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Yadav B, Singh D, Mantri S, Rishi V. Genome-wide Methylation Dynamics and Context-dependent Gene Expression Variability in Differentiating Preadipocytes. J Endocr Soc 2024; 8:bvae121. [PMID: 38966711 PMCID: PMC11222978 DOI: 10.1210/jendso/bvae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Indexed: 07/06/2024] Open
Abstract
Obesity, characterized by the accumulation of excess fat, is a complex condition resulting from the combination of genetic and epigenetic factors. Recent studies have found correspondence between DNA methylation and cell differentiation, suggesting a role of the former in cell fate determination. There is a lack of comprehensive understanding concerning the underpinnings of preadipocyte differentiation, specifically when cells are undergoing terminal differentiation (TD). To gain insight into dynamic genome-wide methylation, 3T3 L1 preadipocyte cells were differentiated by a hormone cocktail. The genomic DNA was isolated from undifferentiated cells and 4 hours, 2 days postdifferentiated cells, and 15 days TD cells. We employed whole-genome bisulfite sequencing (WGBS) to ascertain global genomic DNA methylation alterations at single base resolution as preadipocyte cells differentiate. The genome-wide distribution of DNA methylation showed similar overall patterns in pre-, post-, and terminally differentiated adipocytes, according to WGBS analysis. DNA methylation decreases at 4 hours after differentiation initiation, followed by methylation gain as cells approach TD. Studies revealed novel differentially methylated regions (DMRs) associated with adipogenesis. DMR analysis suggested that though DNA methylation is global, noticeable changes are observed at specific sites known as "hotspots." Hotspots are genomic regions rich in transcription factor (TF) binding sites and exhibit methylation-dependent TF binding. Subsequent analysis indicated hotspots as part of DMRs. The gene expression profile of key adipogenic genes in differentiating adipocytes is context-dependent, as we found a direct and inverse relationship between promoter DNA methylation and gene expression.
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Affiliation(s)
- Binduma Yadav
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
- Regional Center for Biotechnology, Faridabad, Haryana 160014, India
| | - Dalwinder Singh
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
- Department of Anatomy and Cell Biology, Western University, London, Ontario N6A 5C1, Canada
| | - Shrikant Mantri
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
| | - Vikas Rishi
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
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Doukbi E, Ancel P, Dutour A, Soghomonian A, Ahmed S, Castejon V, Piperoglou C, Gariboldi V, Lenoir M, Lechevallier E, Gondran-Tellier B, Boissier R, Ebbo M, Vély F, Gaborit B. Human epicardial fat has a beige profile and contains higher type 2 innate lymphoid cells than subcutaneous fat. Obesity (Silver Spring) 2024; 32:1302-1314. [PMID: 38747118 DOI: 10.1002/oby.24023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 06/28/2024]
Abstract
OBJECTIVE Epicardial adipose tissue (EAT) is a visceral fat that has been associated with coronary artery disease and atrial fibrillation. Previous work has revealed that EAT exhibits beige features. METHODS First, a new pan-genomic microarray analysis was performed on previously collected paired human EAT and thoracic subcutaneous AT (thSAT) from the EPICAR study (n = 31) to decipher a specific immune signature and its link with browning genes. Then, adaptive (T and B cells) and innate lymphoid cell (ILC1, ILC2, and ILC3) immunophenotyping assay panels, including CD127, CD117, and prostaglandin D2 receptor 2, were performed on prospectively collected paired human multiorgan donors (n = 18; INTERFACE study). RESULTS In the EPICAR study, a positive correlation between the T helper cell subtype Th2 immune pathway and browning genes was found in EAT versus thSAT (r = 0.82; p < 0.0001). In the INTERFACE study, this correlation was also observed (r = 0.31; p = 0.017), and a preponderance of CD4+T cells, CD8+T cells, and a few B cells was observed in all ATs (p < 0.0001). An increase in ILCs was observed in visceral AT (VAT) (i.e., EAT + VAT; 30 ± 5 ILCs per gram of AT) compared with subcutaneous counterparts (i.e., thSAT + abdominal SAT; 8 ± 2 ILCs per gram of AT; p = 0.001), with ILC1 being the most frequent (ILC1 > ILC3 > ILC2). Numbers of ILCs per gram of AT correlated with several Th2 or browning genes (IL-13, TNF receptor superfamily member 9 [TNFRSF9], and alkaline phosphatase, biomineralization associated [ALPL]). Interestingly, a specific increase in EAT-ILC2 compared with other ATs was observed, including a significant proportion expressing CD69 and/or CD25 activation markers (97.9% ± 1.2%; p < 0.0001). Finally, more natural killer cells were observed in EAT + VAT than in thSAT + abdominal SAT (p = 0.01). Exclusion of patients with coronary artery disease in the EPICAR and INTERFACE studies did not modify the main findings. Gene expression phenotyping confirmed specific upregulation of Th2 pathway and browning genes (IL-33 and uncoupling protein 1 [UCP-1]) in EAT. CONCLUSIONS This is the first study, to our knowledge, to provide a comparison between innate and adaptive lymphoid cells in human EAT. Further studies are ongoing to decipher whether these cells could be involved in EAT beiging.
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Affiliation(s)
- Elisa Doukbi
- Aix-Marseille University, National Institute for Health and Medical Research (INSERM), National Research Institute for Agriculture, Food and the Environment (INRAE), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
| | - Patricia Ancel
- Aix-Marseille University, National Institute for Health and Medical Research (INSERM), National Research Institute for Agriculture, Food and the Environment (INRAE), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
| | - Anne Dutour
- Aix-Marseille University, National Institute for Health and Medical Research (INSERM), National Research Institute for Agriculture, Food and the Environment (INRAE), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
- Department of Endocrinology, Metabolic Diseases and Nutrition, Pole Endocrinology-Nutrition-Diabetes-Obesity, Public Assistance Marseille Hospitals, Marseille, France
| | - Astrid Soghomonian
- Aix-Marseille University, National Institute for Health and Medical Research (INSERM), National Research Institute for Agriculture, Food and the Environment (INRAE), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
- Department of Endocrinology, Metabolic Diseases and Nutrition, Pole Endocrinology-Nutrition-Diabetes-Obesity, Public Assistance Marseille Hospitals, Marseille, France
| | - Shaista Ahmed
- Aix-Marseille University, National Institute for Health and Medical Research (INSERM), National Research Institute for Agriculture, Food and the Environment (INRAE), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
- Heart Repair and Regeneration Laboratory, Department of Endocrinology, Metabolism, and Cardiovascular System, Faculty of Sciences and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Victoria Castejon
- Aix-Marseille University, National Institute for Health and Medical Research (INSERM), National Research Institute for Agriculture, Food and the Environment (INRAE), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
| | - Christelle Piperoglou
- Aix-Marseille University, CNRS, National Institute for Health and Medical Research (INSERM), Marseille-Luminy Immunology Center (CIML), Marseille University Hospital Timone, Public Assistance Marseille Hospitals, Marseille Immunopole, Marseille, France
| | - Vlad Gariboldi
- Aix-Marseille University, National Institute for Health and Medical Research (INSERM), National Research Institute for Agriculture, Food and the Environment (INRAE), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
- Department of Cardiac Surgery, Marseille University Hospital Timone, Public Assistance Marseille Hospitals, Marseille, France
| | - Marien Lenoir
- Division of Paediatric Cardiac Surgery, Marseille University Hospital Timone, Public Assistance Marseille Hospitals, Marseille, France
| | - Eric Lechevallier
- Department of Urology Surgery, Conception Hospital, Public Assistance Marseille Hospitals, Marseille, France
| | - Bastien Gondran-Tellier
- Department of Urology Surgery, Conception Hospital, Public Assistance Marseille Hospitals, Marseille, France
| | - Romain Boissier
- Department of Urology Surgery, Conception Hospital, Public Assistance Marseille Hospitals, Marseille, France
| | - Mikael Ebbo
- Aix-Marseille University, CNRS, National Institute for Health and Medical Research (INSERM), Marseille-Luminy Immunology Center (CIML), Marseille University Hospital Timone, Public Assistance Marseille Hospitals, Marseille Immunopole, Marseille, France
- Internal Medicine Department, Marseille University Hospital Timone, Public Assistance Marseille Hospitals, Marseille, France
| | - Frédéric Vély
- Aix-Marseille University, CNRS, National Institute for Health and Medical Research (INSERM), Marseille-Luminy Immunology Center (CIML), Marseille University Hospital Timone, Public Assistance Marseille Hospitals, Marseille Immunopole, Marseille, France
| | - Bénédicte Gaborit
- Aix-Marseille University, National Institute for Health and Medical Research (INSERM), National Research Institute for Agriculture, Food and the Environment (INRAE), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
- Department of Endocrinology, Metabolic Diseases and Nutrition, Pole Endocrinology-Nutrition-Diabetes-Obesity, Public Assistance Marseille Hospitals, Marseille, France
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3
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Macário MS, Nascimento CS, Sousa FCB, Oliveira IRS, Vesco APD, Barbosa LT, Sousa KRS. Identification of reference genes for studies of quantitative gene expression in male and female quail tissues. Anim Biotechnol 2023; 34:2400-2413. [PMID: 35792778 DOI: 10.1080/10495398.2022.2092744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In industrial poultry, quail production has gained increasing prominence over the years. It is known that the intensification of genetic studies has contributed greatly to this growth, through techniques, such as analysis of gene expression by PCR, for example. This study aimed to evaluate stability and recommend reference genes for quantitative real-time PCR in different tissues from male and female broiler quails. The stability of 10 housekeeping genes (GAPDH, RPL5, MRPS27, MRPS30, TFRC, HMBS, EEF1, LDHA, B2M, and UBC) by means Bestkeeper, NormFinder, GeNorm softwares with ΔCq method. The tissues analyzed were: heart, thigh muscle, brain, and spleen, considering that they are tissues commonly used in nutrigenomic, immunological, and poultry performance research. As expected, the reference genes tested showed varying stability depending on the tissue evaluated. According to the present study, the most stable housekeeping genes were MRPS30, TFRC, and HMBS in heart; MRPS30, EEF1, and HMBS in thigh muscle; B2M, GAPDH, and UBC in brain; and EEF1, LDHA, and HMBS in spleen. Therefore, it is recommended to be used as reference genes for gene expression studies of male and female quails.
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Affiliation(s)
- M S Macário
- Department of Animal Science, Universidade Federal de Sergipe, São Cristóvão, Brazil
| | - C S Nascimento
- Núcleo de Graduação em Ciências Agrárias e da Terra, Universidade Federal de Sergipe, Nossa Senhora da Glória, Brazil
| | - F C B Sousa
- Department of Animal Science, Universidade Federal do Piauí, Bom Jesus, Brazil
| | - I R S Oliveira
- Department of Animal Science, Universidade Federal de Sergipe, São Cristóvão, Brazil
| | - A P D Vesco
- Department of Animal Science, Universidade Federal de Sergipe, São Cristóvão, Brazil
| | - L T Barbosa
- Department of Animal Science, Universidade Federal de Sergipe, São Cristóvão, Brazil
| | - K R S Sousa
- Department of Animal Science, Universidade Federal do Maranhão, Chapadinha, Brazil
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Pérez-Gómez JM, Porcel-Pastrana F, De La Luz-Borrero M, Montero-Hidalgo AJ, Gómez-Gómez E, Herrera-Martínez AD, Guzmán-Ruiz R, Malagón MM, Gahete MD, Luque RM. LRP10, PGK1 and RPLP0: Best Reference Genes in Periprostatic Adipose Tissue under Obesity and Prostate Cancer Conditions. Int J Mol Sci 2023; 24:15140. [PMID: 37894825 PMCID: PMC10606769 DOI: 10.3390/ijms242015140] [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: 09/04/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Obesity (OB) is a metabolic disorder characterized by adipose tissue dysfunction that has emerged as a health problem of epidemic proportions in recent decades. OB is associated with multiple comorbidities, including some types of cancers. Specifically, prostate cancer (PCa) has been postulated as one of the tumors that could have a causal relationship with OB. Particularly, a specialized adipose tissue (AT) depot known as periprostatic adipose tissue (PPAT) has gained increasing attention over the last few years as it could be a key player in the pathophysiological interaction between PCa and OB. However, to date, no studies have defined the most appropriate internal reference genes (IRGs) to be used in gene expression studies in this AT depot. In this work, two independent cohorts of PPAT samples (n = 20/n = 48) were used to assess the validity of a battery of 15 literature-selected IRGs using two widely used techniques (reverse transcription quantitative PCR [RT-qPCR] and microfluidic-based qPCR array). For this purpose, ΔCt method, GeNorm (v3.5), BestKeeper (v1.0), NormFinder (v.20.0), and RefFinder software were employed to assess the overall trends of our analyses. LRP10, PGK1, and RPLP0 were identified as the best IRGs to be used for gene expression studies in human PPATs, specifically when considering PCa and OB conditions.
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Grants
- PID2022-1381850B-I00 Spanish Ministry of Science, Innovation, and Universities
- PID2019-105564RB-I00 Spanish Ministry of Science, Innovation, and Universities
- FPU18-06009 Spanish Ministry of Science, Innovation, and Universities
- PRE2020-094225 Spanish Ministry of Science, Innovation, and Universities
- FPU18-02485 Spanish Ministry of Science, Innovation, and Universities
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Affiliation(s)
- Jesús M. Pérez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Francisco Porcel-Pastrana
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Marina De La Luz-Borrero
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Antonio J. Montero-Hidalgo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Enrique Gómez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Urology Service, Reina Sofia University Hospital, 14004 Cordoba, Spain
| | - Aura D. Herrera-Martínez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, 14004 Cordoba, Spain
| | - Rocío Guzmán-Ruiz
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - María M. Malagón
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Manuel D. Gahete
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Raúl M. Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
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Guaita-Cespedes M, Grillo-Risco R, Hidalgo MR, Fernández-Veledo S, Burks DJ, de la Iglesia-Vayá M, Galán A, Garcia-Garcia F. Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies. Biol Sex Differ 2023; 14:20. [PMID: 37072826 PMCID: PMC10114345 DOI: 10.1186/s13293-023-00506-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/07/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND As the housekeeping genes (HKG) generally involved in maintaining essential cell functions are typically assumed to exhibit constant expression levels across cell types, they are commonly employed as internal controls in gene expression studies. Nevertheless, HKG may vary gene expression profile according to different variables introducing systematic errors into experimental results. Sex bias can indeed affect expression display, however, up to date, sex has not been typically considered as a biological variable. METHODS In this study, we evaluate the expression profiles of six classical housekeeping genes (four metabolic: GAPDH, HPRT, PPIA, and UBC, and two ribosomal: 18S and RPL19) to determine expression stability in adipose tissues (AT) of Homo sapiens and Mus musculus and check sex bias and their overall suitability as internal controls. We also assess the expression stability of all genes included in distinct whole-transcriptome microarrays available from the Gene Expression Omnibus database to identify sex-unbiased housekeeping genes (suHKG) suitable for use as internal controls. We perform a novel computational strategy based on meta-analysis techniques to identify any sexual dimorphisms in mRNA expression stability in AT and to properly validate potential candidates. RESULTS Just above half of the considered studies informed properly about the sex of the human samples, however, not enough female mouse samples were found to be included in this analysis. We found differences in the HKG expression stability in humans between female and male samples, with females presenting greater instability. We propose a suHKG signature including experimentally validated classical HKG like PPIA and RPL19 and novel potential markers for human AT and discarding others like the extensively used 18S gene due to a sex-based variability display in adipose tissue. Orthologs have also been assayed and proposed for mouse WAT suHKG signature. All results generated during this study are readily available by accessing an open web resource ( https://bioinfo.cipf.es/metafun-HKG ) for consultation and reuse in further studies. CONCLUSIONS This sex-based research proves that certain classical housekeeping genes fail to function adequately as controls when analyzing human adipose tissue considering sex as a variable. We confirm RPL19 and PPIA suitability as sex-unbiased human and mouse housekeeping genes derived from sex-specific expression profiles, and propose new ones such as RPS8 and UBB.
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Affiliation(s)
- Maria Guaita-Cespedes
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026, Valencia, Spain
| | - Rubén Grillo-Risco
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Marta R Hidalgo
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Sonia Fernández-Veledo
- Department of Endocrinology and Nutrition and Research Unit, University Hospital of Tarragona Joan XXIII, Institut d'Investigaciò Sanitària Pere Virgili (IISPV), Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Deborah Jane Burks
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Molecular Neuroendocrinology Laboratory, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - María de la Iglesia-Vayá
- Imaging Unit FISABIO-CIPF, Fundación Para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, 46012, Valencia, Spain
| | - Amparo Galán
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
- Molecular Neuroendocrinology Laboratory, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
| | - Francisco Garcia-Garcia
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
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Zhao L, Yang H, Li X, Zhou Y, Liu T, Zhao Y. Transcriptome-based selection and validation of optimal reference genes in perirenal adipose developing of goat ( Capra hircus). Front Vet Sci 2022; 9:1055866. [PMID: 36467654 PMCID: PMC9712442 DOI: 10.3389/fvets.2022.1055866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/02/2022] [Indexed: 06/15/2024] Open
Abstract
Brown adipose tissue (BAT) is mainly present in young mammals and is important for maintaining body temperature in neonatal mammals because of its ability to produce non-shivering thermogenesis. There is usually a large amount of BAT around the kidneys of newborn kids, but the BAT gradually "whiting" after birth. Screening and validating appropriate reference genes is a prerequisite for further studying the mechanism of goat brown adipose tissue "whiting" during the early stages. In this study, the expression stability of 17 candidate reference genes: 12 COPS8, SAP18, IGF2R, PARL, SNRNP200, ACTG1, CLTA, GANAB, GABARAP, PCBP2, CTSB, and CD151) selected based on previous transcriptome data as new candidate reference genes, 3 (PFDN5, CTNNB1, and EIF3M) recommended in previous studies, and 2 traditional reference genes (ACTB and GAPDH) was evaluated. Real-time quantitative PCR (RT-qPCR) technology was used to detect the expression level of candidate reference genes during goat BAT "whiting". Four algorithms: Normfinder, geNorm, ΔCt method, and BestKeeper, and two comprehensive algorithms: ComprFinder and RefFinder, were used to analyze the stability of each candidate reference genes. GABARAP, CLTA, GAPDH, and ACTB were identified as the most stable reference genes, while CTNNB1, CTSB, and EIF3M were the least stable. Moreover, two randomly selected target genes IDH2 and RBP4, were effectively normalized using the selected most stable reference genes. These findings collectively suggest that GABARAP, CLTA, GAPDH, and ACTB are relatively stable reference genes that can potentially be used for the development of perirenal fat in goats.
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Validation of quantitative real-time PCR reference genes and spatial expression profiles of detoxication-related genes under pesticide induction in honey bee, Apis mellifera. PLoS One 2022; 17:e0277455. [DOI: 10.1371/journal.pone.0277455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
Recently, pesticides have been suggested to be one of the factors responsible for the large-scale decline in honey bee populations, including colony collapse disorder. The identification of the genes that respond to pesticide exposure based on their expression is essential for understanding the xenobiotic detoxification metabolism in honey bees. For the accurate determination of target gene expression by quantitative real-time PCR, the expression stability of reference genes should be validated in honey bees exposed to various pesticides. Therefore, in this study, to select the optimal reference genes, we analyzed the amplification efficiencies of five candidate reference genes (RPS5, RPS18, GAPDH, ARF1, and RAD1a) and their expression stability values using four programs (geNorm, NormFinder, BestKeeper, and RefFinder) across samples of five body parts (head, thorax, gut, fat body, and carcass) from honey bees exposed to seven pesticides (acetamiprid, imidacloprid, flupyradifurone, fenitrothion, carbaryl, amitraz, and bifenthrin). Among these five candidate genes, a combination of RAD1a and RPS18 was suggested for target gene normalization. Subsequently, expression levels of six genes (AChE1, CYP9Q1, CYP9Q2, CYP9Q3, CAT, and SOD1) were normalized with a combination of RAD1a and RPS18 in the different body parts from honey bees exposed to pesticides. Among the six genes in the five body parts, the expression of SOD1 in the head, fat body, and carcass was significantly induced by six pesticides. In addition, among seven pesticides, flupyradifurone statistically induced expression levels of five genes in the fat body.
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McLaughlin T, Schnittger I, Nagy A, Zanley E, Xu Y, Song Y, Nieman K, Tremmel JA, Dey D, Boyd J, Sacks H. Relationship Between Coronary Atheroma, Epicardial Adipose Tissue Inflammation, and Adipocyte Differentiation Across the Human Myocardial Bridge. J Am Heart Assoc 2021; 10:e021003. [PMID: 34726081 PMCID: PMC8751937 DOI: 10.1161/jaha.121.021003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background Inflammation in epicardial adipose tissue (EAT) may contribute to coronary atherosclerosis. Myocardial bridge is a congenital anomaly in which the left anterior descending coronary artery takes a "tunneled" course under a bridge of myocardium: while atherosclerosis develops in the proximal left anterior descending coronary artery, the bridged portion is spared, highlighting the possibility that geographic separation from inflamed EAT is protective. We tested the hypothesis that inflammation in EAT was related to atherosclerosis by comparing EAT from proximal and bridge depots in individuals with myocardial bridge and varying degrees of atherosclerotic plaque. Methods and Results Maximal plaque burden was quantified by intravascular ultrasound, and inflammation was quantified by pericoronary EAT signal attenuation (pericoronary adipose tissue attenuation) from cardiac computed tomography scans. EAT overlying the proximal left anterior descending coronary artery and myocardial bridge was harvested for measurement of mRNA and microRNA (miRNA) using custom chips by Nanostring; inflammatory cytokines were measured in tissue culture supernatants. Pericoronary adipose tissue attenuation was increased, indicating inflammation, in proximal versus bridge EAT, in proportion to atherosclerotic plaque. Individuals with moderate-high versus low plaque burden exhibited greater expression of inflammation and hypoxia genes, and lower expression of adipogenesis genes. Comparison of gene expression in proximal versus bridge depots revealed differences only in participants with moderate-high plaque: inflammation was higher in proximal and adipogenesis lower in bridge EAT. Secreted inflammatory cytokines tended to be higher in proximal EAT. Hypoxia-inducible factor 1a was highly associated with inflammatory gene expression. Seven miRNAs were differentially expressed by depot: 3192-5P, 518D-3P, and 532-5P were upregulated in proximal EAT, whereas miR 630, 575, 16-5P, and 320E were upregulated in bridge EAT. miR 630 correlated directly with plaque burden and inversely with adipogenesis genes. miR 3192-5P, 518D-3P, and 532-5P correlated inversely with hypoxia/oxidative stress, peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PCG1a), adipogenesis, and angiogenesis genes. Conclusions Inflammation is specifically elevated in EAT overlying atherosclerotic plaque, suggesting that EAT inflammation is caused by atherogenic molecular signals, including hypoxia-inducible factor 1a and/or miRNAs in an "inside-to-out" relationship. Adipogenesis was suppressed in the bridge EAT, but only in the presence of atherosclerotic plaque, supporting cross talk between the vasculature and EAT. miR 630 in EAT, expressed differentially according to burden of atherosclerotic plaque, and 3 other miRNAs appear to inhibit key genes related to adipogenesis, angiogenesis, hypoxia/oxidative stress, and thermogenesis in EAT, highlighting a role for miRNA in mediating cross talk between the coronary vasculature and EAT.
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Affiliation(s)
- Tracey McLaughlin
- Division of Endocrinology Stanford University School of Medicine Stanford CA
| | - Ingela Schnittger
- Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA
| | - Anna Nagy
- Division of Endocrinology Stanford University School of Medicine Stanford CA
| | - Elizabeth Zanley
- Division of Endocrinology Stanford University School of Medicine Stanford CA
| | - Yue Xu
- Division of Endocrinology Stanford University School of Medicine Stanford CA
| | - Yanqiu Song
- Cardiovascular Institute Tianjin Chest Hospital Tianjin China
| | - Koen Nieman
- Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA
| | - Jennifer A Tremmel
- Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA
| | - Damini Dey
- Department of Biomedical Sciences and Medicine Cedars-Sinai Medical Center Biomedical Imaging Research Institute Los Angeles CA
| | - Jack Boyd
- Department of Cardiothoracic Surgery Stanford University School of Medicine Stanford CA
| | - Harold Sacks
- Division of Endocrinology Department of Medicine David Geffen School of Medicine at UCLA Los Angeles CA
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Fan X, Yao H, Liu X, Shi Q, Lv L, Li P, Wang R, Tang T, Qi K. High-Fat Diet Alters the Expression of Reference Genes in Male Mice. Front Nutr 2020; 7:589771. [PMID: 33330591 PMCID: PMC7732482 DOI: 10.3389/fnut.2020.589771] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022] Open
Abstract
Quantitative PCR (qPCR), the most accurate and sensitive technique for quantifying mRNA expression, and choice of appropriate reference genes for internal error controlling in qPCR are essential to understanding the molecular mechanisms that drive the obesity epidemic and its comorbidities. In this study, using the high-fat diet (HFD)-induced obese mouse model, we assessed the expression of 10 commonly used reference genes to validate gene-expression stability in adipose tissue, liver, and muscle across different time points (4, 8, 12, and 16 weeks after HFD feeding) during the process of obesity. The data were analyzed by the GeNorm, NormFinder, BestKeeper, and Delta-Ct method, and the results showed that the most stable reference genes were different for a specific organ or tissue in a specific time point; however, PPIA, RPLP0, and YWHAZ were the top three most stable reference genes in qPCR experiments on adipose, hepatic tissues, and muscles of mice in diet-induced obesity. In addition, the mostly used genes ACTB and GAPDH were more unstable in the fat and liver, the ACTB mRNA levels were increased in four adipose tissues, and the GAPDH mRNA levels were decreased in four adipose tissues and liver after HFD feeding. These results suggest that PPIA, RPLP0, or YWHAZ may be more appropriate to be used as reference gene than ACTB and GAPDH in the adipose tissue and liver of mice during the process of high-fat diet-induced obesity.
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Affiliation(s)
- Xiuqin Fan
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Hongyang Yao
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xuanyi Liu
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Qiaoyu Shi
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | | | - Ping Li
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Rui Wang
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tiantian Tang
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Kemin Qi
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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10
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Feng X, Cao X, Zhu R, Huang J. Selection and validation of reference genes for RT-qPCR in adipose and longissimus dorsi muscle tissues of buffalo. Anim Biotechnol 2020; 33:526-535. [DOI: 10.1080/10495398.2020.1811715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Xiaodan Cao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
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11
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Jeon JH, Moon K, Kim Y, Kim YH. Reference gene selection for qRT-PCR analysis of season- and tissue-specific gene expression profiles in the honey bee Apis mellifera. Sci Rep 2020; 10:13935. [PMID: 32811887 PMCID: PMC7435199 DOI: 10.1038/s41598-020-70965-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/07/2020] [Indexed: 01/10/2023] Open
Abstract
Honey bees are both important pollinators and model insects due to their highly developed sociality and colony management. To better understand the molecular mechanisms underlying honey bee colony management, it is important to investigate the expression of genes putatively involved in colony physiology. Although quantitative real-time PCR (qRT-PCR) can be used to quantify the relative expression of target genes, internal reference genes (which are stably expressed across different conditions) must first be identified to ensure accurate normalisation of target genes. To identify reliable reference genes in honey bee (Apis mellifera) colonies, therefore, we evaluated seven candidate genes (ACT, EIF, EF1, RPN2, RPS5, RPS18 and GAPDH) in samples collected from three honey bee tissue types (head, thorax and abdomen) across all four seasons using three analysis programmes (NormFinder, BestKeeper and geNorm). Subsequently, we validated various normalisation methods using each of the seven reference genes and a combination of multiple genes by calculating the expression of catalase (CAT). Although the genes ranked as the most stable gene were slightly different on conditions and analysis methods, our results suggest that RPS5, RPS18 and GAPDH represent optimal honey bee reference genes for target gene normalisation in qRT-PCR analysis of various honey bee tissue samples collected across seasons.
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Affiliation(s)
- Ji Hyang Jeon
- Department of Applied Biology, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
| | - KyungHwan Moon
- Department of Ecological Science, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
| | - YeongHo Kim
- Department of Ecological Science, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
| | - Young Ho Kim
- Department of Applied Biology, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea. .,Department of Ecological Science, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea.
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12
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Validation of reference genes in human epicardial adipose tissue and left ventricular myocardium in heart failure. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00303-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Toczylowski K, Hirnle T, Harasiuk D, Zabielski P, Lewczuk A, Dmitruk I, Ksiazek M, Sulik A, Gorski J, Chabowski A, Baranowski M. Plasma concentration and expression of adipokines in epicardial and subcutaneous adipose tissue are associated with impaired left ventricular filling pattern. J Transl Med 2019; 17:310. [PMID: 31533725 PMCID: PMC6751580 DOI: 10.1186/s12967-019-2060-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/06/2019] [Indexed: 12/11/2022] Open
Abstract
Background Adipokines in serum derive mainly from subcutaneous and visceral adipose tissues. Epicardial adipose tissue (EAT), being a relatively small but unique fat depot, probably does not make an important contribution to systemic concentrations of adipokines. However, proximity of EAT to cardiac muscle and coronary arteries allows cells and proteins to penetrate between tissues. It is hypothesized that overexpression of proinflammatory cytokines in EAT plays an important role in pathophysiology of the heart. The aim of the study was to analyze the relationship between echocardiographic heart parameters and adipokines in plasma, epicardial, and subcutaneous fat in patients with obesity and type 2 diabetes mellitus (T2DM). Additionally, we evaluate proinflammatory properties of EAT by comparing that depot with subcutaneous adipose tissue. Methods The study included 55 male individuals diagnosed with coronary artery disease (CAD) who underwent planned coronary artery bypass graft. Plasma concentrations of leptin, adiponectin, resistin, visfatin, apelin, IL-6, and TNF-α, as well as their mRNA and protein expressions in EAT and subcutaneous adipose tissue (SAT) were determined. Results Obesity and diabetes were associated with increased leptin and decreased adiponectin plasma levels, higher protein expression of leptin and IL-6 in SAT, and higher visfatin protein expression in EAT. Impaired left ventricular (LV) diastolic function was associated with increased plasma concentrations of leptin, resistin, IL-6, and adiponectin, as well as with increased expressions of resistin, apelin, and adiponectin in SAT, and leptin in EAT. Conclusions Obesity and T2DM in individuals with CAD have a limited effect on adipokines. Expression of adipokines in EAT and SAT is linked to certain heart parameters, however diastolic dysfunction of the LV is strongly associated with circulating adipokines.
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Affiliation(s)
- Kacper Toczylowski
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274, Bialystok, Poland
| | - Tomasz Hirnle
- Department of Cardiac Surgery, Medical University of Bialystok, Sklodowskiej 24A, 15-276, Bialystok, Poland
| | - Dorota Harasiuk
- Department of Physiology, Medical University of Bialystok, Mickiewicza 2C, 15-222, Bialystok, Poland
| | - Piotr Zabielski
- Department of Physiology, Medical University of Bialystok, Mickiewicza 2C, 15-222, Bialystok, Poland
| | - Anna Lewczuk
- Department of Cardiac Surgery, Medical University of Bialystok, Sklodowskiej 24A, 15-276, Bialystok, Poland
| | - Iwona Dmitruk
- Department of Cardiac Surgery, Medical University of Bialystok, Sklodowskiej 24A, 15-276, Bialystok, Poland
| | - Monika Ksiazek
- Department of Physiology, Medical University of Bialystok, Mickiewicza 2C, 15-222, Bialystok, Poland
| | - Artur Sulik
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274, Bialystok, Poland
| | - Jan Gorski
- Department of Physiology, Medical University of Bialystok, Mickiewicza 2C, 15-222, Bialystok, Poland
| | - Adrian Chabowski
- Department of Physiology, Medical University of Bialystok, Mickiewicza 2C, 15-222, Bialystok, Poland
| | - Marcin Baranowski
- Department of Physiology, Medical University of Bialystok, Mickiewicza 2C, 15-222, Bialystok, Poland.
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14
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Yokoyama T, Omotehara T, Hirano T, Kubota N, Yanai S, Hasegawa C, Takada T, Mantani Y, Hoshi N. Identification of reference genes for quantitative PCR analyses in developing mouse gonads. J Vet Med Sci 2018; 80:1534-1539. [PMID: 30175754 PMCID: PMC6207531 DOI: 10.1292/jvms.18-0417] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Stable reference genes are important for gene expression analyses such as quantitative
PCR. The stability of 15 candidate reference genes that can be used to developing mouse
gonads was thoroughly verified using combinations of multiple algorithms. The expression
of these genes fluctuated greatly depending on the analysis period and/or gender.
Peptidylprolyl isomerase A (Ppia) and polymerase (RNA) II (DNA directed)
polypeptide A (Polr2a) were the reference genes that were used stably for
a wide analysis period in developing mouse gonads. Furthermore, the stable reference genes
corresponding to the analysis period and/or gender were ranked. These results are useful
for the selection of the optimal reference gene required for high-precision
measurements.
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Affiliation(s)
- Toshifumi Yokoyama
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Takuya Omotehara
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan.,Department of Anatomy, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku, Tokyo 160-8402, Japan
| | - Tetsushi Hirano
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan.,Division of Drug and Structural Research, Life Science Research Center, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Naoto Kubota
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Shogo Yanai
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Chinatsu Hasegawa
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Tadashi Takada
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yohei Mantani
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Nobuhiko Hoshi
- Department of Animal Science, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
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15
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Dai M, Lin Y, El-Amouri SS, Kohls M, Pan D. Comprehensive evaluation of blood-brain barrier-forming micro-vasculatures: Reference and marker genes with cellular composition. PLoS One 2018; 13:e0197379. [PMID: 29763456 PMCID: PMC5953434 DOI: 10.1371/journal.pone.0197379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 05/01/2018] [Indexed: 01/04/2023] Open
Abstract
Primary brain microvessels (BrMV) maintain the cellular characters and molecular signatures as displayed in vivo, and serve as a vital tool for biomedical research of the blood-brain barrier (BBB) and the development/optimization of brain drug delivery. The variations of relative purities or cellular composition among different BrMV samples may have significant consequences in data interpretation and research outcome, especially for experiments with high-throughput genomics and proteomics technologies. In this study, we aimed to identify suitable reference gene (RG) for accurate normalization of real-time RT-qPCR analysis, and determine the proper marker genes (MG) for relative purity assessment in BrMV samples. Out of five housekeeping genes, β-actin was selected as the most suitable RG that was validated by quantifying mRNA levels of alpha-L-iduronidase in BrMV isolated from mice with one or two expressing alleles. Four marker genes highly/selectively expressed in BBB-forming capillary endothelial cells were evaluated by RT-qPCR for purity assessment, resulting in Cldn5 and Pecam1 as most suitable MGs that were further confirmed by immunofluorescent analysis of cellular components. Plvap proved to be an indicator gene for the presence of fenestrated vessels in BrMV samples. This study may contribute to the building blocks toward overarching research needs on the blood-brain barrier.
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Affiliation(s)
- Mei Dai
- Division of Experimental Hematology & Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Yi Lin
- Division of Experimental Hematology & Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Salim S. El-Amouri
- Division of Experimental Hematology & Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Mara Kohls
- Department of Pediatrics, School of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Dao Pan
- Division of Experimental Hematology & Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, School of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
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16
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Kishibe M, Baida G, Bhalla P, Lavker RM, Schlosser B, Iinuma S, Yoshida S, Dudley JT, Budunova I. Important role of kallikrein 6 for the development of keratinocyte proliferative resistance to topical glucocorticoids. Oncotarget 2018; 7:69479-69488. [PMID: 27283773 PMCID: PMC5342492 DOI: 10.18632/oncotarget.9926] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/13/2016] [Indexed: 11/25/2022] Open
Abstract
One of the major adverse effects of topical glucocorticoids is cutaneous atrophy often followed by development of resistance to steroids (tachyphylaxis). Previously we showed that after two weeks, interfollicular mouse keratinocytes acquired resistance to anti-proliferative effects of glucocorticoid fluocinolone acetonide (FA). One of the top genes activated by FA during tachyphylaxis was Klk6 encoding kallikrein-related peptidase 6, known to enhance keratinocyte proliferation. KLK6 was also strongly induced by chronic glucocorticoids in human skin. Double immunostaining showed that KLK6+ keratinocytes, localized in suprabasal layer of mouse skin, were frequently adjacent to proliferating 5-bromo-2'-deoxyuridine-positive basal keratinocytes. We used KLK6 knockout (KO) mice to evaluate KLK6 role in skin regeneration after steroid-induced atrophy. KLK6 KOs had thinner epidermis and decreased keratinocyte proliferation. The keratinocytes in wild type and KLK6 KO epidermis were equally sensitive to acute anti-proliferative effect of FA. However, the development of proliferative resistance during chronic treatment was reduced in KO epidermis. This was not due to the changes in glucocorticoid receptor (GR) expression or function as GR protein level and induction of GR-target genes were similar in wild type and KLK6 KO skin. Overall, these results suggest a novel mechanism of epidermal regeneration after glucocorticoid-induced atrophy via KLK6 activation.
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Affiliation(s)
- Mari Kishibe
- Department of Dermatology, Asahikawa Medical University, Japan
| | - Gleb Baida
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Pankaj Bhalla
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Robert M Lavker
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | | | - Sin Iinuma
- Department of Dermatology, Asahikawa Medical University, Japan
| | - Shigetaka Yoshida
- Department of Functional Anatomy and Neuroscience, Asahikawa Medical University, Japan
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irina Budunova
- Department of Dermatology, Northwestern University, Chicago, IL, USA
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17
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Della Latta V, Cabiati M, Burchielli S, Frenzilli G, Bernardeschi M, Cecchettini A, Viglione F, Morales MA, Del Ry S. Lung inflammation after bleomycin treatment in mice: Selection of an accurate normalization strategy for gene expression analysis in an ex-vivo and in-vitro model. Int J Biochem Cell Biol 2017; 88:145-154. [PMID: 28526615 DOI: 10.1016/j.biocel.2017.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 04/10/2017] [Accepted: 05/08/2017] [Indexed: 01/01/2023]
Abstract
Pulmonary fibrosis (PF) is the most common and aggressive interstitial lung disease, characterized by a patchy development of fibrosis leading to progressive destruction of the normal lung architecture which is preceded by an inflammatory process. Gene expression studies are important to understand the development of PF but the accuracy and reproducibility of Real-Time PCR depend on appropriate normalization strategies. This study aimed to analyze the expression variability of eight commonly used reference genes during the initial inflammatory phase of bleomycin-induced PF in a mouse model and to verify whether the selected reference genes could be applied to an in-vitro model of BLM-treated primary murine lung fibroblasts. Wild-type C57BL/6 mice (n=40) were used. Real-Time PCR was carried out on lung tissue of mice either BLM (BLM-tm) or physiological solution-treated (PSS-tm), and in primary lung fibroblasts, isolated from healthy C57BL/6 mice. Histological analysis was performed to confirm the inflammation development. During inflammation, the most stable genes resulted: PPIA, HPRT-1 and SDHA for both models; the normalization strategy was tested analyzing mRNA expression of PTX-3 and TNF-α which resulted up-regulated both in ex-vivo and in-vitro with respect to PSS-tm/fibroblasts. Histological analysis supported the results. This study identified a new set of reference genes expressed both in the in-vitro and ex-vivo models. A higher expression of both markers in BLM-tm with respect to PSS-tm indicated that BLM might lead to increased PTX-3 local production by a co-regulation with TNF-α at lung level.
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Affiliation(s)
- Veronica Della Latta
- CNR Institute of Clinical Physiology, Laboratory of Biochemistry and Molecular Biology, Pisa, Italy
| | - Manuela Cabiati
- CNR Institute of Clinical Physiology, Laboratory of Biochemistry and Molecular Biology, Pisa, Italy
| | | | - Giada Frenzilli
- University of Pisa, Dept. Experimental and Clinical Medicine, Pisa, Italy
| | | | | | - Federica Viglione
- CNR Institute of Clinical Physiology, Laboratory of Biochemistry and Molecular Biology, Pisa, Italy
| | - Maria-Aurora Morales
- CNR Institute of Clinical Physiology, Laboratory of Biochemistry and Molecular Biology, Pisa, Italy
| | - Silvia Del Ry
- CNR Institute of Clinical Physiology, Laboratory of Biochemistry and Molecular Biology, Pisa, Italy.
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18
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Kim BS, Tilstam PV, Springenberg-Jung K, Boecker AH, Schmitz C, Heinrichs D, Hwang SS, Stromps JP, Ganse B, Kopp R, Knobe M, Bernhagen J, Pallua N, Bucala R. Characterization of adipose tissue macrophages and adipose-derived stem cells in critical wounds. PeerJ 2017; 5:e2824. [PMID: 28070458 PMCID: PMC5217526 DOI: 10.7717/peerj.2824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/22/2016] [Indexed: 01/14/2023] Open
Abstract
Background Subcutaneous adipose tissue is a rich source of adipose tissue macrophages and adipose-derived stem cells which both play a key role in wound repair. While macrophages can be divided into the classically-activated M1 and the alternatively-activated M2 phenotype, ASCs are characterized by the expression of specific stem cell markers. Methods In the present study, we have investigated the expression of common macrophage polarization and stem cell markers in acutely inflamed adipose tissue. Subcutaneous adipose tissue adjacent to acutely inflamed wounds of 20 patients and 20 healthy subjects were harvested and underwent qPCR and flow cytometry analysis. Results Expression levels of the M1-specific markers CD80, iNOS, and IL-1b were significantly elevated in inflammatory adipose tissue when compared to healthy adipose tissue, whereas the M2-specific markers CD163 and TGF-β were decreased. By flow cytometry, a significant shift of adipose tissue macrophage populations towards the M1 phenotype was confirmed. Furthermore, a decrease in the mesenchymal stem cell markers CD29, CD34, and CD105 was observed whereas CD73 and CD90 remained unchanged. Discussion This is the first report describing the predominance of M1 adipose tissue macrophages and the reduction of stem cell marker expression in acutely inflamed, non-healing wounds.
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Affiliation(s)
- Bong-Sung Kim
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany.,Department of Medicine, Yale University, New Haven, United States.,Institute of Biochemistry and Molecular Cell Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | | | - Katrin Springenberg-Jung
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Arne Hendrick Boecker
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Corinna Schmitz
- Institute of Biochemistry and Molecular Cell Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Daniel Heinrichs
- Institute of Biochemistry and Molecular Cell Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Soo Seok Hwang
- Department of Immunology, Yale University, New Haven, United States
| | - Jan Philipp Stromps
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Bergita Ganse
- Department of Orthopedic Trauma Surgery, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Ruedger Kopp
- Department of Intensive Care Medicine, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Matthias Knobe
- Department of Orthopedic Trauma Surgery, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Juergen Bernhagen
- Department of Vascular Biology, Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität München (LMU), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München (LMU), Munich, Germany
| | - Norbert Pallua
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Richard Bucala
- Department of Medicine, Yale University, New Haven, United States
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Rabelo K, Trugilho MRO, Costa SM, Pereira BAS, Moreira OC, Ferreira ATS, Carvalho PC, Perales J, Alves AMB. The effect of the dengue non-structural 1 protein expression over the HepG2 cell proteins in a proteomic approach. J Proteomics 2016; 152:339-354. [PMID: 27826075 DOI: 10.1016/j.jprot.2016.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 10/14/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
Abstract
Dengue is an important mosquito borne viral disease in the world. Dengue virus (DENV) encodes a polyprotein, which is cleaved in ten proteins, including the non-structural protein 1 (NS1). In this work, we analyzed the effect of NS1 expression in one hepatic cell line, HepG2, through a shotgun proteomic approach. Cells were transfected with pcENS1 plasmid, which encodes the DENV2 NS1 protein, or the controls pcDNA3 (negative control) and pMAXGFP (GFP, a protein unrelated to dengue). Expression of NS1 was detected by immunofluorescence, western blot and flow cytometry. We identified 14,138 peptides that mapped to 4,756 proteins in all analyzed conditions. We found 41 and 81 differentially abundant proteins when compared to cells transfected with plasmids pcDNA3 and pMAXGFP, respectively. Besides, 107 proteins were detected only in the presence of NS1. We identified clusters of proteins involved mainly in mRNA process and viral RNA replication. Down regulation expression of one protein (MARCKS), identified by the proteomic analysis, was also confirmed by real time PCR in HepG2 cells infected with DENV2. Identification of proteins modulated by the presence of NS1 may improve our understanding of its role in virus infection and pathogenesis, contributing to development of new therapies and vaccines. BIOLOGICAL SIGNIFICANCE Dengue is an important viral disease, with epidemics in tropical and subtropical regions of the world. The disease is complex, with different manifestations, in which the liver is normally affected. The NS1 is found in infected cells associated with plasma membrane and secreted into the circulation as a soluble multimer. This protein is essential for virus viability, although its function is not elucidated. Some reports indicate that the NS1 can be used as a protective antigen for the development of a dengue vaccine, while others suggest its involvement in viral pathogenesis. In this work, we report an in-depth comprehensive proteomic profiling resulting from the presence of NS1 in HepG2 cells. These results can contribute to a better understanding of the NS1 role during infection.
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Affiliation(s)
- Kíssila Rabelo
- Laboratory of Biotechnology and Physiology of Viral Infections, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Monique R O Trugilho
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Simone M Costa
- Laboratory of Biotechnology and Physiology of Viral Infections, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Bernardo A S Pereira
- Laboratory of Biotechnology and Physiology of Viral Infections, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Otacílio C Moreira
- Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - André T S Ferreira
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Paulo C Carvalho
- Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Jonas Perales
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Ada M B Alves
- Laboratory of Biotechnology and Physiology of Viral Infections, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
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20
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Klein C, Ninni S, Coisne A, Staels B, Montaigne D. Omentin-1, epicardial fat and coronary artery disease. Atherosclerosis 2016; 255:224-225. [PMID: 27769510 DOI: 10.1016/j.atherosclerosis.2016.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Cedric Klein
- CHU de Lille, Department of Echocardiography and Cardiovascular explorations, Lille, France; European Genomic Institute for Diabetes (E.G.I.D), FR 3508, F-59000, Lille, France; Univ Lille, F-59000, Lille, France; Inserm UMR 1011, F-59000, Lille, France; Institut Pasteur de Lille, F-59000, Lille, France.
| | - Sandro Ninni
- CHU de Lille, Department of Echocardiography and Cardiovascular explorations, Lille, France; European Genomic Institute for Diabetes (E.G.I.D), FR 3508, F-59000, Lille, France; Univ Lille, F-59000, Lille, France; Inserm UMR 1011, F-59000, Lille, France; Institut Pasteur de Lille, F-59000, Lille, France
| | - Augustin Coisne
- CHU de Lille, Department of Echocardiography and Cardiovascular explorations, Lille, France; European Genomic Institute for Diabetes (E.G.I.D), FR 3508, F-59000, Lille, France; Univ Lille, F-59000, Lille, France; Inserm UMR 1011, F-59000, Lille, France; Institut Pasteur de Lille, F-59000, Lille, France
| | - Bart Staels
- European Genomic Institute for Diabetes (E.G.I.D), FR 3508, F-59000, Lille, France; Univ Lille, F-59000, Lille, France; Inserm UMR 1011, F-59000, Lille, France; Institut Pasteur de Lille, F-59000, Lille, France; CHU de Lille, Department of Biology, Lille, France
| | - David Montaigne
- CHU de Lille, Department of Echocardiography and Cardiovascular explorations, Lille, France; European Genomic Institute for Diabetes (E.G.I.D), FR 3508, F-59000, Lille, France; Univ Lille, F-59000, Lille, France; Inserm UMR 1011, F-59000, Lille, France; Institut Pasteur de Lille, F-59000, Lille, France
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21
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Morales MA, Mendoza BM, Lavine LC, Lavine MD, Walsh DB, Zhu F. Selection of Reference Genes for Expression Studies of Xenobiotic Adaptation in Tetranychus urticae. Int J Biol Sci 2016; 12:1129-39. [PMID: 27570487 PMCID: PMC4997057 DOI: 10.7150/ijbs.16319] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 07/08/2016] [Indexed: 11/25/2022] Open
Abstract
Quantitative real-time PCR (qRT-PCR) is an extensively used, high-throughput method to analyze transcriptional expression of genes of interest. An appropriate normalization strategy with reliable reference genes is required for calculating gene expression across diverse experimental conditions. In this study, we aim to identify the most stable reference genes for expression studies of xenobiotic adaptation in Tetranychus urticae, an extremely polyphagous herbivore causing significant yield reduction of agriculture. We chose eight commonly used housekeeping genes as candidates. The qRT-PCR expression data for these genes were evaluated from seven populations: a susceptible and three acaricide resistant populations feeding on lima beans, and three other susceptible populations which had been shifted host from lima beans to three other plant species. The stability of the candidate reference genes was then assessed using four different algorithms (comparative ΔCt method, geNorm, NormFinder, and BestKeeper). Additionally, we used an online web-based tool (RefFinder) to assign an overall final rank for each candidate gene. Our study found that CycA and Rp49 are best for investigating gene expression in acaricide susceptible and resistant populations. GAPDH, Rp49, and Rpl18 are best for host plant shift studies. And GAPDH and Rp49 were the most stable reference genes when investigating gene expression under changes in both experimental conditions. These results will facilitate research in revealing molecular mechanisms underlying the xenobiotic adaptation of this notorious agricultural pest.
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Affiliation(s)
- Mariany Ashanty Morales
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
| | | | - Laura Corley Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Mark Daniel Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Douglas Bruce Walsh
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
| | - Fang Zhu
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
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22
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Differences between perivascular adipose tissue surrounding the heart and the internal mammary artery: possible role for the leptin-inflammation-fibrosis-hypoxia axis. Clin Res Cardiol 2016; 105:887-900. [DOI: 10.1007/s00392-016-0996-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/19/2016] [Indexed: 12/18/2022]
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23
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Gentile AM, Lhamyani S, Coín-Aragüez L, Oliva-Olivera W, Zayed H, Vega-Rioja A, Monteseirin J, Romero-Zerbo SY, Tinahones FJ, Bermúdez-Silva FJ, El Bekay R. RPL13A and EEF1A1 Are Suitable Reference Genes for qPCR during Adipocyte Differentiation of Vascular Stromal Cells from Patients with Different BMI and HOMA-IR. PLoS One 2016; 11:e0157002. [PMID: 27304673 PMCID: PMC4909211 DOI: 10.1371/journal.pone.0157002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/23/2016] [Indexed: 12/21/2022] Open
Abstract
Real-time or quantitative PCR (qPCR) is a useful technique that requires reliable reference genes for data normalization in gene expression analysis. Adipogenesis is among the biological processes suitable for this technique. The selection of adequate reference genes is essential for qPCR gene expression analysis of human Vascular Stromal Cells (hVSCs) during their differentiation into adipocytes. To the best of our knowledge, there are no studies validating reference genes for the analyses of visceral and subcutaneous adipose tissue hVSCs from subjects with different Body Mass Index (BMI) and Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) index. The present study was undertaken to analyze this question. We first analyzed the stability of expression of five potential reference genes: CYC, GAPDH, RPL13A, EEF1A1, and 18S ribosomal RNA, during in vitro adipogenic differentiation, in samples from these types of patients. The expression of RPL13A and EEF1A1 was not affected by differentiation, thus being these genes the most stable candidates, while CYC, GAPDH, and 18S were not suitable for this sort of analysis. This work highlights that RPL13A and EEF1A1 are good candidates as reference genes for qPCR analysis of hVSCs differentiation into adipocytes from subjects with different BMI and HOMA-IR.
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Affiliation(s)
| | - Said Lhamyani
- IBIMA, Universidad de Málaga, Campus Teatinos s/n, 29010, Málaga, España
| | - Leticia Coín-Aragüez
- CIBER Pathophysiology of obesity and nutrition CB06/03, Carlos III Health Institute, Malaga, 29010, Spain, Laboratory of Biomedical Research, Virgen de la Victoria Clinical University Hospital, Málaga, 29010, Spain
| | - Wilfredo Oliva-Olivera
- CIBER Pathophysiology of obesity and nutrition CB06/03, Carlos III Health Institute, Malaga, 29010, Spain, Laboratory of Biomedical Research, Virgen de la Victoria Clinical University Hospital, Málaga, 29010, Spain
| | - Hatem Zayed
- Biomedical Sciences Program, Health Sciences Department, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Antonio Vega-Rioja
- Unidad de Gestión Clínica de Alergia Intercentros, Hospital Universitario Virgen Macarena, Sevilla, Spain
- * E-mail: (AVR); (FJBS); (REB)
| | - Javier Monteseirin
- Unidad de Gestión Clínica de Alergia Intercentros, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - Silvana-Yanina Romero-Zerbo
- Unidad de Gestion Clínica Intercentros de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Regional Universitario de Málaga/Universidad de Málaga, 29009, Málaga, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Málaga, Spain
| | - Francisco-José Tinahones
- CIBER Pathophysiology of obesity and nutrition CB06/03, Carlos III Health Institute, Malaga, 29010, Spain, Laboratory of Biomedical Research, Virgen de la Victoria Clinical University Hospital, Málaga, 29010, Spain
- Endocrinology Service, Virgen de la Victoria Clinical University Hospital, Malaga, 29010, Spain
| | - Francisco-Javier Bermúdez-Silva
- Unidad de Gestion Clínica Intercentros de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Regional Universitario de Málaga/Universidad de Málaga, 29009, Málaga, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Málaga, Spain
- * E-mail: (AVR); (FJBS); (REB)
| | - Rajaa El Bekay
- CIBER Pathophysiology of obesity and nutrition CB06/03, Carlos III Health Institute, Malaga, 29010, Spain, Laboratory of Biomedical Research, Virgen de la Victoria Clinical University Hospital, Málaga, 29010, Spain
- * E-mail: (AVR); (FJBS); (REB)
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24
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Jatav P, Sodhi M, Sharma A, Mann S, Kishore A, Shandilya UK, Mohanty AK, Kataria RS, Yadav P, Verma P, Kumar S, Malakar D, Mukesh M. Identification of internal control genes in milk-derived mammary epithelial cells during lactation cycle of Indian zebu cow. Anim Sci J 2016; 87:344-53. [DOI: 10.1111/asj.12384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/11/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Pradeep Jatav
- National Bureau of Animal Genetic Resources; Haryana India
| | - Monika Sodhi
- National Bureau of Animal Genetic Resources; Haryana India
| | - Ankita Sharma
- National Bureau of Animal Genetic Resources; Haryana India
| | - Sandeep Mann
- National Bureau of Animal Genetic Resources; Haryana India
| | - Amit Kishore
- National Bureau of Animal Genetic Resources; Haryana India
| | | | | | | | - Poonam Yadav
- National Bureau of Animal Genetic Resources; Haryana India
| | - Preeti Verma
- National Bureau of Animal Genetic Resources; Haryana India
| | | | | | - Manishi Mukesh
- National Bureau of Animal Genetic Resources; Haryana India
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25
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Taube M, Andersson-Assarsson JC, Lindberg K, Pereira MJ, Gäbel M, Svensson MK, Eriksson JW, Svensson PA. Evaluation of reference genes for gene expression studies in human brown adipose tissue. Adipocyte 2015; 4:280-5. [PMID: 26451284 DOI: 10.1080/21623945.2015.1039884] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/03/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022] Open
Abstract
Human brown adipose tissue (BAT) has during the last 5 year been subjected to an increasing research interest, due to its putative function as a target for future obesity treatments. The most commonly used method for molecular studies of human BAT is the quantitative polymerase chain reaction (qPCR). This method requires normalization to a reference gene (genes with uniform expression under different experimental conditions, e.g. similar expression levels between human BAT and WAT), but so far no evaluation of reference genes for human BAT has been performed. Two different microarray datasets with samples containing human BAT were used to search for genes with low variability in expression levels. Seven genes (FAM96B, GNB1, GNB2, HUWE1, PSMB2, RING1 and TPT1) identified by microarray analysis, and 8 commonly used reference genes (18S, B2M, GAPDH, LRP10, PPIA, RPLP0, UBC, and YWHAZ) were selected and further analyzed by quantitative PCR in both BAT containing perirenal adipose tissue and subcutaneous adipose tissue. Results were analyzed using 2 different algorithms (Normfinder and geNorm). Most of the commonly used reference genes displayed acceptably low variability (geNorm M-values <0.5) in the samples analyzed, but the novel reference genes identified by microarray displayed an even lower variability (M-values <0.25). Our data suggests that PSMB2, GNB2 and GNB1 are suitable novel reference genes for qPCR analysis of human BAT and we recommend that they are included in future gene expression studies of human BAT.
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26
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Gaborit B, Venteclef N, Ancel P, Pelloux V, Gariboldi V, Leprince P, Amour J, Hatem SN, Jouve E, Dutour A, Clément K. Human epicardial adipose tissue has a specific transcriptomic signature depending on its anatomical peri-atrial, peri-ventricular, or peri-coronary location. Cardiovasc Res 2015; 108:62-73. [PMID: 26239655 DOI: 10.1093/cvr/cvv208] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 07/23/2015] [Indexed: 11/14/2022] Open
Abstract
AIMS Human epicardial adipose tissue (EAT) is a visceral and perivascular fat that has been shown to act locally on myocardium, atria, and coronary arteries. Its abundance has been linked to coronary artery disease (CAD) and atrial fibrillation. However, its physiological function remains highly debated. The aim of this study was to determine a specific EAT transcriptomic signature, depending on its anatomical peri-atrial (PA), peri-ventricular (PV), or peri-coronary location. METHODS AND RESULTS Samples of EAT and thoracic subcutaneous fat, obtained from 41 patients paired for cardiovascular risk factors, CAD, and atrial fibrillation were analysed using a pangenomic approach. We found 2728 significantly up-regulated genes in the EAT vs. subcutaneous fat with 400 genes being common between PA, PV, and peri-coronary EAT. These common genes were related to extracellular matrix remodelling, inflammation, infection, and thrombosis pathways. Omentin (ITLN1) was the most up-regulated gene and secreted adipokine in EAT (fold-change >12, P < 0.0001). Among EAT-enriched genes, we observed different patterns depending on adipose tissue location. A beige expression phenotype was found in EAT but PV EAT highly expressed uncoupled protein 1 (P = 0.01). Genes overexpressed in peri-coronary EAT were implicated in proliferation, O-N glycan biosynthesis, and sphingolipid metabolism. PA EAT displayed an atypical pattern with genes implicated in cardiac muscle contraction and intracellular calcium signalling pathway. CONCLUSION This study opens new perspectives in understanding the physiology of human EAT and its local interaction with neighbouring structures.
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Affiliation(s)
- Bénédicte Gaborit
- Institute of Cardiometabolism and Nutrition, ICAN, Heart and Nutrition Department, Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris F-75013, France Sorbonne Universities, University Pierre et Marie Curie-Paris 6, UMRS 1166, Paris F-75006, France INSERM, Nutriomics (team6 and Team3), UMR_S U1166, Paris F-75013, France Aix-Marseille Université, Faculté de Médecine, Department 'Nutrition, Obésité et Risque Thrombotique', INSERM, UMR 1062, INRA 1260, 13385 Marseille, France
| | - Nicolas Venteclef
- Institute of Cardiometabolism and Nutrition, ICAN, Heart and Nutrition Department, Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris F-75013, France Sorbonne Universities, University Pierre et Marie Curie-Paris 6, UMRS 1166, Paris F-75006, France INSERM, UMRS_S1138, Paris F-75006, France
| | - Patricia Ancel
- Institute of Cardiometabolism and Nutrition, ICAN, Heart and Nutrition Department, Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris F-75013, France Sorbonne Universities, University Pierre et Marie Curie-Paris 6, UMRS 1166, Paris F-75006, France INSERM, Nutriomics (team6 and Team3), UMR_S U1166, Paris F-75013, France Aix-Marseille Université, Faculté de Médecine, Department 'Nutrition, Obésité et Risque Thrombotique', INSERM, UMR 1062, INRA 1260, 13385 Marseille, France
| | - Véronique Pelloux
- Institute of Cardiometabolism and Nutrition, ICAN, Heart and Nutrition Department, Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris F-75013, France Sorbonne Universities, University Pierre et Marie Curie-Paris 6, UMRS 1166, Paris F-75006, France INSERM, Nutriomics (team6 and Team3), UMR_S U1166, Paris F-75013, France
| | - Vlad Gariboldi
- Assistance-Publique Hôpitaux de Marseille, Cardiac Surgery, La Timone Hospital,13005 Marseille, France
| | - Pascal Leprince
- Institute of Cardiometabolism and Nutrition, ICAN, Heart and Nutrition Department, Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris F-75013, France Sorbonne Universities, University Pierre et Marie Curie-Paris 6, UMRS 1166, Paris F-75006, France Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Heart Department, 73013 Paris, France
| | - Julien Amour
- Institute of Cardiometabolism and Nutrition, ICAN, Heart and Nutrition Department, Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris F-75013, France Sorbonne Universities, University Pierre et Marie Curie-Paris 6, UMRS 1166, Paris F-75006, France Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Heart Department, 73013 Paris, France
| | - Stéphane N Hatem
- Institute of Cardiometabolism and Nutrition, ICAN, Heart and Nutrition Department, Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris F-75013, France Sorbonne Universities, University Pierre et Marie Curie-Paris 6, UMRS 1166, Paris F-75006, France INSERM, Nutriomics (team6 and Team3), UMR_S U1166, Paris F-75013, France Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Heart Department, 73013 Paris, France
| | - Elisabeth Jouve
- Assistance-Publique Hôpitaux de Marseille, Medical Evaluation Department, CIC-CPCET, 13005 Marseille, France
| | - Anne Dutour
- Aix-Marseille Université, Faculté de Médecine, Department 'Nutrition, Obésité et Risque Thrombotique', INSERM, UMR 1062, INRA 1260, 13385 Marseille, France
| | - Karine Clément
- Institute of Cardiometabolism and Nutrition, ICAN, Heart and Nutrition Department, Assistance-Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris F-75013, France Sorbonne Universities, University Pierre et Marie Curie-Paris 6, UMRS 1166, Paris F-75006, France INSERM, Nutriomics (team6 and Team3), UMR_S U1166, Paris F-75013, France
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27
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Rocha SC, Pessoa MTC, Neves LDR, Alves SLG, Silva LM, Santos HL, Oliveira SMF, Taranto AG, Comar M, Gomes IV, Santos FV, Paixão N, Quintas LEM, Noël F, Pereira AF, Tessis ACSC, Gomes NLS, Moreira OC, Rincon-Heredia R, Varotti FP, Blanco G, Villar JAFP, Contreras RG, Barbosa LA. 21-Benzylidene digoxin: a proapoptotic cardenolide of cancer cells that up-regulates Na,K-ATPase and epithelial tight junctions. PLoS One 2014; 9:e108776. [PMID: 25290152 PMCID: PMC4188576 DOI: 10.1371/journal.pone.0108776] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023] Open
Abstract
Cardiotonic steroids are used to treat heart failure and arrhythmia and have promising anticancer effects. The prototypic cardiotonic steroid ouabain may also be a hormone that modulates epithelial cell adhesion. Cardiotonic steroids consist of a steroid nucleus and a lactone ring, and their biological effects depend on the binding to their receptor, Na,K-ATPase, through which, they inhibit Na+ and K+ ion transport and activate of several intracellular signaling pathways. In this study, we added a styrene group to the lactone ring of the cardiotonic steroid digoxin, to obtain 21-benzylidene digoxin (21-BD), and investigated the effects of this synthetic cardiotonic steroid in different cell models. Molecular modeling indicates that 21-BD binds to its target Na,K-ATPase with low affinity, adopting a different pharmacophoric conformation when bound to its receptor than digoxin. Accordingly, 21-DB, at relatively high µM amounts inhibits the activity of Na,K-ATPase α1, but not α2 and α3 isoforms. In addition, 21-BD targets other proteins outside the Na,K-ATPase, inhibiting the multidrug exporter Pdr5p. When used on whole cells at low µM concentrations, 21-BD produces several effects, including: 1) up-regulation of Na,K-ATPase expression and activity in HeLa and RKO cancer cells, which is not found for digoxin, 2) cell specific changes in cell viability, reducing it in HeLa and RKO cancer cells, but increasing it in normal epithelial MDCK cells, which is different from the response to digoxin, and 3) changes in cell-cell interaction, altering the molecular composition of tight junctions and elevating transepithelial electrical resistance of MDCK monolayers, an effect previously found for ouabain. These results indicate that modification of the lactone ring of digoxin provides new properties to the compound, and shows that the structural change introduced could be used for the design of cardiotonic steroid with novel functions.
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Affiliation(s)
- Sayonarah C. Rocha
- Laboratório de Bioquímica Celular, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Marco T. C. Pessoa
- Laboratório de Bioquímica Celular, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Luiza D. R. Neves
- Laboratório de Bioquímica Celular, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Silmara L. G. Alves
- Laboratório de Síntese Orgânica, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Luciana M. Silva
- Laboratório de Biologia Celular e Inovação Biotecnológica, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil
| | - Herica L. Santos
- Laboratório de Bioquímica Celular, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Soraya M. F. Oliveira
- Laboratório de Bioinformática, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Alex G. Taranto
- Laboratório de Bioinformática, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Moacyr Comar
- Laboratório de Bioinformática, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Isabella V. Gomes
- Laboratório de Biologia Celular e Mutagenicidade, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Fabio V. Santos
- Laboratório de Biologia Celular e Mutagenicidade, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Natasha Paixão
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Luis E. M. Quintas
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - François Noël
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Antonio F. Pereira
- Laboratório de Bioquímica Microbiana, Instituto de Microbiologia Paulo Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ana C. S. C. Tessis
- Laboratório de Bioquímica Microbiana, Instituto de Microbiologia Paulo Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rio de Janeiro, RJ, Brazil
| | - Natalia L. S. Gomes
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Otacilio C. Moreira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Ruth Rincon-Heredia
- Department of Physiology, Biophysics and Neurosciences, Center for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Fernando P. Varotti
- Laboratório de Bioquímica de Parasitos, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Gustavo Blanco
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Jose A. F. P. Villar
- Laboratório de Síntese Orgânica, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
| | - Rubén G. Contreras
- Department of Physiology, Biophysics and Neurosciences, Center for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Leandro A. Barbosa
- Laboratório de Bioquímica Celular, Universidade Federal de São João del Rei, Campus Centro-Oeste Dona Lindú, Divinópolis, MG, Brazil
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Mo F, Zhao J, Liu N, Cao LH, Jiang SX. Validation of reference genes for RT-qPCR analysis of CYP4T expression in crucian carp. Genet Mol Biol 2014; 37:500-7. [PMID: 25249772 PMCID: PMC4171773 DOI: 10.1590/s1415-47572014000400005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/24/2014] [Indexed: 12/19/2022] Open
Abstract
Reference genes are commonly used for normalization of target gene expression during RT-qPCR analysis. However, no housekeeping genes or reference genes have been identified to be stable across different tissue types or under different experimental conditions. To identify the most suitable reference genes for RT-qPCR analysis of target gene expression in the hepatopancreas of crucian carp (Carassius auratus) under various conditions (sex, age, water temperature, and drug treatments), seven reference genes, including beta actin (ACTB), beta-2 microglobulin (B2M), embryonic elongation factor-1 alpha (EEF1A), glyceraldehyde phosphate dehydrogenase (GAPDH), alpha tubulin (TUBA), ribosomal protein l8 (RPL8) and glucose-6-phosphate dehydrogenase (G6PDH), were evaluated in this study. The stability and ranking of gene expression were analyzed using three different statistical programs: GeNorm, Normfinder and Bestkeeper. The expression errors associated with selection of the genes were assessed by the relative quantity of CYP4T. The results indicated that all the seven genes exhibited variability under the experimental conditions of this research, and the combination of ACTB/TUBA/EEF1A or of ACTB/EEF1A was the best candidate that raised the accuracy of quantitative analysis of gene expression. The findings highlighted the importance of validation of housekeeping genes for research on gene expression under different conditions of experiment and species.
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Affiliation(s)
- Fei Mo
- Nanjing Agricultural University, China
| | - Jie Zhao
- Nanjing Agricultural University, China
| | - Na Liu
- Nanjing Agricultural University, China
| | - Li-hua Cao
- Nanjing Agricultural University, China; Guangdong Agribusiness Group Corporation, China
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29
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Zhang Y, Zhang XD, Liu X, Li YS, Ding JP, Zhang XR, Zhang YH. Reference gene screening for analyzing gene expression across goat tissue. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1665-71. [PMID: 25049756 PMCID: PMC4092887 DOI: 10.5713/ajas.2013.13199] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/18/2013] [Accepted: 06/03/2013] [Indexed: 02/03/2023]
Abstract
Real-time quantitative PCR (qRT-PCR) is one of the important methods for investigating the changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of real-time quantitative PCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We used real-time quantitative PCR to detect the expression levels of eight reference gene candidates (18S, TBP, HMBS, YWHAZ, ACTB, HPRT1, GAPDH and EEF1A2) in ten tissues types sourced from Boer goats. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in genes expression stability. When all tissues were considered, 18S, TBP and HMBS is the optimal reference combination for calibrating quantitative PCR analysis of gene expression from goat tissues. Dividing data set by tissues, ACTB was the most stable in stomach, small intestine and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney and GAPDH in muscle. Overall, this study provided valuable information about the goat reference genes that can be used in order to perform a proper normalisation when relative quantification by qRT-PCR studies is undertaken.
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Affiliation(s)
- Yu Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiao-Dong Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xing Liu
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yun-Sheng Li
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Jian-Ping Ding
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiao-Rong Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yun-Hai Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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30
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Association and expression analysis of porcine ACLY gene related to growth and carcass quality traits in Italian Large White and Italian Duroc breeds. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Identification and validation of suitable reference genes for RT-qPCR analysis in mouse testis development. Mol Genet Genomics 2014; 289:1157-69. [PMID: 24952483 DOI: 10.1007/s00438-014-0877-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 06/05/2014] [Indexed: 10/25/2022]
Abstract
RT-qPCR is a commonly used method for evaluating gene expression; however, its accuracy and reliability are dependent upon the choice of appropriate reference gene(s), and there is limited information available on suitable reference gene(s) that can be used in mouse testis at different stages. In this study, using the RT-qPCR method, we investigated the expression variations of six reference genes representing different functional classes (Actb, Gapdh, Ppia, Tbp, Rps29, Hprt1) in mice testis during embryonic and postnatal development. The expression stabilities of putative reference genes were evaluated using five algorithms: geNorm, NormFinder, Bestkeeper, the comparative delta C(t) method and integrated tool RefFinder. Analysis of the results showed that Ppia, Gapdh and Actb were identified as the most stable genes and the geometric mean of Ppia, Gapdh and Actb constitutes an appropriate normalization factor for gene expression studies. The mRNA expression of AT1 as a test gene of interest varied depending upon which of the reference gene(s) was used as an internal control(s). This study suggested that Ppia, Gapdh and Actb are suitable reference genes among the six genes used for RT-qPCR normalization and provide crucial information for transcriptional analyses in future studies of gene expression in the developing mouse testis.
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Olias P, Adam I, Meyer A, Scharff C, Gruber AD. Reference genes for quantitative gene expression studies in multiple avian species. PLoS One 2014; 9:e99678. [PMID: 24926893 PMCID: PMC4057121 DOI: 10.1371/journal.pone.0099678] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/19/2014] [Indexed: 11/18/2022] Open
Abstract
Quantitative real-time PCR (qPCR) rapidly and reliably quantifies gene expression levels across different experimental conditions. Selection of suitable reference genes is essential for meaningful normalization and thus correct interpretation of data. In recent years, an increasing number of avian species other than the chicken has been investigated molecularly, highlighting the need for an experimentally validated pan-avian primer set for reference genes. Here we report testing a set for 14 candidate reference genes (18S, ABL, GAPDH, GUSB, HMBS, HPRT, PGK1, RPL13, RPL19, RPS7, SDHA, TFRC, VIM, YWHAZ) on different tissues of the mallard (Anas platyrhynchos), domestic chicken (Gallus gallus domesticus), common crane (Grus grus), white-tailed eagle (Haliaeetus albicilla), domestic turkey (Meleagris gallopavo f. domestica), cockatiel (Nymphicus hollandicus), Humboldt penguin (Sphenicus humboldti), ostrich (Struthio camelus) and zebra finch (Taeniopygia guttata), spanning a broad range of the phylogenetic tree of birds. Primer pairs for six to 11 genes were successfully established for each of the nine species. As a proof of principle, we analyzed expression levels of 10 candidate reference genes as well as FOXP2 and the immediate early genes, EGR1 and CFOS, known to be rapidly induced by singing in the avian basal ganglia. We extracted RNA from microbiopsies of the striatal song nucleus Area X of adult male zebra finches after they had sang or remained silent. Using three different statistical algorithms, we identified five genes (18S, PGK1, RPS7, TFRC, YWHAZ) that were stably expressed within each group and also between the singing and silent conditions, establishing them as suitable reference genes. In conclusion, the newly developed pan-avian primer set allows accurate normalization and quantification of gene expression levels in multiple avian species.
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Affiliation(s)
- Philipp Olias
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Iris Adam
- Institute of Biology, Department of Animal Behavior, Freie Universität Berlin, Berlin, Germany
| | - Anne Meyer
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Constance Scharff
- Institute of Biology, Department of Animal Behavior, Freie Universität Berlin, Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
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Analysis of g.265T>C SNP of fatty acid synthase gene and expression study in skeletal muscle and backfat tissues of Italian Large White and Italian Duroc pigs. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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34
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Reference gene selection for quantitative real-time RT-PCR normalization in the half-smooth tongue sole (Cynoglossus semilaevis) at different developmental stages, in various tissue types and on exposure to chemicals. PLoS One 2014; 9:e91715. [PMID: 24667563 PMCID: PMC3965400 DOI: 10.1371/journal.pone.0091715] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 02/14/2014] [Indexed: 12/20/2022] Open
Abstract
Quantitative real time RT-PCR has been described as the most sensitive method for the detection of low abundance mRNA. To date, no reference genes have been screened in the half-smooth tongue sole (Cynoglossus semilaevis). The aim of this study was to select the most stable genes for quantitative real-time RT-PCR. Eight housekeeping genes (18S, TUBA, B2M, ACTB, EF1A, GAPDH, RPL17 and UBCE) were tested at different developmental stages, in different tissues, and following exposure to the drug SB-431542. Using geNorm, BestKeeper and NormFinder software, GAPDH/B2M, GAPDH/18S and UBCE/GAPDH were identified as the most suitable genes from samples taken of different developmental stages while 18S/RPL17 were consistently ranked as the best reference genes for different tissue types. Furthermore, TUBA/B2M, TUBA/UBCE and B2M/TUBA were found to be the most suitable genes in samples treated with the drug, SB-431542 by geNorm, BestKeeper and NormFinder respectively. Across both different developmental stages and tissue types, the combination of 18S and GAPDH was the most stable reference gene analyzed by Ref-Finder. To test and verify the screened reference genes, the expression profiles of LEFTY-normalized to the combination of GAPDH/18S and ACTB were presented. These results will be useful for future gene-expression studies in the half-smooth tongue sole.
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ZHANG JUAN, TANG HONGJU, ZHANG YUQING, DENG RUYUAN, SHAO LI, LIU YUN, LI FENGYING, WANG XIAO, ZHOU LIBIN. Identification of suitable reference genes for quantitative RT-PCR during 3T3-L1 adipocyte differentiation. Int J Mol Med 2014; 33:1209-18. [DOI: 10.3892/ijmm.2014.1695] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/27/2014] [Indexed: 11/06/2022] Open
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Wu H, Taki FA, Zhang Y, Dobbins DL, Pan X. Evaluation and identification of reliable reference genes for toxicological study in Caenorhabditis elegans. Mol Biol Rep 2014; 41:3445-55. [PMID: 24510408 DOI: 10.1007/s11033-014-3206-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 01/27/2014] [Indexed: 12/26/2022]
Abstract
To identify reliable reference genes for toxicological studies, 16 commonly-used reference genes were selected as candidates to evaluate their expression stabilities under experimental conditions in Caenorhabditis elegans. Sixteen candidates were composed of 12 protein-coding genes and 4 non-coding RNAs, they were act-2, ama-1, arp-6, cdc-42, csq-1, eif-3.C, idhg-1, mdh, pmp-3, rbd-1, tba-1, Y45F10D.4, 18S rRNA, Ce234, U18, and U6. Larval stage 1 synchronized hermaphrodites were exposed to benzo-α-pyrene (BαP), chlorpyrifos, diazinon, gossypol, zinc oxide nanoparticles, and the vehicle control DMSO for 30 h, respectively. Expression stabilities of candidate genes were analyzed using 4 independent evaluating approaches (BestKeeper, the delta Ct approach, geNorm, and NormFinder) followed by a comprehensive method. Results showed that there were slight differences in ranking order between evaluation methods due to their different assumptions and computations. The results also showed that responses of candidate genes to different chemicals were distinct, 18S rRNA was the best for BαP and chlorpyrifos, tba-1 was the most stable gene for diazinon and gossypol treatments, while pmp-3 was more stable for zinc oxide exposure. Additionally, results demonstrated that combinations of multiple genes were more reliable than individual gene, suggesting selecting two or more candidates as reference genes may generate more reliable results for toxicological studies.
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Affiliation(s)
- Hongmei Wu
- School of Public Health, Wenzhou Medical College, Wenzhou, 325035, China
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Comparative study of candidate housekeeping genes for quantification of target gene messenger RNA expression by real-time PCR in patients with inflammatory bowel disease. Inflamm Bowel Dis 2013; 19:2840-7. [PMID: 24141710 DOI: 10.1097/01.mib.0000435440.22484.e8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Mucosal expression of immunological mediators is modified in inflammatory bowel disease (IBD). Quantification of target gene messenger RNA (mRNA) transcripts depends on the normalization to a housekeeping or reference gene. Stability of housekeeping gene expression is critical for the accurate measurement of transcripts of the target gene. No studies have addressed the optimization of reference gene performance for mRNA studies in healthy intestinal mucosa and during mucosal inflammation. METHODS RNA was extracted from endoscopically obtained intestinal biopsies from healthy control subjects and patients with active IBD or non-IBD inflammatory diseases. Comparative analysis of 10 candidate housekeeping genes for quantitative real-time PCR was carried out according to predefined criteria, including use of the Web-based RefFinder platform. RESULTS We demonstrate that intestinal inflammation may significantly affect the stability of mucosal expression of housekeeping genes. Commonly used controls, such as glyceraldehyde-3-phosphate dehydrogenase, β-actin, or β2-microglobulin displayed high variability within the control group and/or between the healthy and inflamed mucosae. In contrast, we have identified novel genes with optimal stability, which may be used as appropriate housekeeping controls. The ribosomal proteins encoding genes (RPLPO and RPS9) were the most stable because their expression was not affected by interindividual differences, the presence of inflammation, or intestinal location. Normalization ofthe mRNA expression of mucosal tumor necrosis factor-α was highly dependent on the specific reference gene and varied significantly when normalized to genes with high or low stability. CONCLUSIONS Validation for optimal performance of the housekeeping gene is required for target mRNA quantification in healthy intestine and IBD-associated lesions. Suboptimal reference gene expression may explain conflicting results from published studies on IBD gene expression.
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Kianianmomeni A, Hallmann A. Validation of reference genes for quantitative gene expression studies in Volvox carteri using real-time RT-PCR. Mol Biol Rep 2013; 40:6691-9. [PMID: 24057254 DOI: 10.1007/s11033-013-2784-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
Abstract
Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is a sensitive technique for analysis of gene expression under a wide diversity of biological conditions. However, the identification of suitable reference genes is a critical factor for analysis of gene expression data. To determine potential reference genes for normalization of qRT-PCR data in the green alga Volvox carteri, the transcript levels of ten candidate reference genes were measured by qRT-PCR in three experimental sample pools containing different developmental stages, cell types and stress treatments. The expression stability of the candidate reference genes was then calculated using the algorithms geNorm, NormFinder and BestKeeper. The genes for 18S ribosomal RNA (18S) and eukaryotic translation elongation factor 1α2 (eef1) turned out to have the most stable expression levels among the samples both from different developmental stages and different stress treatments. The genes for the ribosomal protein L23 (rpl23) and the TATA-box binding protein (tbpA) showed equivalent transcript levels in the comparison of different cell types, and therefore, can be used as reference genes for cell-type specific gene expression analysis. Our results indicate that more than one reference gene is required for accurate normalization of qRT-PCRs in V. carteri. The reference genes in our study show a much better performance than the housekeeping genes used as a reference in previous studies.
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Affiliation(s)
- Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615, Bielefeld, Germany,
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Marchal E, Hult EF, Huang J, Tobe SS. Sequencing and validation of housekeeping genes for quantitative real-time PCR during the gonadotrophic cycle of Diploptera punctata. BMC Res Notes 2013; 6:237. [PMID: 23777660 PMCID: PMC3750588 DOI: 10.1186/1756-0500-6-237] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 06/11/2013] [Indexed: 11/16/2022] Open
Abstract
Background Quantitative RT-PCR (q-RT-PCR) is a powerful tool that allows for the large scale analysis of small changes in gene expression. Accurate and reliable results depend on the use of stable reference genes for normalization. However, the expression of some widely used housekeeping genes can vary under different experimental setups. To our knowledge, no validation studies have been reported for reference genes in cockroaches. The aim of the current study is the identification and validation of a set of eight housekeeping genes during the first gonadotrophic cycle of the cockroach, Diploptera punctata. This study made use of two different algorithms (geNorm and Normfinder) to evaluate the stability of gene expression. Results Candidate housekeeping genes were sequenced: β-actin (Actin), elongation factor 1 alpha (EF1a), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), armadillo (Arm), ribosomal protein L32 (RpL32), succinate dehydrogenase (SDHa), annexin IX (AnnIX) and α-tubulin (Tub). The expression of these eight genes was analyzed in corpora allata (CA) and ovaries of adult female D. punctata. Both geNorm, as well as Normfinder characterized SDHa, EF1a and Arm as being the most stably expressed in the corpora allata. In the ovary, the geNorm calculation showed Tub, EF1a and RpL32 to be most stable, whereas Normfinder identified Tub, EF1a and Arm as the best. In ovary, the least stable gene was Actin, challenging its usefulness in normalization. As a proof of principle, the expression of follicle cell protein 3c and CYP15A1 was monitored during the first gonadotrophic cycle. Conclusion Arm and EF1a form the most stably expressed combination of two reference genes out of the eight candidates that were tested in the corpora allata. Our results show that the combined use of Tub, EF1a and RpL32 ensures an accurate normalization of gene expression levels in ovary of D. punctata. Our study has indicated that neither Actin nor AnnIX should be used for normalization of transcript levels when studying the first gonadotrophic cycle in CA or ovary of D. punctata. The results stress the necessity for validation of reference genes in q-RT-PCR studies in cockroaches.
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Affiliation(s)
- Elisabeth Marchal
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Canada
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Riemer AB, Keskin DB, Reinherz EL. Identification and validation of reference genes for expression studies in human keratinocyte cell lines treated with and without interferon-γ - a method for qRT-PCR reference gene determination. Exp Dermatol 2012; 21:625-9. [PMID: 22775998 DOI: 10.1111/j.1600-0625.2012.01537.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Based on the exquisite sensitivity, reproducibility and wide dynamic range of quantitative reverse-transcription real-time polymerase chain reaction (qRT-PCR), it is currently the gold standard for gene expression studies. Target gene expression is calculated relative to a stably expressed reference gene. An ideal reference should be uniformly expressed during all experimental conditions within the given experimental system. However, no commonly applicable 'best' reference gene has been identified. Thus, endogenous controls must be determined for every experimental system. As no appropriate reference genes have been reported for immunological studies in keratinocytes, we aimed at identifying and validating a set of endogenous controls for these settings. An extensive validation of sixteen possible endogenous controls in a panel of 8 normal and transformed keratinocyte cell lines in experimental conditions with and without interferon-γ was performed. RNA and cDNA quality was stringently controlled. Candidate reference genes were assessed by TaqMan(®) qRT-PCR. Two different statistical algorithms were used to determine the most stably and reproducibly expressed housekeeping genes. mRNA abundance was compared and reference genes with widely different ranges of expression than possible target genes were excluded. Subsequent geNorm and NormFinder analyses identified GAPDH, PGK1, IPO8 and PPIA as the most stably expressed genes in the keratinocyte panel under the given experimental conditions. We conclude that the geometric means of expression values of these four genes represents a robust normalization factor for qRT-PCR analyses in interferon-γ-dependent gene expression studies in keratinocytes. The methodology and results herein may help other researchers by facilitating their choice of reference genes.
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Affiliation(s)
- Angelika B Riemer
- Cancer Vaccine Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
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Chechi K, Blanchard PG, Mathieu P, Deshaies Y, Richard D. Brown fat like gene expression in the epicardial fat depot correlates with circulating HDL-cholesterol and triglycerides in patients with coronary artery disease. Int J Cardiol 2012; 167:2264-70. [PMID: 22727960 DOI: 10.1016/j.ijcard.2012.06.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/01/2012] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND Recent evidence indicates that epicardial adipose tissue (EAT) expresses uncoupling protein-1 (UCP1), a marker of brown adipocytes. However, the putative effects of the presence of brown adipocytes in EAT remain unknown. METHODS The mRNA expression of genes related to brown adipocyte-mediated thermogenesis was measured in the fat samples collected from the epicardial-, mediastinal- and subcutaneous-depots of patients undergoing coronary artery bypass grafting. Both univariate and multivariate analyses were then utilized to determine any association between gene expression and the anthropometrics and fasting blood chemistries of these patients. RESULTS EAT exhibited significantly higher expression of UCP1 and cytochrome c oxidase subunit-IV (COX-IV) compared to mediastinal- and subcutaneous-fat depots (P ≤ 0.05). EAT expression of UCP1 (r=0.50), COX-IV (r=0.37) and lipoprotein lipase (LPL) (r=0.58) positively associated with circulating levels of HDL-cholesterol (P ≤ 0.05). In addition, EAT expression of LPL, acyl coA dehydrogenase-short, -medium and -long chain genes associated negatively with circulating TG levels (P ≤ 0.05). CONCLUSIONS Abundance of UCP-1 in the EAT relative to other fat depots confirms the presence of brown adipocytes in human EAT. Furthermore, the correlations among the EAT expression of thermogenesis-related genes with the circulating HDL and TG levels indicate that presence of active brown adipocytes shares a functional association with the circulating plasma lipids in humans.
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Affiliation(s)
- Kanta Chechi
- Faculty of Medicine, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, Canada G1V4G5
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