1
|
Souza JLN, Lopes CDA, Leal-Silva T, Vieira-Santos F, Amorim CCO, Padrão LDLS, Antunes Porto AR, Fujiwara RT, Russo RC, Bueno LL. Evaluation of reference genes for gene expression analysis by real-time quantitative PCR (qPCR) in different tissues from mice infected by Ascaris suum. Microb Pathog 2024; 189:106567. [PMID: 38364877 DOI: 10.1016/j.micpath.2024.106567] [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] [Received: 10/03/2023] [Revised: 01/19/2024] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
Human ascariasis is the most prevalent helminth infection, affecting 445 million people worldwide. To better understand the impact of the immune system on the pathophysiology of individuals infected with Ascaris suum, mice have been used as experimental models. The RT-qPCR technique is a critical auxiliary tool of investigation used to quantify mRNA levels. However, proper normalization using reference genes is essential to ensure reliable outcomes to avoid analytical errors and false results. Despite the importance of reference genes for experimental A. suum infection studies, no specific reference genes have been identified yet. Therefore, we conducted a study to assess five potential reference genes (GAPDH, 18s, ACTB, B2M, and HPRT1) in different tissues (liver, lungs, small and large intestines) affected by A. suum larval migration in C57BL/6j mice. Tissue collection was carried out to analyze parasite burden and confirm the presence of larvae during the peak of migration in each tissue. Upon confirmation, we analyzed different genes in the tissues and found no common gene with stable expression. Our results highlight the importance of analyzing different genes and using different software programs to ensure reliable relative expression results. Based on our findings, B2M was ranked as the ideal reference gene for the liver, while 18S was the most stable gene in the lung and small intestine. ACTB, or a combination of ACTB with GAPDH, was deemed suitable as reference genes for the large intestine due to their stable expression and less variation between the control and infected groups. To further demonstrate the impact of using different reference genes, we normalized the expression of a chemokine gene (CXCL9) in all tissues. Significant differences in CXCL9 expression levels were observed between different groups in all tissues except for the large intestine. This underscores the importance of selecting appropriate reference genes to avoid overestimating target gene expression levels and encountering normalization-related issues that can lead to false results. In conclusion, our study highlights the significance of using reliable reference genes for accurate RT-qPCR analysis, especially in the context of A. suum infection studies in different tissues. Proper normalization is crucial to ensure the validity of gene expression data and avoid potential pitfalls in interpreting results.
Collapse
Affiliation(s)
- Jorge Lucas Nascimento Souza
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Camila de Almeida Lopes
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thais Leal-Silva
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flaviane Vieira-Santos
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Chiara Cássia Oliveira Amorim
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiza de Lima Silva Padrão
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Rafaela Antunes Porto
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ricardo Toshio Fujiwara
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Remo Castro Russo
- Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lilian Lacerda Bueno
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| |
Collapse
|
2
|
Vasu M, Ahlawat S, Choudhary V, Kaur R, Arora R, Sharma R, Sharma U, Chhabra P, Mir MA, Kumar Singh M. Identification and validation of stable reference genes for expression profiling of target genes in diverse ovine tissues. Gene 2024; 897:148067. [PMID: 38092161 DOI: 10.1016/j.gene.2023.148067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023]
Abstract
Quantitative PCR (qPCR) is a widely-used technique for quantifying the expression of target genes across various tissues, as well as under different pathological and physiological conditions. One of the challenges associated with this method is the need to identify optimal reference genes (RGs) that maintain consistent expression levels under diverse experimental settings, thereby ensuring accurate biological interpretation. In this study, we conducted a thorough analysis of 18 candidate RGs (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) across 10 ovine tissues (muscle, skin, kidney, liver, intestine, rumen, lung, testis, heart, and spleen) obtained from five individual sheep. We aimed to identify genes with stable expression across these tissues. A literature-based survey helped us shortlist candidate genes representing various functional classes from multiple livestock species. We employed four algorithms: geNorm, NormFinder, BestKeeper, and Delta Ct (ΔCt), to rank these genes based on their stability. A consistent trend in the rankings was observed across these different algorithms. RefFinder was then used for a comprehensive ranking, integrating the outputs from the various methods. ACTB, PPIB, BACH1, and B2M emerged as the most stable RGs, while RPS9, RPS15, and PGK1 displayed variable expression. We validated our findings through qPCR analysis of four target genes (ACTN2, CRYAB, DLK1, and TRIM54) in the skin samples from two different sheep breeds. Based on these results, we recommend ACTB, PPIB, BACH1, and B2M as reliable internal control genes for qPCR experiments involving diverse ovine tissues.
Collapse
Affiliation(s)
- Mahanthi Vasu
- ICAR-National Bureau of Animal Genetic Resources, Karnal; ICAR-National Dairy Research Institute, Karnal
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal.
| | - Vikas Choudhary
- District Disease Diagnostic Laboratory, Karnal, Department of Animal Husbandry and Dairying, Haryana
| | - Rashmeet Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - M A Mir
- Mountain Research Centre for Sheep and Goat, Shuhama (Aulestang), SKUAST-Kashmir
| | | |
Collapse
|
3
|
Lucas Nascimento Souza J, Cavalcante Silva F, da Silva CG, Maria Fortaleza Neves Bomfim I, Rocha de Medeiros H, Giotto Zaros L. Analysis of the stability of the reference genes GAPDH, SDHA and RPL-19 in sheep from a semi-arid region infected by gastrointestinal nematodes. BMC Vet Res 2023; 19:147. [PMID: 37679739 PMCID: PMC10483723 DOI: 10.1186/s12917-023-03709-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
Analyzing the stability of reference genes already described as universal is an important methodology to lead gene expression analysis because different studies have shown that the expression of universal reference genes may vary between experimental treatments. In this sense, the glyceraldehyde 3-phosphate dehydrogenase (GAPDH), Succinate dehydrogenase complex subunit A (SDHA) and Ribosomal Protein L-19 (RPL-19) reference genes (already described in other studies with sheep from different regions, breeds and infectious agents or in organisms evolutionarily close to sheep) were investigated in the abomasum, small and large intestines of resistant and susceptible crossbred sheep groups to gastrointestinal nematode infections in the Semi-arid region in Northeast of Brazil. The animals were naturally infected to determine the resistance or susceptibility status by counting eggs per gram (EPG) of feces from the gastrointestinal tract after 33 weeks of observations of infection evolution. Relative gene expression was performed by RT-qPCR methodology using Sybr green and relative gene expression stability was tested by different software programs such as REST, BestKeeper, geNorm and Normfinder. Our results showed the susceptible animals had increase in egg counts per gram of feces than resistant animals (p < 0.001), and both groups showed a mixed infection by nematodes of the genus Haemonchus, Trichostrongylus, Oesophagostomum and Trichuris. Furthermore, we show the importance of analyzing different genes in different software programs and the importance to choose ideal reference genes. In this sense, GAPDH was the most stable gene in the abomasum, whereas SDHA was the most stable in the small and large intestines. In addition, we discuss about variables which can interfere in relative expression such as breed, species, climate and tissue. However, utilizing other reference genes already described in other studies with the same and different variables should be performed.
Collapse
Affiliation(s)
- Jorge Lucas Nascimento Souza
- Graduate Program in Parasitary Biology, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Fernanda Cavalcante Silva
- Graduate Program in Animal Production, Jundiaí Agricultural School, Federal University of Rio Grande do Norte, Macaíba, Rio Grande do Norte, Brazil
| | - Carlikelly Gleicy da Silva
- Graduate Program in Parasitary Biology, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Henrique Rocha de Medeiros
- Jundiaí Agricultural School, Federal University of Rio Grande do Norte, Macaíba, Rio Grande do Norte, Brazil
| | - Lilian Giotto Zaros
- Department of Microbiology and Parasitology, Biosciences Centre, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil.
| |
Collapse
|
4
|
Criado M, Pérez V, Arteche-Villasol N, Elguezabal N, Molina E, Benavides J, Gutiérrez-Expósito D. Evaluation of the innate immune response of caprine neutrophils against Mycobacterium avium subspecies paratuberculosis in vitro. Vet Res 2023; 54:61. [PMID: 37464437 DOI: 10.1186/s13567-023-01193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/22/2023] [Indexed: 07/20/2023] Open
Abstract
Neutrophils constitute an essential component of the innate immune response, readily killing most bacteria through phagocytosis, degranulation, and the release of neutrophil extracellular traps (NETs) among other mechanisms. These cells play an unclear role in mycobacterial infections such as Mycobacterium avium subspecies paratuberculosis (Map), the etiological agent of paratuberculosis, and its response is particularly understudied in ruminants. Herein, a wide set of techniques were adapted, or newly developed, to study the in vitro response of caprine neutrophils after Map infection. Immunofluorescence was used to demonstrate, simultaneously, chemotaxis, phagocytosis, degranulation, and NETs. The quantification of neutrophil phagocytic activity against Map at a 1:10 multiplicity of infection (MOI), through flow cytometry, showed values that varied from 4.54 to 5.63% of phagocyting neutrophils. By immunofluorescence, a 73.3 ± 14.5% of the fields showed NETs, and the mean release of DNA, attributable to NETosis, calculated through a fluorometric method, was 16.2 ± 3.5%. In addition, the RNA expression of TGF-β, TNF and IL-1β cytokines, measured through reverse transcription qPCR, was significantly higher in the two latter. Overall, neutrophil response was proportional to the number of bacteria. This work confirms that the simultaneous study of several neutrophil mechanisms, and the combination of different methodologies, are essential to reach a comprehensive understanding of neutrophil response against pathogens, demonstrates that, in vitro, caprine neutrophils display a strong innate response against Map, using their entire repertoire of effector functions, and sets the basis for further in vitro and in vivo studies on the role of neutrophils in paratuberculosis.
Collapse
Affiliation(s)
- Miguel Criado
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Grulleros, León, Spain.
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain.
| | - Valentín Pérez
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Noive Arteche-Villasol
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Natalia Elguezabal
- Departamento de Sanidad Animal, NEIKER-BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, 48160, Derio, Vizcaya, Spain
| | - Elena Molina
- Departamento de Sanidad Animal, NEIKER-BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, 48160, Derio, Vizcaya, Spain
| | - Julio Benavides
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Grulleros, León, Spain
| | - Daniel Gutiérrez-Expósito
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| |
Collapse
|
5
|
He H, Li Z, Ni M, Xing S, Yu L, Xu H, Zhuo D, Li M. Screening and stability analysis of reference genes in fasting caecotrophy model in rabbits. Mol Biol Rep 2021; 49:1057-1065. [PMID: 34743273 DOI: 10.1007/s11033-021-06927-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/01/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The selection and validation of stably expressed reference genes is key for accurately quantifying the mRNA abundance of genes under different treatments. In the rabbit model of fasting caecotrophy, reports about the selection of stable reference genes are not available. METHODS AND RESULTS This study aims to screen suitable reference genes in different tissues (including uterus, cecum, and liver) of rabbits between control and fasting caecotrophy groups. RT-qPCR was used to analyze the expression levels of eight commonly used reference genes (including GAPDH, 18S rRNA, B2M, CYP, HPRT1, β-actin, H2afz, Ywhaz), and RefFinder (including geNorm, NormFinder, and BestKeeper) was used to analyze the expression stability of these reference genes. Our results showed that the most stable reference genes were different in different tissues and treatments. In the control and fasting caecotrophy groups, CYP, GAPDH and HPRT1 were proven to be the top stable reference genes in the uterus, cecum, and liver tissues, respectively. GAPDH and Ywhaz were proven to be the top two stable reference genes among uterus, cecum, and liver in both control and fasting caecotrophy groups. CONCLUSIONS Our results indicated that the combined analysis of three or more reference genes (GAPDH, HPRT1, and Ywhaz) are recommended to be used for RT-qPCR normalization in the rabbit model of fasting caecotrophy, and that GAPDH is a better choice than the other reference genes for normalizing the relative expression of target genes in different tissues of fasting caecotrophy rabbits.
Collapse
Affiliation(s)
- Hui He
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Zhichao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Mengke Ni
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Shanshan Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Lei Yu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China.
| | - Dehu Zhuo
- College of Medicine, Zhengzhou University, Zhengzhou, 450046, People's Republic of China.
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China.
| |
Collapse
|
6
|
A Bilayer Osteochondral Scaffold with Self‐Assembled Monomeric Collagen Type‐I, Type‐II, and Polymerized Chondroitin Sulfate Promotes Chondrogenic and Osteogenic Differentiation of Mesenchymal Stem Cells. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
7
|
Onaga T, Sakai A, Kajita M, Fukuda H, Yasui Y, Hayashi H. Messenger RNA expression and localization of xenin in the gastrointestinal tract in sheep. Domest Anim Endocrinol 2021; 74:106523. [PMID: 32795864 DOI: 10.1016/j.domaniend.2020.106523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/27/2020] [Accepted: 07/10/2020] [Indexed: 10/23/2022]
Abstract
The present study aimed to determine the primary sequence of ovine xenin and clarify the mRNA expression and peptide localization of xenin in the gastrointestinal tract in sheep. The colocalization of xenin and glucose-dependent insulinotropic polypeptide was also compared in the antrum and duodenum. Analysis of the nucleotide sequence of ovine xenin revealed a high degree (97.9%) of sequence homology of the sequence between sheep and cattle, and the amino acids sequence determined for ovine xenin coincided (100%) with that of other mammalian species. Real-time quantitative PCR for ovine xenin did not show regional difference in the mRNA expression ratio of xenin. In contrast to the real-time quantitative PCR results, anti-xenin positive cells were abundantly localized in the abomasal antrum (P < 0.01) and at a lesser amount in the duodenum, but no antixenin positive cells were observed in the other regions. Anti-xenin single-positive cells were in a majority in the abomasal antrum, whereas anti-xenin single-positive cells, and anti-GIP single-positive cells, and double-positive cells were even colocalized in the duodenum. These results suggest that abomasal antrum is a major source of xenin in the ovine gastrointestinal tract.
Collapse
Affiliation(s)
- T Onaga
- Laboratory of Veterinary Physiology and Nutrition, Division of Biosciences, Department of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan.
| | - A Sakai
- Laboratory of Veterinary Physiology and Nutrition, Division of Biosciences, Department of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan
| | - M Kajita
- Laboratory of Veterinary Physiology and Nutrition, Division of Biosciences, Department of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan
| | - H Fukuda
- Laboratory of Veterinary Physiology and Nutrition, Division of Biosciences, Department of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan
| | - Y Yasui
- Laboratory of Veterinary Physiology and Nutrition, Division of Biosciences, Department of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan
| | - H Hayashi
- Laboratory of Veterinary Physiology, Division of Biosciences, Department of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan
| |
Collapse
|
8
|
Sassu EL, Kangethe RT, Settypalli TBK, Chibssa TR, Cattoli G, Wijewardana V. Development and evaluation of a real-time PCR panel for the detection of 20 immune markers in cattle and sheep. Vet Immunol Immunopathol 2020; 227:110092. [PMID: 32673891 DOI: 10.1016/j.vetimm.2020.110092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/05/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
Abstract
The establishment of a panel of immune markers is of paramount importance to understand the different transcription patterns of infectious diseases in livestock. The array of commercially available immunological assays for cattle and sheep is currently limited, due to the lack of antibodies for these species. Even though SYBR Green based real time quantitative PCR (qPCR) is the most commonly used method to study cytokine transcription in ruminants, a lack of standardization impairs its implementation in the study of different ruminant diseases. In order to obtain reliable qPCR results, several variables need to be considered: choice of reference genes for optimal normalization, variation of annealing temperature among primer sets, and assay specificity and sensitivity. In this study, we developed and validated a panel of immune markers in bovine and ovine samples using SYBR Green based qPCR in a cost-effective way with multiple primer sets optimised to amplify at a common thermal cycling temperature. Twenty primer sets were designed to quantify immune markers (IL-1b, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-13, IL-15, IL-18, IL-23, TNF-α, IFN-γ, IFN-α, Ki-67, NFkB-65, TLR-3, TLR-4, TLR-8 and Rig-1) in ovine and bovine templates. For optimal normalization and selection of suitable reference genes, primer sets that measure the transcription of five reference genes were also included in the panel. The amplification efficiency, linearity and specificity was validated for all target genes. Optimal amplification conditions were achieved in both ovine and bovine samples for all gene targets, with the exception of Ki67. Relative quantification studies were performed on ovine and bovine mRNA obtained from sheep peripheral blood mononuclear cells (PBMCs) stimulated with three different treatments (PMA/Ionomycin, Concanavalin A (Con A) and pokeweed mitogen (PWM)). Pokeweed and ConA efficiently induced gene transcription of most of the targeted genes, while PMA/Ionomycin showed a weaker induction. Finally, we further assessed usability of our panel by running it on bovine monocyte derived dendritic cells (MoDCs) stimulated with different vaccines. Results confirmed the induction of a specific pro-inflammatory gene transcription pattern by rabies vaccine, which resembles the one occurring during viral infection. Altogether, we validated the efficiency and usability of an extended real-time PCR panel that gives the possibility to rapidly measure a broad spectrum of ovine and bovine immune markers by using a single set of reagents and protocol thus representing a valid and cost-effective tool for research purposes.
Collapse
Affiliation(s)
- Elena L Sassu
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Richard T Kangethe
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Tirumala Bharani K Settypalli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Tesfaye Rufael Chibssa
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| | - Viskam Wijewardana
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria.
| |
Collapse
|
9
|
Capellini FM, Vencia W, Amadori M, Mignone G, Parisi E, Masiello L, Vivaldi B, Ferrari A, Razzuoli E. Characterization of MDCK cells and evaluation of their ability to respond to infectious and non-infectious stressors. Cytotechnology 2019; 72:97-109. [PMID: 31802289 PMCID: PMC7002637 DOI: 10.1007/s10616-019-00360-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/28/2019] [Indexed: 01/08/2023] Open
Abstract
The Madin-Darby Canine Kidney (MDCK) cell line is widely used as epithelial cell model in studies ranging from viral infection to environmental pollutants, and vaccines production. However, little is known about basal expression of genes involved in innate immunity, and the ability to respond to infectious and non-infectious stressors. Therefore, the aims of our study were to evaluate the basal level of expression of pivotal genes in the innate immune response and cell cycle regulation, as well as to evaluate the ability of this cell line to respond to infectious or non-infectious stressors. As surmised in our working hypothesis, we demonstrated the constitutive expression of genes involved in the innate immune response and cell defense alike, including TLRs, Interleukins, Myd88, p65/NF-kB and p53. Moreover, we described the ability of this cell line to respond to LPS and cadmium (Cd2+) in terms of gene expression and cytokine release. These data confirm the possibility of using this cell line as a model in studies of host/pathogen interaction and response to non-infectious stressors.
Collapse
Affiliation(s)
- Francesca Maria Capellini
- Laboratory of Diagnostic, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e valle d'Aosta, S.S Genova, piazza Borgo pila 24-39, 16129, Genoa, Italy
| | - Walter Vencia
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e valle d'Aosta, piazza Borgo pila 24-39, 16129, Genoa, Italy
| | - Massimo Amadori
- Laboratory of Cellular Immunology, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, via A. Bianchi 9, 25124, Brescia, Italy
| | - Giulia Mignone
- Laboratory of Diagnostic, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e valle d'Aosta, S.S Genova, piazza Borgo pila 24-39, 16129, Genoa, Italy
| | - Erica Parisi
- Laboratory of Diagnostic, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e valle d'Aosta, S.S Genova, piazza Borgo pila 24-39, 16129, Genoa, Italy
| | - Lucia Masiello
- Laboratory of Chemistry, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e valle d'Aosta, piazza Borgo pila 24-39, 16129, Genoa, Italy
| | - Barbara Vivaldi
- Laboratory of Chemistry, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e valle d'Aosta, piazza Borgo pila 24-39, 16129, Genoa, Italy
| | - Angelo Ferrari
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e valle d'Aosta, piazza Borgo pila 24-39, 16129, Genoa, Italy
| | - Elisabetta Razzuoli
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e valle d'Aosta, piazza Borgo pila 24-39, 16129, Genoa, Italy.
| |
Collapse
|
10
|
Fan H, Hou Y, Sahana G, Gao H, Zhu C, Du L, Zhao F, Wang L. A Transcriptomic Study of the Tail Fat Deposition in Two Types of Hulun Buir Sheep According to Tail Size and Sex. Animals (Basel) 2019; 9:ani9090655. [PMID: 31491862 PMCID: PMC6770480 DOI: 10.3390/ani9090655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 01/19/2023] Open
Abstract
Simple Summary Based on tail types, Hulun Buir sheep were divided into two lines including small and big fat-tailed, but these two lines have similar genetic background. In this study, we investigated the morphology and transcription level differences of tail fat between these two lines. The RNA-seq analyses indicated several differentially expressed genes when compared between sexes or two tail sizes. Interestingly, we also found an obvious sex difference in the fat metabolism in Hulun Buir sheep. Two different co-expression networks were only shown either in male or in female sheep. Our findings will provide theoretical background in understanding the genetic mechanism of fat deposition in sheep. Abstract Hulun Buir sheep of similar genetic background were divided into two lines based on tail types: Small- and big fat-tailed. To explore the molecular mechanism of fat deposition in sheep tails, we firstly evaluated the morphology and transcription level differences of tail fat between these two lines. RNA-Seq technology was used to identify differentially expressed genes (DEGs) in phenotypic extremes of tail sizes. Five comparisons were performed taking into account two factors, sex and tail type. We screened out 373 DEGs between big-tailed and small-tailed Hulun Buir sheep, and 775 and 578 DEGs between two types of tails in male and female sheep, respectively. The results showed an obvious sex difference in the fat metabolism in sheep based on gene ontology (GO), pathway, and network analyses. Intriguingly, there were two different co-expression networks only respectively shown in male and female sheep, which were insulin-related network acting on upstream pathways and PPARG-related network effect in downstream pathways. Furthermore, these two networks were linked by a classic pathway of regulating adipogenesis. This is the first study to investigate the sex differences of fat metabolism in domestic animals, and it demonstrates a new experimental way to study fat metabolism. Our findings will provide theoretical background in understanding the tail-size phenotype in sheep and can be exploited in breeding small-tailed sheep.
Collapse
Affiliation(s)
- Hongying Fan
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Mariculture, Ocean University of China, Qingdao 266000, China
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing 100101, China
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Hongding Gao
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Caiye Zhu
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixin Du
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuping Zhao
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lixian Wang
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
11
|
Li C, Li M, Li X, Ni W, Xu Y, Yao R, Wei B, Zhang M, Li H, Zhao Y, Liu L, Ullah Y, Jiang Y, Hu S. Whole-Genome Resequencing Reveals Loci Associated With Thoracic Vertebrae Number in Sheep. Front Genet 2019; 10:674. [PMID: 31379930 PMCID: PMC6657399 DOI: 10.3389/fgene.2019.00674] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/27/2019] [Indexed: 12/31/2022] Open
Abstract
The number of vertebrae, especially thoracic vertebrae, is an important economic trait that may influence carcass length and meat production in animals. However, the genetic basis of vertebrae number in sheep is still poorly understood. To detect the candidate genes, 400 increased number of thoracic vertebrae (T14L6) and 200 normal (T13L6) Kazakh sheep were collected. We generated and sequenced 60 pools of genomic DNA (each pool prepared by mixing genomic DNA from 10 sheep with the same thoracic traits), with an average depth of coverage of 25.65×. We identified a total of 42,075,402 SNPs and 11 putatively selected genomic regions, including the VRTN gene and the HoxA gene family that regulate vertebral development. The most prominent areas of selective elimination were located in a region of chromosome 7, including VRTN, which regulates spinal development and morphology. Further investigation indicated that the expression level of the VRTN gene during fetal development was significantly higher in sheep with more thoracic vertebrae than in those with a normal number of thoracic vertebrae. A genome-wide comparison between sheep with increased and normal numbers of thoracic vertebrae showed that the VRTN gene is the major selection locus for the number of thoracic vertebrae in sheep and has the potential to be utilized in sheep breeding in the future.
Collapse
Affiliation(s)
- Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, China.,College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Ming Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Bin Wei
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yue Zhao
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yaseen Ullah
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, China
| |
Collapse
|
12
|
Does kisspeptin participate in GABA-mediated modulation of GnRH and GnRH receptor biosynthesis in the hypothalamic-pituitary unit of follicular-phase ewes? Pharmacol Rep 2019; 71:636-643. [PMID: 31176893 DOI: 10.1016/j.pharep.2019.02.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND The inverse relationship between GnRH transcript level and GABA neurons activity has suggested that GABA at the hypothalamic level may exert a suppressive effect on subsequent steps of the GnRH biosynthesis. In the present study, we analyzed the effects of GABA type A receptor agonist (muscimol) or antagonist (bicuculline) on molecular mechanisms governing GnRH/LH secretion in follicular-phase sheep. METHODS ELISA technique was used to investigate the effects of muscimol and/or bicuculline on levels of post-translational products of genes encoding GnRH ligand and GnRH receptor (GnRHR) in the preoptic area (POA), anterior (AH) and ventromedial (VMH) hypothalamus, stalk/median eminence (SME), and GnRHR in the anterior pituitary (AP). Real-time PCR was chosen for determination of the effect of drugs on kisspeptin (Kiss 1) mRNA level in POA and VMH including arcuate nucleus (VMH/ARC), and on Kiss1 receptor (Kiss1r) mRNA abundance in POA-hypothalamic structures. These analyses were supplemented by RIA method for measurement of plasma LH concentration. RESULTS The study demonstrated that muscimol and bicuculline significantly decreased or increased GnRH biosynthesis in all analyzed structures, respectively, and led to analogous changes in plasma LH concentration. Similar muscimol- and bicuculline-related alterations were observed in levels of GnRHR. However, the expression of Kiss 1 and Kiss1r mRNAs in selected POA-hypothalamic areas of either muscimol- and bicuculline-treated animals remained unaltered. CONCLUSIONS Our data suggest that GABAergic neurotransmission is involved in the regulatory pathways of GnRH/GnRHR biosynthesis and then GnRH/LH release in follicular-phase sheep conceivably via indirect mechanisms that exclude involvement of Kiss 1 neurons.
Collapse
|
13
|
Toscano JHB, Lopes LG, Giraldelo LA, da Silva MH, Okino CH, de Souza Chagas AC. Identification of appropriate reference genes for local immune-related studies in Morada Nova sheep infected with Haemonchus contortus. Mol Biol Rep 2018; 45:1253-1262. [DOI: 10.1007/s11033-018-4281-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/24/2018] [Indexed: 01/23/2023]
|
14
|
Wang S, Wang J, Lv X. Selection of reference genes for expression analysis in mouse models of acute alcoholic liver injury. Int J Mol Med 2018; 41:3527-3536. [PMID: 29512759 DOI: 10.3892/ijmm.2018.3527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/08/2018] [Indexed: 11/06/2022] Open
Abstract
Investigations of hepatic gene expression are crucial for determining the molecular factors involved in acute alcoholic liver injury. The results of liver molecular investigations may reveal etiologically important genomic alterations. Therefore, it is necessary to normalize gene expression data to identify stable genes, which may be used as a reference under different experimental conditions. The aim of the present study was to apply reverse transcription‑quantitative polymerase chain reaction analysis and use analysis software to investigate the expression stability of candidate reference genes in hepatic tissues from mice with acute alcoholic liver injury. The acute alcoholic liver injury models were established by the intragastric administration of alcohol (5 mg/kg) in Imprinting Control Region mice. Total RNA was isolated from the mouse livers, following which the expression levels of seven reference genes, β-actin, glyceraldehyde 3-phosphate dehydrogenase (Gadph), glucuronidase β, hypoxanthine phosphoribosyltransferase 1 (Hprt1), 18S ribosomal RNA, TATA binding protein and β‑2 microglobulin, were examined, and gene expression stability was assessed using the geNorm, NormFinder and BestKeeper tools. The geNorm analysis revealed that the gene with the lowest variability was Hprt1. Hprt1 and Gapdh were validated as the optimal reference gene pair in all samples from all groups. The NormFinder and BestKeeper results showed that Hprt1 was the most stable gene in all samples. Alcohol induces endoplasmic reticulum (ER) stress, causing changes in the expression levels of ER stress‑associated genes. The stability of Hprt1 was verified by the expression analysis of ER stress‑associated genes, and gene expression levels in the ethanol groups were upregulated, with a significant difference in expression, compared with those in the control group. Therefore, Hprt1 was selected as the most stable gene, and Hprt1 and Gapdh were determined to be the optimum gene pair in mouse models of acute alcoholic liver injury. The reliability of the Hprt1 gene was confirmed by expression analysis of ER stress‑associated genes.
Collapse
Affiliation(s)
- Sheng Wang
- School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Jianqing Wang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Xiongwen Lv
- School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, P.R. China
| |
Collapse
|
15
|
Ciechanowska M, Łapot M, Paruszewska E, Radawiec W, Przekop F. The influence of dopaminergic system inhibition on biosynthesis of gonadotrophin-releasing hormone (GnRH) and GnRH receptor in anoestrous sheep; hierarchical role of kisspeptin and RFamide-related peptide-3 (RFRP-3). Reprod Fertil Dev 2018; 30:672-680. [DOI: 10.1071/rd16309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/14/2017] [Indexed: 11/23/2022] Open
Abstract
This study aimed to explain how prolonged inhibition of central dopaminergic activity affects the cellular processes governing gonadotrophin-releasing hormone (GnRH) and LH secretion in anoestrous sheep. For this purpose, the study included two experimental approaches: first, we investigated the effect of infusion of sulpiride, a dopaminergic D2 receptor antagonist (D2R), on GnRH and GnRH receptor (GnRHR) biosynthesis in the hypothalamus and on GnRHR in the anterior pituitary using an immunoassay. This analysis was supplemented by analysis of plasma LH levels by radioimmunoassay. Second, we used real-time polymerase chain reaction to analyse the influence of sulpiride on the levels of kisspeptin (Kiss1) mRNA in the preoptic area and ventromedial hypothalamus including arcuate nucleus (VMH/ARC), and RFamide-related peptide-3 (RFRP-3) mRNA in the paraventricular nucleus (PVN) and dorsomedial hypothalamic nucleus. Sulpiride significantly increased plasma LH concentration and the levels of GnRH and GnRHR in the hypothalamic–pituitary unit. The abolition of dopaminergic activity resulted in a significant increase in transcript level of Kiss1 in VMH/ARC and a decrease of RFRP-3 in PVN. The study demonstrates that dopaminergic neurotransmission through D2R is involved in the regulatory pathways of GnRH and GnRHR biosynthesis in the hypothalamic–pituitary unit of anoestrous sheep, conceivably via mechanisms in which Kiss1 and RFRP-3 participate.
Collapse
|
16
|
Schulze F, Malhan D, El Khassawna T, Heiss C, Seckinger A, Hose D, Rösen-Wolff A. A tissue-based approach to selection of reference genes for quantitative real-time PCR in a sheep osteoporosis model. BMC Genomics 2017; 18:975. [PMID: 29258442 PMCID: PMC5735898 DOI: 10.1186/s12864-017-4356-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In order to better understand the multifactorial nature of osteoporosis, animal models are utilized and compared to healthy controls. Female sheep are well established as a model for osteoporosis induced by ovariectomy, calcium and vitamin D low diet, application of steroids, or a combination of these treatments. Transcriptional studies can be performed by applying quantitative real time PCR (RT-qPCR). RT-qPCR estimates mRNA-levels of target genes in relation to reference genes. A chosen set of reference genes should not show variation under experimental conditions. Currently, no standard reference genes are accepted for all tissue types and experimental conditions. Studies examining reference genes for sheep are rare and only one study described stable reference in mandibular bone. However, this type of bone differs from trabecular bone where most osteoporotic fractures occur. The present study aimed at identifying a set of reference genes for relative quantification of transcriptional activity of ovine spine bone and ovine in vitro differentiated mesenchymal stromal cells (MSC) for reliable comparability. METHODS Twelve candidate reference genes belonging to different functional classes were selected and their expression was measured from cultured ovMSCs (n = 18) and ovine bone samples (n = 16), respectively. RefFinder was used to rank the candidate genes. RESULTS We identified B2M, GAPDH, RPL19 and YWHAZ as the best combination of reference genes for normalization of RT-qPCR results for transcriptional analyses of these ovine samples. CONCLUSION This study demonstrates the importance of applying a set of reference genes for RT-qPCR analysis in sheep. Based on our data we recommend using four identified reference genes for relative quantification of gene expression studies in ovine bone or for in vitro experiments with osteogenically differentiated ovine MSCs.
Collapse
Affiliation(s)
- Felix Schulze
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Deeksha Malhan
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany
| | - Thaqif El Khassawna
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany
| | - Christian Heiss
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany.,Department of Trauma, Hand and Reconstructive Surgery, University Hospital of Giessen-Marburg, Rudolf-Buchheim-Strasse 7, 35385, Giessen, Germany
| | - Anja Seckinger
- Labor für Myelomforschung, Medizinische Klinik V, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Dirk Hose
- Labor für Myelomforschung, Medizinische Klinik V, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Angela Rösen-Wolff
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
| |
Collapse
|
17
|
Li C, Li X, Ma Q, Zhang X, Cao Y, Yao Y, You S, Wang D, Quan R, Hou X, Liu Z, Zhan Q, Liu L, Zhang M, Yu S, Ni W, Hu S. Genome-wide analysis of circular RNAs in prenatal and postnatal pituitary glands of sheep. Sci Rep 2017; 7:16143. [PMID: 29170496 PMCID: PMC5700919 DOI: 10.1038/s41598-017-16344-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/10/2017] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of animal non-coding RNAs and play an impor-tant role in animal growth and development. However, the expression and function of circRNAs in the pituitary gland of sheep are unclear. Transcriptome profiling of circRNAs in the pituitary gland of sheep may enable us to understand their biological functions. In the present study, we identified 10,226 circRNAs from RNA-seq data in the pituitary gland of prenatal and postnatal sheep. Reverse transcription PCR and DNA sequencing analysis confirmed the presence of several circRNAs. Real-time RT-PCR analysis showed that sheep circRNAs are resistant to RNase R digestion and are expressed in prenatal and postnatal pituitary glands. GO and KEGG enrichment analysis showed that host genes of differentially expressed circRNAs are involved in the regulation of hormone secretion as well as in several pathways related to these processes. We determined that numerous circRNAs interact with pituitary-specific miRNAs that are involved in the biologic functions of the pituitary gland. Moreover, several circRNAs contain at least one IRES element and open reading frame, indicating their potential to encode proteins. Our study provides comprehensive expression profiles of circRNAs in the pituitary gland, thereby offering a valuable resource for circRNA biology in sheep.
Collapse
Affiliation(s)
- Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qiman Ma
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiangyu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shuang You
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Zhijin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qianqian Zhan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| |
Collapse
|
18
|
Li C, Li X, Yao Y, Ma Q, Ni W, Zhang X, Cao Y, Hazi W, Wang D, Quan R, Hou X, Liu Z, Zhan Q, Liu L, Zhang M, Yu S, Hu S. Genome-wide analysis of circular RNAs in prenatal and postnatal muscle of sheep. Oncotarget 2017; 8:97165-97177. [PMID: 29228601 PMCID: PMC5722553 DOI: 10.18632/oncotarget.21835] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep. A total of 6113 circRNAs were detected from the RNA-seq data. Several circRNAs were identified using reverse transcription PCR, DNA sequencing and RNase R digestion experiments. The expression levels of several circRNAs in prenatal and postnatal muscle were confirmed by Real-Time RT-PCR. The gene ontology (GO) and KEGG enrichment analysis of the host gene of the circRNAs showed that these circRNAs were mainly involved in the growth and development of muscle related signaling pathways. These circRNAs might sponge microRNAs (miRNAs) in predicted circRNA-miRNA-mRNA networks. The circRNAs expression profiles in muscle provided an important reference for the study of circRNAs in sheep.
Collapse
Affiliation(s)
- Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qiman Ma
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiangyu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Zhijin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qianqian Zhan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| |
Collapse
|
19
|
Higgitt RL, Buss PE, van Helden PD, Miller MA, Parsons SDC. Development of gene expression assays measuring immune responses in the spotted hyena (Crocuta crocuta). AFRICAN ZOOLOGY 2017. [DOI: 10.1080/15627020.2017.1309300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Roxanne L Higgitt
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Peter E Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa
| | - Paul D van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Michele A Miller
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Sven DC Parsons
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| |
Collapse
|
20
|
Mahakapuge TAN, Scheerlinck JPY, Rojas CAA, Every AL, Hagen J. Assessment of reference genes for reliable analysis of gene transcription by RT-qPCR in ovine leukocytes. Vet Immunol Immunopathol 2016; 171:1-6. [PMID: 26964711 DOI: 10.1016/j.vetimm.2015.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/21/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
With the availability of genetic sequencing data, quantitative reverse transcription PCR (RT-qPCR) is increasingly being used for the quantification of gene transcription across species. Too often there is little regard to the selection of reference genes and the impact that a poor choice has on data interpretation. Indeed, RT-qPCR provides a snapshot of relative gene transcription at a given time-point, and hence is highly dependent on the stability of the transcription of the reference gene(s). Using ovine efferent lymph cells and peripheral blood mono-nuclear cells (PBMCs), the two most frequently used leukocytes in immunological studies, we have compared the stability of transcription of the most commonly used ovine reference genes: YWHAZ, RPL-13A, PGK1, B2M, GAPDH, HPRT, SDHA and ACTB. Using established algorithms for reference gene normalization "geNorm" and "Norm Finder", PGK1, GAPDH and YWHAZ were deemed the most stably transcribed genes for efferent leukocytes and PGK1, YWHAZ and SDHA were optimal in PBMCs. These genes should therefore be considered for accurate and reproducible RT-qPCR data analysis of gene transcription in sheep.
Collapse
Affiliation(s)
- T A N Mahakapuge
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia.
| | - J-P Y Scheerlinck
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - C A Alvarez Rojas
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - A L Every
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - J Hagen
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia; Department of Life Sciences, Imperial College London, SW7 2AZ London, UK
| |
Collapse
|
21
|
Olivier TT, Viljoen IM, Hofmeyr J, Hausler GA, Goosen WJ, Tordiffe ASW, Buss P, Loxton AG, Warren RM, Miller MA, van Helden PD, Parsons SDC. Development of a Gene Expression Assay for the Diagnosis ofMycobacterium bovisInfection in African Lions (Panthera leo). Transbound Emerg Dis 2015; 64:774-781. [DOI: 10.1111/tbed.12436] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 11/26/2022]
Affiliation(s)
- T. T. Olivier
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| | - I. M. Viljoen
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| | - J. Hofmeyr
- Veterinary Wildlife Services; Kruger National Park; Skukuza South Africa
| | - G. A. Hausler
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| | - W. J. Goosen
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| | - A. S. W. Tordiffe
- Department of Paraclinical Sciences; Faculty of Veterinary Science; University of Pretoria; Pretoria South Africa
- National Zoological Gardens of South Africa; Pretoria South Africa
| | - P. Buss
- Veterinary Wildlife Services; Kruger National Park; Skukuza South Africa
| | - A. G. Loxton
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| | - R. M. Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| | - M. A. Miller
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| | - P. D. van Helden
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| | - S. D. C. Parsons
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for TB Research/Division of Molecular Biology and Human Genetics; Faculty of Medicine and Health Sciences; Stellenbosch University; Tygerberg South Africa
| |
Collapse
|
22
|
Jiang X, Xue Y, Zhou H, Li S, Zhang Z, Hou R, Ding Y, Hu K. Evaluation of reference gene suitability for quantitative expression analysis by quantitative polymerase chain reaction in the mandibular condyle of sheep. Mol Med Rep 2015; 12:5633-40. [PMID: 26238421 PMCID: PMC4581798 DOI: 10.3892/mmr.2015.4128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 05/08/2015] [Indexed: 11/29/2022] Open
Abstract
Reference genes are commonly used as a reliable approach to normalize the results of quantitative polymerase chain reaction (qPCR), and to reduce errors in the relative quantification of gene expression. Suitable reference genes belonging to numerous functional classes have been identified for various types of species and tissue. However, little is currently known regarding the most suitable reference genes for bone, specifically for the sheep mandibular condyle. Sheep are important for the study of human bone diseases, particularly for temporomandibular diseases. The present study aimed to identify a set of reference genes suitable for the normalization of qPCR data from the mandibular condyle of sheep. A total of 12 reference genes belonging to various functional classes were selected, and the expression stability of the reference genes was determined in both the normal and fractured area of the sheep mandibular condyle. RefFinder, which integrates the following currently available computational algorithms: geNorm, NormFinder, BestKeeper, and the comparative ΔCt method, was used to compare and rank the candidate reference genes. The results obtained from the four methods demonstrated a similar trend: RPL19, ACTB, and PGK1 were the most stably expressed reference genes in the sheep mandibular condyle. As determined by RefFinder comprehensive analysis, the results of the present study suggested that RPL19 is the most suitable reference gene for studies associated with the sheep mandibular condyle. In addition, ACTB and PGK1 may be considered suitable alternatives.
Collapse
Affiliation(s)
- Xin Jiang
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yang Xue
- State Key Laboratory of Military Stomatology, Department of Oral Biology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Hongzhi Zhou
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Shouhong Li
- Department of Oral and Maxillofacial Surgery, Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei 442008, P.R. China
| | - Zongmin Zhang
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Rui Hou
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yuxiang Ding
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Kaijin Hu
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| |
Collapse
|
23
|
Selection of reference genes for gene expression studies related to intramuscular fat deposition in Capra hircus skeletal muscle. PLoS One 2015; 10:e0121280. [PMID: 25794179 PMCID: PMC4368700 DOI: 10.1371/journal.pone.0121280] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/29/2015] [Indexed: 01/12/2023] Open
Abstract
The identification of suitable reference genes is critical for obtaining reliable results from gene expression studies using quantitative real-time PCR (qPCR) because the expression of reference genes may vary considerably under different experimental conditions. In most cases, however, commonly used reference genes are employed in data normalization without proper validation, which may lead to incorrect data interpretation. Here, we aim to select a set of optimal reference genes for the accurate normalization of gene expression associated with intramuscular fat (IMF) deposition during development. In the present study, eight reference genes (PPIB, HMBS, RPLP0, B2M, YWHAZ, 18S, GAPDH and ACTB) were evaluated by three different algorithms (geNorm, NormFinder and BestKeeper) in two types of muscle tissues (longissimus dorsi muscle and biceps femoris muscle) across different developmental stages. All three algorithms gave similar results. PPIB and HMBS were identified as the most stable reference genes, while the commonly used reference genes 18S and GAPDH were the most variably expressed, with expression varying dramatically across different developmental stages. Furthermore, to reveal the crucial role of appropriate reference genes in obtaining a reliable result, analysis of PPARG expression was performed by normalization to the most and the least stable reference genes. The relative expression levels of PPARG normalized to the most stable reference genes greatly differed from those normalized to the least stable one. Therefore, evaluation of reference genes must be performed for a given experimental condition before the reference genes are used. PPIB and HMBS are the optimal reference genes for analysis of gene expression associated with IMF deposition in skeletal muscle during development.
Collapse
|
24
|
Puech C, Dedieu L, Chantal I, Rodrigues V. Design and evaluation of a unique SYBR Green real-time RT-PCR assay for quantification of five major cytokines in cattle, sheep and goats. BMC Vet Res 2015; 11:65. [PMID: 25889787 PMCID: PMC4369058 DOI: 10.1186/s12917-015-0382-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/27/2015] [Indexed: 11/24/2022] Open
Abstract
Background Today, when more than 60% of animal diseases are zoonotic, understanding their origin and development and identifying protective immune responses in ruminants are major challenges. Robust, efficient and cost-effective tools are preconditions to solve these challenges. Cytokines play a key role in the main mechanisms by which the immune system is balanced in response to infectious pathogens. The cytokine balance has thus become the focus of research to characterize immune response in ruminants. Currently, SYBR Green reverse transcriptase quantitative PCR (RT-qPCR) is the most widely method used to investigate cytokine gene expression in ruminants, but the conditions in which the many assays are carried out vary considerably and need to be properly evaluated. Accordingly, the quantification of gene expression by RT-qPCR requires normalization by multiple reference genes. The objective of the present study was thus to develop an RT-qPCR assay to simultaneously quantify the expression of several cytokines and reference genes in three ruminant species. In this paper, we detail each stage of the experimental protocol, check validation parameters and report assay performances, following MIQE guidelines. Results Ten novel primer sets were designed to quantify five cytokine genes (IL-4, IL-10, IL-12B, IFN-γ and TNF-α) and five reference genes (ACTB, GAPDH, H3F3A, PPIA and YWHAZ) in cattle, sheep, and goats. All the primer sets were designed to span exon-exon boundaries and use the same hybridization temperature. Each stage of the RT-qPCR method was detailed; their specificity and efficiency checked, proved and are reported here, demonstrating the reproducibility of our method, which is capable of detecting low levels of cytokine mRNA up to one copy whatever the species. Finally, we checked the stability of candidate reference gene expression, performed absolute quantification of cytokine and reference gene mRNA in whole blood samples and relative expression of cytokine mRNA in stimulated PBMC samples. Conclusions We have developed a novel RT-qPCR assay for the simultaneous relative quantification of five major cytokines in cattle, sheep and goats, and their accurate normalization by five reference genes. This accurate and easily reproducible tool can be used to investigate ruminant immune responses and is widely accessible to the veterinary research community. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0382-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Carinne Puech
- INRA, UMR1309 CMAEE, Montpellier, F-34398, France. .,CIRAD, UMR CMAEE, Montpellier, F-34398, France.
| | | | | | - Valérie Rodrigues
- INRA, UMR1309 CMAEE, Montpellier, F-34398, France. .,CIRAD, UMR CMAEE, Montpellier, F-34398, France.
| |
Collapse
|
25
|
Jarczak J, Kaba J, Bagnicka E. The validation of housekeeping genes as a reference in quantitative Real Time PCR analysis. Gene 2014; 549:280-5. [DOI: 10.1016/j.gene.2014.07.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 10/25/2022]
|
26
|
Schoen K, Plendl J, Gabler C, Kaessmeyer S. Identification of stably expressed reference genes for RT-qPCR data normalization in defined localizations of cyclic bovine ovaries. Anat Histol Embryol 2014; 44:200-11. [PMID: 25092559 DOI: 10.1111/ahe.12128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 05/27/2014] [Indexed: 01/22/2023]
Abstract
Ovaries are highly complex organs displaying morphological, molecular and functional differences between their cortical zona parenchymatosa and medullary zona vasculosa, and also between the different cyclic luteal stages. Objective of the present study was to validate expression stability of twelve putative reference genes (RGs) in bovine ovaries, considering the intrinsic heterogeneity of bovine ovarian tissue with regard to different luteal stages and intra-ovarian localizations. The focus was on identifying RGs, which are suitable to normalize RT-qPCR results of ovaries collected from clinical healthy cattle, irrespective of localization and the hormonal stage. Expression profiles of twelve potential reference genes (GAPDH, ACTB, YWHAZ, HPRT1, SDHA, UBA52, POLR2C, RPS9, ACTG2, H3F3B, RPS18 and RPL19) were analysed. Evaluation of gene expression differences was performed using genorm, normfinder, and bestkeeper software. The most stably expressed genes according to genorm, normfinder and bestkeeper approaches contained the candidates H3F3B, RPS9, YWHAZ, RPS18, POLR2C and UBA52. Of this group, the genes YWHAZ, H3F3B and RPS9 could be recommended as best-suited RGs for normalization purposes on healthy bovine ovaries irrespective of the luteal stage or intra-ovarian localization.
Collapse
Affiliation(s)
- K Schoen
- Department of Veterinary Medicine, Institute of Veterinary Anatomy, Freie Universität Berlin, Koserstraße 20, 14195, Berlin, Germany
| | - J Plendl
- Department of Veterinary Medicine, Institute of Veterinary Anatomy, Freie Universität Berlin, Koserstraße 20, 14195, Berlin, Germany
| | - C Gabler
- Department of Veterinary Medicine, Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, 14163, Berlin, Germany
| | - S Kaessmeyer
- Department of Veterinary Medicine, Institute of Veterinary Anatomy, Freie Universität Berlin, Koserstraße 20, 14195, Berlin, Germany
| |
Collapse
|
27
|
Modesto P, Peletto S, Pisoni G, Cremonesi P, Castiglioni B, Colussi S, Caramelli M, Bronzo V, Moroni P, Acutis PL. Evaluation of internal reference genes for quantitative expression analysis by real-time reverse transcription-PCR in somatic cells from goat milk. J Dairy Sci 2013; 96:7932-44. [PMID: 24119819 DOI: 10.3168/jds.2012-6383] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 08/10/2013] [Indexed: 11/19/2022]
Abstract
Reverse transcription (RT) quantitative real-time PCR (qPCR) is the most accurate and easy-to-perform technique to measure the expression level of a selected gene of interest by quantifying mRNA transcripts. The use of reference genes is commonly accepted as the most reliable approach to normalize RT-qPCR data and reduce possible errors generated in the quantification of gene expression. The optimal number and choice of reference genes are experimentally validated for specific tissues or cell types and experimental designs. To date, data on qPCR normalization in goats are scarce and the most suitable reference genes in this species have been identified for only a limited number of tissues. The aim of this study was to determine an optimal combination of stably expressed reference genes in caprine milk somatic cells (MSC) from healthy and infected mammary glands. For the purpose, we performed RT-qPCR for 10 commonly used reference genes from various functional classes and then determined their expression level in MSC from goats intramammary challenged with Staphylococcus aureus and in MSC from healthy controls, with a view to select genes whose stability would be unaffected under infection conditions. The geNorm and NormFinder algorithms were used for validating the reference genes. Furthermore, to demonstrate the importance of normalization of gene expression with appropriate reference genes, we tested the effect of using a combination of the least stable genes for expression analysis evaluation. On the basis of our evaluation, we recommend the use of a panel of reference genes that should include G6PD, YWHAZ, and ACTB for caprine MSC gene expression profiling. The expression of the 2 genes of interest, pentraxin-related protein (PTX3) and secreted phosphoprotein 1 (SPP1), was evaluated by RT-qPCR in all samples collected pre- and postinfection, and the recommended reference genes were used to normalize the data. Our study provides a validated panel of optimal reference genes for the identification of genes differentially expressed by qRT-PCR in caprine MSC. Moreover, we provided a set of intron-spanning primer sequences that could be suitable for gene expression experiments using SYBR Green chemistry on other caprine tissues and cells.
Collapse
Affiliation(s)
- P Modesto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, 10154 Turin, Italy; Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, Università degli Studi di Milano, 20133 Milan, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Reference gene selection for quantitative PCR studies in sheep neutrophils. Int J Mol Sci 2013; 14:11484-95. [PMID: 23722658 PMCID: PMC3709743 DOI: 10.3390/ijms140611484] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 05/15/2013] [Accepted: 05/15/2013] [Indexed: 11/16/2022] Open
Abstract
Reference genes are essential for studying mRNA expression with quantitative PCR (qPCR). We investigated 11 potential neutrophil reference genes (RPL19, GAPDH, ACTB, B2M, HPRT, G6PD, TFRC, PGK1, YWHAZ, SDHA and GYPC) for sheep under disease conditions of foot rot (FR) and with or without Se supplementation. Initial screening was based on gene expression level (<28 Cq cycles) and variability (SD < 1.5 Cq cycles) and excluded TFRC, GYPC and HPRT from further analysis. Expression stability of the remaining genes was evaluated using four software programs: geNorm, NormFinder, BestKeeper and the comparative delta Cq method. The neutrophil reference genes, G6PD, YWHAZ, GAPDH, RPL19 and SDHA, consistently ranked among the top five most stable genes under these experimental conditions. The SDHA gene expression was not stable in FR-diseased sheep receiving Se treatment and, thus, cannot be recommended as a reference gene. The commonly used genes, PGK1, ACTB and B2M, were not reliable reference genes, underscoring the need to validate neutrophil reference genes under different experimental conditions. Multiple references genes rather than a single gene may provide more robust and reliable results. The best pair of reference genes was SDHA/G6PD in healthy sheep and GADPH/YWHAZ in FR-diseased sheep.
Collapse
|
29
|
Vorachek WR, Bobe G, Hall JA. Reference gene selection for quantitative PCR studies in bovine neutrophils. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.410a3002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
30
|
Selection of suitable reference genes for normalization of quantitative real-time PCR in cartilage tissue injury and repair in rabbits. Int J Mol Sci 2012. [PMID: 23203068 PMCID: PMC3509584 DOI: 10.3390/ijms131114344] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
When studying the altered expression of genes associated with cartilage regeneration by quantitative real-time RT-PCR (RT-qPCR), reference genes with highly stable expression during different stages of chondrocyte developmental are necessary to normalize gene expression accurately. Until now, no reports evaluating expression changes of commonly used reference genes in rabbit articular cartilage have been published. In this study, defects were made in rabbit articular cartilage, with or without insulin-like growth factor 1 (IGF-1) treatment, to create different chondrocyte living environments. The stability and intensity of the expressions of the candidate reference genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S Ribosomal RNA (18S rRNA), cyclophilin (CYP), hypoxanthine phosphoribosyl transferase (HPRT1), and beta-2-microglobulin (B2M) were evaluated. The data were analyzed by geNorm and NormFinder. B2M and 18S rRNA were identified to be suitable reference genes for rabbit cartilage tissues.
Collapse
|