CC, Viner ME, Donkin SS, White HM. Hepatic patatin-like phospholipase domain-containing protein 3 sequence, single nucleotide polymorphism presence, protein confirmation, and responsiveness to energy balance in dairy cows. J Dairy Sci 2014; 97:5167-75. [PMID: 24931521 DOI: 10.3168/jds.2014-7910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/02/2014] [Indexed: 12/24/2022]
Abstract
Patatin-like phospholipase domain-containing protein 3 (PNPLA3), commonly known as adiponutrin, is part of a novel subfamily of triglyceride lipase enzymes with potential effects on triglyceride metabolism in adipose and hepatic tissues. The predicted bovine PNPLA3 sequence has been identified, but expression of the gene had not been examined. The objectives of this study were to confirm the predicted bovine PNPLA3 gene sequence, determine expression of the bovine PNPLA3 gene in response to whole-animal energy balance, identify single nucleotide polymorphisms present in dairy cows, and verify the presence of the protein in the liver. Using liver biopsy samples collected from cows at +28d relative to calving (DRTC), RNA was isolated and used to generate a cDNA template for amplification of the entire predicted coding sequence of PNPLA3 via PCR. To determine if energy balance alters the expression of PNPLA3, RNA was isolated and mRNA expression quantified in liver samples from mid-lactation cows after a 5-d ad libitum period (n=5) and after a subsequent 5-d 50% feed restriction period (n=5), and in samples collected from cows at -14, +1, +14, and +28 DRTC (n=16). The presence of PNPLA3 protein was detected by Western blot in liver protein samples collected at +28 DRTC. Expression of hepatic PNPLA3 was decreased after a period of feed restriction (8.14 vs. 1.08±2.17 arbitrary units, ad libitum vs. fasted). Expression of PNPLA3 mRNA was decreased at +1 and +14 DRTC compared with -14 DRTC (23.35, 7.28, 10.17, and 14.5±4.9 arbitrary units, -14, +1, +14, and +28 DRTC, respectively). The presence of PNPLA3 protein was detected as a 55-kDa band in hepatic protein isolations from liver tissue collected at +28 DRTC. These data confirm the presence and sequence of the bovine hepatic PNPLA3 gene and single nucleotide polymorphisms. Furthermore, these data indicate responsiveness of bovine hepatic PNPLA3 to energy balance.
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Affiliation(s)
| | - Molly E Viner
- Department of Animal Science, University of Connecticut, Storrs 06269
| | - Shawn S Donkin
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - H M White
- Department of Dairy Science, University of Wisconsin, Madison 53706.
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