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Tiwari M, Sodhi M, Sharma M, Sharma V, Mukesh M. Hypoxia related genes modulate in similar fashion in skin fibroblast cells of yak (Bos grunniens) adapted to high altitude and native cows (Bos indicus) adapted to tropical climate during hypoxia stress. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:1675-1687. [PMID: 38814473 DOI: 10.1007/s00484-024-02695-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/07/2024] [Accepted: 04/27/2024] [Indexed: 05/31/2024]
Abstract
The present study was conducted to understand transcriptional response of skin fibroblast of yak (Bos grunniens) and cows of Bos indicus origin to hypoxia stress. Six primary fibroblast cell lines derived from three individuals each of Ladakhi yak (Bos grunniens) and Sahiwal cows (Bos indicus) were exposed to low oxygen concentration for a period of 24 h, 48 h and 72 h. The expression of 10 important genes known to regulate hypoxia response such as HIF1A, VEGFA, EPAS1, ATP1A1, GLUT1, HMOX1, ECE1, TNF-A, GPx and SOD were evaluated in fibroblast cells of Ladakhi yak (LAY-Fb) and Sahiwal cows (SAC-Fb) during pre- and post-hypoxia stress. A panel of 10 reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) were also evaluated for their expression stability to perform accurate normalization. The expression of HIF1A was significantly (p < 0.05) induced in both LAY-Fb (2.29-fold) and SAC-Fb (2.07-fold) after 24 h of hypoxia stress. The angiogenic (VEGFA), metabolic (GLUT1) and antioxidant genes (SOD and GPx) were also induced after 24 h of hypoxia stress. However, EPAS1 and ATP1A1 induced significantly (p < 0.05) after 48 h whereas, ECE1 expression induced significantly (p < 0.05) at 72 h after exposure to hypoxia. The TNF-alpha which is a pro-inflammatory gene induced significantly (p < 0.05) at 24 h in SAC-Fb and at 72 h in LAY-Fb. The induction of hypoxia associated genes indicated the utility of skin derived fibroblast as cellular model to evaluate transcriptome signatures post hypoxia stress in populations adapted to diverse altitudes.
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Affiliation(s)
- Manish Tiwari
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Monika Sodhi
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manish Sharma
- DRDO-Defence Institute of Physiology and Allied Sciences, New Delhi, India
| | - Vishal Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manishi Mukesh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India.
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2
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Vasisth R, Gurao A, Chitkara M, Kumar G, Sriranga KR, Mukesh M, Dige MS, Singh P, Aggarwal RAK, Kataria RS. Selection of reference genes for normalizing gene expression data across seasons in spermatozoa of water buffalo (Bubalus bubalis). INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:1397-1409. [PMID: 38602552 DOI: 10.1007/s00484-024-02675-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/04/2023] [Accepted: 03/01/2024] [Indexed: 04/12/2024]
Abstract
Selection of the most stably expressed reference genes is key to monitoring accurate target gene expression across any tissue or cell type. The mRNA in spermatozoa stores valuable information related to changes in spermatogenesis due to variations in environmental conditions, especially during heat stress, which affects various sperm functions. Semen quality in buffalo bulls is significantly influenced by the seasons. In the study, a panel of nine genes was evaluated to identify the most stably expressed internal control gene (ICG) for the normalization of real-time gene expression data generated across various seasons for Murrah buffalo bulls' spermatozoa. Sperm cells were purified from the semen samples collected during different seasons, with temperature-humidity index (THI) ranging from 80.80 ± 1.47 (hot summer) to 55.88 ± 1.98 (winter), using the BoviPure™ gradient purification method. The RNA isolated from the purified spermatozoa fraction was quality checked prior to reverse transcription and subjected to qPCR (quantitative real-time PCR) based expression analysis. An automated 'endoGene' pipeline was employed to apply the geNorm, NormFinder, and BestKeeper algorithms for data analysis. The result indicated that GAPDH and PP1A were the most stably expressed among the gene panel, whereas ATPSF1 and ACTB were the two least stable expressed reference genes. Further, the most suitable ICGs identified were validated by normalization of real time expression data of heat stress and sperm quality genes, HSFY2 and AKAP4, respectively. The genes identified would help in generating the most reliable results for the expression profiling of the genes dictating sperm quality and heat stress cope-up mechanism in buffalo spermatozoa, collected during different seasons.
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Affiliation(s)
- Rashi Vasisth
- ICAR- National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
- ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Ankita Gurao
- ICAR- National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Meenakshi Chitkara
- ICAR- National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
- ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Gautam Kumar
- ICAR- National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
- ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | | | - Manishi Mukesh
- ICAR- National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | | | - Pawan Singh
- ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | | | - Ranjit Singh Kataria
- ICAR- National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
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Verma D, Chauhan MS, Mishra SK, Babu KR, Singh KP, Rani S, Kumar P, Singh MK, Gurao A, Kataria RS. Sequence characterization and comparative expression profile of buffalo WNT10B gene in adult and fetal tissues. Anim Biotechnol 2023; 34:3774-3782. [PMID: 37345902 DOI: 10.1080/10495398.2023.2225091] [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: 06/23/2023]
Abstract
In this study, Wingless-type MMTV (mouse mammary tumor virus) integration site family member (WNT10B) gene was sequence characterized in the Indian water buffalo. Sequence analysis revealed an open reading frame of 1176 nucleotides in buffalo, encoding 391 amino acids long protein. Nineteen nucleotide variations were observed between cattle and buffalo resulting in six amino acid changes. Phylogenetic analysis showed the clustering of ruminant species together. Real-time expression analysis of WNT10B in tissues collected from different organs of fetal and adult buffalo, revealed, the gene being abundantly expressed in the rumen and liver of the fetus. The fetal ovary, heart, kidney, lung, testis and mammary gland showed moderate expression, while in adult tissues, expression was high in the ovary, testis, brain, kidney, small intestine and liver, whereas lower expression was observed in the adult rumen. Significant differences in WNT10B expression levels were found for the brain, small intestine, testes, kidney, heart, rumen, and ovary when adult and fetal tissues were compared. A moderate level of genetic variation was found between cattle and buffalo WNT10B and expression patterns in a variety of tissues in adult buffalo implies that in addition to possible roles in adipogenesis and hematopoiesis, the WNT10B gene might be playing a significant role in other regulatory pathways as well.
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Affiliation(s)
- Deepu Verma
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | | | | | | | | | - Saroj Rani
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Prem Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | | | - Ankita Gurao
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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Li Z, Li R, Ren H, Qin C, Su J, Song X, Wang S, Liu Q, Liu Y, Cui K. Role of Different Members of the AGPAT Gene Family in Milk Fat Synthesis in Bubalus bubalis. Genes (Basel) 2023; 14:2072. [PMID: 38003015 PMCID: PMC10671497 DOI: 10.3390/genes14112072] [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: 10/09/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
During triacylglycerol synthesis, the acylglycerol-3-phosphate acyltransferase (AGPAT) family catalyzes the conversion of lysophosphatidic acid to phosphatidic acid and the acylation of sn-2 fatty acids. However, the catalytic activity of different AGPAT members is different. Therefore, this study aimed to investigate the mechanism through which different AGPATs affect the efficiency of TAG synthesis and fatty acid composition. The conservation of amino acid sequences and protein domains of the AGPAT family was analyzed, and the functions of AGPAT1, AGPAT3, and AGPAT4 genes in buffalo mammary epithelial cells (BMECs) were studied using RNA interference and gene overexpression. Prediction of the protein tertiary structure of the AGPAT family demonstrated that four conservative motifs (motif1, motif2, motif3, and motif6) formed a hydrophobic pocket in AGPAT proteins, except AGPAT6. According to cytological studies, AGPAT1, AGPAT3, and AGPAT4 were found to promote the synthesis and fatty acid compositions of triacylglycerol, especially UFA compositions of triacylglycerol, by regulating ACSL1, FASN, GPAM, DGAT2, and PPARG gene expression. This study provides new insights into the role of different AGPAT gene family members involved in TAG synthesis, and a reference for improving the fatty acid composition of milk.
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Affiliation(s)
- Zhipeng Li
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (R.L.); (H.R.); (C.Q.); (J.S.); (X.S.); (S.W.)
| | - Ruijia Li
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (R.L.); (H.R.); (C.Q.); (J.S.); (X.S.); (S.W.)
| | - Honghe Ren
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (R.L.); (H.R.); (C.Q.); (J.S.); (X.S.); (S.W.)
| | - Chaobin Qin
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (R.L.); (H.R.); (C.Q.); (J.S.); (X.S.); (S.W.)
| | - Jie Su
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (R.L.); (H.R.); (C.Q.); (J.S.); (X.S.); (S.W.)
| | - Xinhui Song
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (R.L.); (H.R.); (C.Q.); (J.S.); (X.S.); (S.W.)
| | - Shuwan Wang
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (R.L.); (H.R.); (C.Q.); (J.S.); (X.S.); (S.W.)
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; (Q.L.); (K.C.)
| | - Yang Liu
- Guangxi Zhuang Autonomous Region Center for Analysis and Test Research, Nanning 530022, China;
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; (Q.L.); (K.C.)
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5
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Formosa A, Acton E, Lee A, Turgeon P, Izhar S, Plant P, Tsoporis JN, Soussi S, Trahtemberg U, Baker A, dos Santos CC. Validation of reference gene stability for miRNA quantification by reverse transcription quantitative PCR in the peripheral blood of patients with COVID-19 critical illness. PLoS One 2023; 18:e0286871. [PMID: 37643172 PMCID: PMC10464995 DOI: 10.1371/journal.pone.0286871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/25/2023] [Indexed: 08/31/2023] Open
Abstract
The COVID-19 pandemic has created an urgency to study the host gene response that leads to variable clinical presentations of the disease, particularly the critical illness response. miRNAs have been implicated in the mechanism of host immune dysregulation and thus hold potential as biomarkers and/or therapeutic agents with clinical application. Hence, further analyses of their altered expression in COVID-19 is warranted. An important basis for this is identifying appropriate reference genes for high quality expression analysis studies. In the current report, NanoString technology was used to study the expression of 798 miRNAs in the peripheral blood of 24 critically ill patients, 12 had COVID-19 and 12 were COVID-19 negative. A list of potentially stable candidate reference genes was generated that included ten miRNAs. The top six were analyzed using reverse transcription quantitative polymerase chain reaction (RT-qPCR) in a total of 41 patients so as to apply standard computational algorithms for validating reference genes, namely geNorm, NormFinder, BestKeeper and RefFinder. There was general agreement among all four algorithms in the ranking of four stable miRNAs: miR-186-5p, miR-148b-3p, miR-194-5p and miR-448. A detailed analysis of their output rankings led to the conclusion that miR-186-5p and miR-148b-3p are appropriate reference genes for miRNA expression studies using PaxGene tubes in the peripheral blood of patients critically ill with COVID-19 disease.
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Affiliation(s)
- Amanda Formosa
- Interdepartmental Division of Critical Care Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
| | - Erica Acton
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
- Molecular Biology & Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Amy Lee
- Molecular Biology & Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Paul Turgeon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shehla Izhar
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
| | - Pamela Plant
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jim N. Tsoporis
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
| | - Sabri Soussi
- Interdepartmental Division of Critical Care Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
| | - Uriel Trahtemberg
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
- Critical Care Department, Galilee Medical Center, Nahariya, Israel
| | - Andrew Baker
- Interdepartmental Division of Critical Care Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
- Department of Critical Care, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Claudia C. dos Santos
- Interdepartmental Division of Critical Care Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- The Keenan Research Centre for Biomedical Sciences, Unity Health Toronto, Toronto, Ontario, Canada
- Department of Critical Care, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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6
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Crawford AH, Hildyard JCW, Wells DJ, Piercy RJ. Identification of quantitative polymerase chain reaction reference genes suitable for normalising gene expression in the brain of normal and dystrophic mice and dogs. Wellcome Open Res 2023; 6:84. [PMID: 37942409 PMCID: PMC10628364 DOI: 10.12688/wellcomeopenres.16707.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 11/10/2023] Open
Abstract
Background: In addition to progressive, debilitating muscle degeneration, ~50% of patients with Duchenne muscular dystrophy (DMD) have associated cognitive and behavioural disorders secondary to deficiency of dystrophin protein in the brain. The brain expresses a variety of dystrophin isoforms (Dp427, Dp140 and Dp71) whose functions remain to be fully elucidated. Detailed comparative analysis of gene expression in healthy and dystrophin-deficient brain is fundamental to understanding the functions of each isoform, and the consequences of their deficiency, with animal models representing a key tool in this endeavour. Reverse transcription quantitative real-time PCR (RT-qPCR) is a widely used method to study gene expression. However, accurate quantitative assessment requires normalisation of expression data using validated reference genes. The aim of this study was to identify a panel of suitable reference genes that can be used to normalise gene expression in the brain of healthy and dystrophic dogs and mice. Methods: Using the DE50-MD dog and mdx mouse models of DMD we performed RT-qPCR from fresh frozen brain tissue and employed the geNorm, BestKeeper and Normfinder algorithms to determine the stability of expression of a panel of candidate reference genes across healthy and dystrophic animals, and across different brain regions. Results: We show that SDHA, UBC and YWHAZ are suitable reference genes for normalising gene expression in healthy and dystrophic canine brain, and GAPDH, RPL13A and CYC1 in healthy and dystrophic murine brain. Notably, there was no overlap in the highest performing reference genes between the two species. Conclusions: Our findings suggest that gene expression normalisation is possible across six regions of the canine brain, and three regions of the murine brain. Our results should facilitate future work to study gene expression in the brains of normal and dystrophic dogs and mice and thus decipher the transcriptional consequences of dystrophin deficiency in the brain.
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Affiliation(s)
- Abbe H. Crawford
- Clinical Science and Services, Royal Veterinary College, London, UK
| | | | - Dominic J. Wells
- Comparative Biomedical Sciences, Royal Veterinary College, London, UK
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Jiang Q, Sherlock DN, Guyader J, Loor JJ. Abundance of Amino Acid Transporters and mTOR Pathway Components in the Gastrointestinal Tract of Lactating Holstein Cows. Animals (Basel) 2023; 13:ani13071189. [PMID: 37048445 PMCID: PMC10093496 DOI: 10.3390/ani13071189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Data from non-ruminants indicate that amino acid (AA) transport into cells can regulate mTOR pathway activity and protein synthesis. Whether mTOR is expressed in the ruminant gastrointestinal tract (GIT) and how it may be related to AA transporters and the AA concentrations in the tissue is unknown. Ruminal papillae and the epithelia of the duodenum, jejunum, and ileum collected at slaughter from eight clinically healthy Holstein in mid-lactation were used. Metabolites and RNA were extracted from tissue for liquid chromatography–mass spectrometry and RT-qPCR analysis. The glycine and asparagine concentrations in the rumen were greater than those in the intestine (p < 0.05), but the concentrations of other AAs were greater in the small intestine than those in the rumen. Among the 20 AAs identified, the concentrations of glutamate, alanine, and glycine were the greatest. The mRNA abundances of AKT1 and MTOR were greater in the small intestine than those in the rumen (p < 0.05). Similarly, the SLC1A1, SLC6A6, SLC7A8, SLC38A1, SLC38A7, and SLC43A2 mRNA abundances were greater (p < 0.05) in the small intestine than those in the rumen. The mRNA abundances of SLC1A5, SLC3A2, and SLC7A5 were greater in the rumen than those in the small intestine (p < 0.05). Overall, the present study provides fundamental data on the relationship between mTOR pathway components and the transport of AAs in different sections of the gastrointestinal tract.
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Affiliation(s)
- Qianming Jiang
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | | | - Jessie Guyader
- Evonik Operations GmbH, Hanau-Wolfgang, 63457 Essen, Germany
| | - Juan J. Loor
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
- Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA
- Correspondence:
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8
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Kumar A, Sodhi M, Mukesh M, Kaur A, Bhakri G, Chaudhary V, Swami P, Sharma V, Mohanty AK, Kataria RS. Identification of stably expressed Internal Control Genes (ICGs) for normalization of expression data in liver of C57BL/6 mice injected with beta casomorphins. PLoS One 2023; 18:e0282994. [PMID: 37145997 PMCID: PMC10162558 DOI: 10.1371/journal.pone.0282994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/28/2023] [Indexed: 05/07/2023] Open
Abstract
In recent years, beta-casomorphin peptides (BCM7/BCM9) derived from the digestion of cow milk have drawn a lot of attention world over because of their proposed impact on human health. In order to evaluate the transcriptional modulation of target genes through RT-qPCR in response to these peptides, availability of appropriate reference or internal control genes (ICGs) will be the key. The present study was planned to identify a panel of stable ICGs in the liver tissue of C57BL/6 mice injected with BCM7/BCM9 cow milk peptides for 3 weeks. A total of ten candidate genes were evaluated as potential ICGs by assessing their expression stability using software suites; geNorm, NormFinder and BestKeeper. The suitability of the identified ICGs was validated by assessing the relative expression levels of target genes, HP and Cu/Zn SOD. Based on geNorm, PPIA and SDHA gene pair was identified to be most stably expressed in liver tissue during the animal trials. Similarly, NormFinder analysis also identified PPIA as the most stable gene. BestKeeper analysis showed crossing point SD value for all the genes in the acceptable range that is closer to 1. Overall, the study identified a panel of stable ICGs for reliable normalization of target genes expression data in mice liver tissues during BCM7/9 peptides trial.
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Affiliation(s)
- Anurag Kumar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Monika Sodhi
- Animal Biotechnology Division, National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manishi Mukesh
- Animal Biotechnology Division, National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Amandeep Kaur
- Animal Biotechnology Division, National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Gaurav Bhakri
- Animal Biotechnology Division, National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Vipul Chaudhary
- Animal Biotechnology Division, National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Preeti Swami
- Animal Biotechnology Division, National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Vishal Sharma
- Animal Biotechnology Division, National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Ashok Kumar Mohanty
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Ranjit S Kataria
- Animal Biotechnology Division, National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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9
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Selection of species specific panel of reference genes in peripheral blood mononuclear cells of native livestock species adapted to trans-Himalayan region of Leh-Ladakh. Sci Rep 2022; 12:18473. [PMID: 36323741 PMCID: PMC9630269 DOI: 10.1038/s41598-022-22588-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 10/17/2022] [Indexed: 01/06/2023] Open
Abstract
The identification of appropriate references genes is an integral component of any gene expression-based study for getting accuracy and reliability in data interpretation. In this study, we evaluated the expression stability of 10 candidate reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) in peripheral blood mononuclear cells of livestock species that are adapted to high altitude hypoxia conditions of Leh-Ladakh. A total of 37 PBMCs samples from six native livestock species of Leh-Ladakh region such as Ladakhi cattle, Ladakhi yak, Ladakhi donkey, Chanthangi goat, Double hump cattle and Zanskar ponies were included in this study. The commonly used statistical algorithms such as geNorm, Normfinder, BestKeeper and RefFinder were employed to assess the stability of these RGs in all the livestock species. Our study has identified different panel of reference genes in each species; for example, EEF1A1, RPL4 in Ladakhi cattle; GAPDH, RPS9, ACTB in Ladakhi yak; HPRT1, B2M, ACTB in Ladakhi donkey; HPRT1, B2M, ACTB in Double hump camel, RPS9, HPRT1 in Changthangi goat, HPRT1 and ACTB in Zanskar ponies. To the best of our knowledge, this is the first systematic attempt to identify panel of RGs across different livestock species types adapted to high altitude hypoxia conditions. In future, the findings of the present study would be quite helpful in conducting any transcriptional studies to understand the molecular basis of high altitude adaptation of native livestock population of Leh-Ladakh.
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Sozoniuk M, Jamioł M, Kankofer M, Kowalczyk K. Reference gene selection in bovine caruncular epithelial cells under pregnancy-associated hormones exposure. Sci Rep 2022; 12:12742. [PMID: 35882953 PMCID: PMC9325760 DOI: 10.1038/s41598-022-17069-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/20/2022] [Indexed: 11/09/2022] Open
Abstract
Examination of transcriptional regulation occurring during pregnancy establishment and maintenance requires the identification of endogenous reference genes characterized by high expression stability. Since the expression of some reference genes may be modulated by pregnancy-associated hormones, the goal of our study was to identify suitable reference genes unaffected by hormonal treatment. In our study bovine caruncular epithelial cells were subjected to progesterone, estrogen and prostaglandin F2α treatment. Ten candidate reference genes (ACTR1A, CNOT11, HDAC1, HPRT1, RPL19, RPS9, SDHA, SUZ12, UXT and ZNF131) were evaluated with the use of four approaches (geNorm, NormFinder, BestKeeper, delta Ct). We found that RPS9 and SUZ12 displayed the highest expression stability in the tested material. Moreover, HPRT1 and SDHA were found inappropriate for RT-qPCR data normalization as they demonstrated the highest expression variability out of all candidates analysed. Hence geNorm calculations shown that the use of just two best-performing genes would be sufficient for obtaining reliable results, we propose that RPS9 and SUZ12 be used as suitable endogenous controls in future studies investigating gene expression in normal and compromised pregnancies.
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Affiliation(s)
- Magdalena Sozoniuk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka Street 15, 20-950, Lublin, Poland
| | - Monika Jamioł
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, Akademicka Street 12, 20-033, Lublin, Poland.
| | - Marta Kankofer
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, Akademicka Street 12, 20-033, Lublin, Poland
| | - Krzysztof Kowalczyk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka Street 15, 20-950, Lublin, Poland
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11
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Verma P, Sharma A, Sodhi M, Tiwari M, Vivek P, Kataria RS, Nirajan SK, Bharti VK, Singh P, Lathwal SS, Sharma V, Masharing N, Mukesh M. Identification of Internal Reference Genes in Peripheral Blood Mononuclear Cells of Cattle Populations Adapted to Hot Arid Normoxia and Cold Arid Hypoxia Environments. Front Genet 2022; 12:730599. [PMID: 35178065 PMCID: PMC8846307 DOI: 10.3389/fgene.2021.730599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
To estimate gene expression in a reliable manner, quantitative real-time polymerase chain reaction data require normalisation using a panel of stably expressed reference genes (RGs). To date, information on an appropriate panel of RGs in cattle populations reared at cold arid high-altitude hypoxia and hot arid tropical normoxia environments is not available. Therefore, the present study was carried out to identify a panel of stably expressed RGs from 10 candidate genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, HMBS, B2M, RPS15, and ACTB) in peripheral blood mononuclear cells (PBMCs) of cattle populations reared at cold arid high-altitude hypoxia and hot arid normoxia environments. Four different statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder were used to assess the stability of these genes. A total of 30 blood samples were collected: six adult heifers each of Ladakhi (LAC) and Holstein Frisian crosses (HFX) and 4 Jersey (JYC) cows from cold arid high-altitude hypoxia environments (group I) and five adult heifers each of Sahiwal (SAC), Karan Fries (KFC), and Holstein Friesian (HFC) cows from hot arid normoxia environments (group II). Combined analysis of group I and group II resulted in identification of a panel of RGs like RPS9, RPS15, and GAPDH that could act as a useful resource to unravel the accurate transcriptional profile of PBMCs from diverse cattle populations adapted to distinct altitudes.
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Affiliation(s)
- Preeti Verma
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ankita Sharma
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Monika Sodhi
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Manish Tiwari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India.,Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, India
| | - Prince Vivek
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ranjit S Kataria
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - S K Nirajan
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Vijay K Bharti
- DRDO-Defense Institute of High-altitude Research, Leh, India
| | - Pawan Singh
- Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, India.,Department of Livestock Production Management, ICAR-National Dairy Research Institute, Karnal, India
| | - S S Lathwal
- Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, India.,Department of Livestock Production Management, ICAR-National Dairy Research Institute, Karnal, India
| | - Vishal Sharma
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Nampher Masharing
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India.,Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, India
| | - Manishi Mukesh
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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12
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Yang X, Tong G, Dong L, Yan T, Xu H, Tang G, Zhang Y, Ma K, Yin J, Kuang Y. Evaluation of qPCR reference genes for taimen (Hucho taimen) under heat stress. Sci Rep 2022; 12:313. [PMID: 35013399 PMCID: PMC8748915 DOI: 10.1038/s41598-021-03872-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/06/2021] [Indexed: 11/09/2022] Open
Abstract
As a powerful and attractive method for detecting gene expression, qRT-PCR has been broadly used in aquaculture research. Understanding the biology of taimen (Hucho taimen) has drawn increasing interest because of its ecological and economic value. Stable reference genes are required for the reliable quantification of gene expression, but such genes have not yet been optimized for taimen. In this study, the stability levels of 10 commonly used candidate reference genes were evaluated using geNorm, NormFinder, BestKeeper, and RefFinder. The expression levels of the 10 genes were detected using 240 samples from 48 experimental groups consisting of 40 individuals treated under four heat-stress conditions (18, 20, 22, and 24 °C) for 24 h and 26 °C for 4, 24, 48, and 72 h. Six tissues (blood, heart, brain, gill, skin, and liver) were collected from each individual. Ribosomal protein S29 (RPS29) and ribosomal protein L19 (RPL19) were the most stable genes among all of the samples, whereas 28S ribosomal RNA (28S rRNA), attachment region binding protein (ARBP), and 18S ribosomal RNA (18S rRNA) were the least stable. These results were verified by an expression analysis of taimen heat-stress genes (heat shock protein 60, hsp60, and heat shock protein 70, hsp70). In conclusion, RPS29 and RPL19 are the optimal reference genes for qRT-PCR analyses of taimen, irrespective of the tissue and experimental conditions. These results allow the reliable study of gene expression in taimen.
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Affiliation(s)
- Xiaoxing Yang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.,Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201303, China
| | - Guangxiang Tong
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.,Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China.,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Harbin, 150070, China
| | - Le Dong
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.,Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201303, China
| | - Ting Yan
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.,Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Huan Xu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.,Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China
| | - Guopan Tang
- Henan University of Animal Husbandry and Economy, Zhengzhou, 450016, China
| | - Yongquan Zhang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Harbin, 150070, China
| | - Kai Ma
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Harbin, 150070, China
| | - Jiasheng Yin
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.,Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China.,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Harbin, 150070, China
| | - Youyi Kuang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China. .,Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150070, China.
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13
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Wu X, Yang W, Ren Z, Cheng J, Luo Y, Wang Y, Yang Z, Yao X, Zhao W, Li Y, Tang K. Reference gene screening for analyzing gene expression in the heart, liver, spleen, lung and kidney of forest musk deer. J Vet Med Sci 2021; 83:1750-1759. [PMID: 34615843 PMCID: PMC8636893 DOI: 10.1292/jvms.21-0281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The screening of reference genes for real-time quantitative PCR (qPCR) in forest musk deer (FMD) tissue is of great significance to the basic research on FMD. However, there are few reports
on the stability analysis of FMD reference genes so far. In this study, We used qPCR to detect the expression levels of 11 reference gene candidates (18S rRNA, beta-actin
[ACTB], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], TATA box-binding protein [TBP], hypoxanthine phosphoribosyltransferase 1
[HPRT1], tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta polypeptide [YWHAZ], hydroxymethylbilane synthase
[HMBS], eukaryotic translation elongation factor 1 alpha 1 [EEF1A1], succinate dehydrogenase complex flavoprotein subunit A [SDHA],
peptidylprolyl isomerase B [PPIB], and ubiquitin C [UBC]) in heart, liver, spleen, lung and kidney of FMD. After removing 18S rRNA on
account of its high expression level, geNorm, NormFinder, BestKeeper and ΔCt algorithms were used to evaluate the expression stability of the remaining genes in the five organs, and further
comprehensive ranking was calculated by RefFinder. According to the results, the selected reference genes with the most stable expression in the heart of FMD are SDHA and
YWHAZ, while in the liver are ACTB and SDHA; in the spleen and lung are YWHAZ and HPRT1; in the kidney
are YWHAZ and PPIB. The use of common reference genes in all five organs is not recommended. The analyses showed that tissue is an important variability
factor in genes expression stability. Meanwhile, the result can be used as a reference for the selection of reference genes for qPCR in further study.
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Affiliation(s)
- Xi Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Wei Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Ziwei Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Jianguo Cheng
- Sichuan Institute of Musk Deer Breeding, Dujiangyan 611830, Sichuan Province, China
| | - Yan Luo
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Yin Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Zexiao Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Xueping Yao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Wei Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Yimeng Li
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Kexin Tang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
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KAUR RAMNEEK, SODHI MONIKA, SHARMA ANKITA, SHARMA VIJAYLAKSHMI, VERMA PREETI, SWAMI SHELESHKUMAR, KATARIA RANJITS, SINGH MANOJK, K PARVESH, MUKESH MANISHI. Molecular characterization and identification of SNPs in ATP1A1 isoform of sodium-phosphate adenosine triphosphatase across diverse breeds of riverine buffaloes (Bubalus bubalis) and Indian native cattle (Bos indicus): A plausible candidate gene for heat tolerance. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2021. [DOI: 10.56093/ijans.v91i7.115898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In the present study, efforts were made to sequence characterize the selected exonic region (18–21) of ATP1A1 gene to identify variations/SNPs in different breeds of Indian riverine buffaloes and native cattle. The sequence characterization of selected intronic/exonic region (17–21) of ATP1A1 gene was carried out in a total of 120 samples which included 6 animals each of 8 buffalo breeds and 72 animals of 12 cattle breeds. Genomic DNA was extracted from the whole blood by enzymatic digestion using proteinase K using phenol:chloroform method.. Three sets of primers were designed using Primer3 software to amplify genomic region from intron 17 to intron 21 of ATP1A1 gene in both cattle and buffaloes. The amplified products were purified by enzymatic method and purified PCR products were sequenced using forward primers in an ABI 3100 Automated DNA Sequencer. The chromatogram of each sequence obtained was checked manually. Base calling was performed with Phred and contig assembly was done via Phrap/Cross_match/Swat tool available in the suite Codon code Aligner v. 3.5.1. The results revealed a total of 26 variations in exons 18–21 of ATP1A1 gene in riverine buffalo. Out of 26 variations, 6 (T27006876C, C27006599T, T27006345C, T27006330C, G27006309T and T27006240C) were distributed across 4 exonic regions and the remaining 20 were located in intronic region whereas in native cattle, only 2 SNPs were identified in exonic regions (18–21). SNP T27007767C was found to be a novel one in 18 intronic region of ATP1A1 gene in Indian cattle breeds. All 7 variations found in exonic region of both buffalo and cattle breeds were synonymous with the predicted changes in amino acids. The variations identified in ATP1A1 gene in the present study could be evaluated in future for their roles in heat tolerance trait in riverine buffaloes and native cattle.
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15
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Bovine Satellite Cells Isolated after 2 and 5 Days of Tissue Storage Maintain the Proliferative and Myogenic Capacity Needed for Cultured Meat Production. Int J Mol Sci 2021; 22:ijms22168376. [PMID: 34445082 PMCID: PMC8395070 DOI: 10.3390/ijms22168376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/03/2023] Open
Abstract
Cultured meat is an emerging alternative food technology which aims to deliver a more ethical, sustainable, and healthy muscle-tissue-derived food item compared to conventional meat. As start-up companies are rapidly forming and accelerating this technology, many aspects of this multi-faceted science have still not been investigated in academia. In this study, we investigated if bovine satellite cells with the ability to proliferate and undergo myogenic differentiation could be isolated after extended tissue storage, for the purpose of increasing the practicality for cultured meat production. Proliferation of bovine satellite cells isolated on the day of arrival or after 2 and 5 days of tissue storage were analyzed by metabolic and DNA-based assays, while their myogenic characteristics were investigated using RT-qPCR and immunofluorescence. Extended tissue storage up to 5 days did not negatively affect proliferation nor the ability to undergo fusion and create myosin heavy chain-positive myotubes. The expression patterns of myogenic and muscle-specific genes were also not affected after tissue storage. In fact, the data indicated a positive trend in terms of myogenic potential after tissue storage, although it was non-significant. These results suggest that the timeframe of which viable myogenic satellite cells can be isolated and used for cultured meat production can be greatly extended by proper tissue storage.
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16
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de Sousa FCB, do Nascimento CS, Macário MDS, Araújo RDS, Barbosa LT, Bayão GFV, Sousa KRS. Selection of reference genes for quantitative real-time PCR normalization in European quail tissues. Mol Biol Rep 2021; 48:67-76. [PMID: 33454906 DOI: 10.1007/s11033-020-06134-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Coturniculture has been standing out as an industrial poultry activity in several countries around the world because of the several adaptive advantages of quails. Research that considers the analysis of gene expression can enhance this activity. This study aimed to analyze the stability of reference genes (RGs) in different tissues of quails (both males and females) for the recommendation of use in gene expression studies by the quantitative reverse transcription-polymerase chain reaction (RT-qPCR). The expression stability of ten RGs (ACTA1, ACTB, B2M, GAPDH, HMBS, SDHA, HPRT1, MRPS27, MRPS30, and RPL5) was analyzed in four tissues (breast muscle, abdominal fat, liver, and intestine), and assessed using the statistical tools geNorm, NormFinder, comparative ΔCq method, and BestKeeper. The HPRT1 gene was the most stable in all quail tissues tested, followed by MRPS27 and MRPS30 in breast muscle, B2M and RPL5 in abdominal fat, HMBS and B2M in the liver, and RPL5 and HMBS in the intestine. These results may help studies using RT-qPCR assays to assess quail tissues from both sexes because they provide data on the most stable genes, which should be tested as candidate RGs for other experimental conditions.
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Affiliation(s)
| | | | - Maíse Dos Santos Macário
- Department of Animal Science, Universidade Federal de Sergipe, São Cristóvão, SE, 49100-000, Brazil
| | | | - Leandro Teixeira Barbosa
- Department of Animal Science, Universidade Federal de Sergipe, São Cristóvão, SE, 49100-000, Brazil
| | - Geraldo Fábio Viana Bayão
- Department of Animal Science, Instituto Federal de Educação, Ciência e Tecnologia do Maranhão, São Luís, MA, 65095-460, Brazil
| | - Katiene Régia Silva Sousa
- Department of Oceanography and Limnology, Universidade Federal do Maranhão, São Luís, MA, 65080-805, Brazil
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17
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Sevrin T, Boquien CY, Gandon A, Grit I, de Coppet P, Darmaun D, Alexandre-Gouabau MC. Fenugreek Stimulates the Expression of Genes Involved in Milk Synthesis and Milk Flow through Modulation of Insulin/GH/IGF-1 Axis and Oxytocin Secretion. Genes (Basel) 2020; 11:E1208. [PMID: 33081164 PMCID: PMC7602737 DOI: 10.3390/genes11101208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
We previously demonstrated galactagogue effect of fenugreek in a rat model of lactation challenge, foreshadowing its use in women's breastfeeding management. To assess longitudinal molecular mechanisms involved in milk synthesis/secretion in dams submitted to fenugreek supplementation, inguinal mammary, pituitary glands and plasma were isolated in forty-three rats nursing large 12 pups-litters and assigned to either a control (CTL) or a fenugreek-supplemented (FEN) diet during lactation. RT-PCR were performed at days 12 and 18 of lactation (L12 and L18) and the first day of involution (Inv1) to measure the relative expression of genes related to both milk synthesis and its regulation in the mammary gland and lactogenic hormones in the pituitary gland. Plasma hormone concentrations were measured by ELISA. FEN diet induced 2- to 3-times higher fold change in relative expression of several genes related to macronutrient synthesis (Fasn, Acaca, Fabp3, B4galt1, Lalba and Csn2) and energy metabolism (Cpt1a, Acads) and in IGF-1 receptor in mammary gland, mainly at L12. Pituitary oxytocin expression and plasma insulin concentration (+77.1%) were also significantly increased. Altogether, these findings suggest fenugreek might extend duration of peak milk synthesis through modulation of the insulin/GH/IGF-1 axis and increase milk ejection by activation of oxytocin secretion.
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Affiliation(s)
- Thomas Sevrin
- FRANCE Bébé Nutrition (FBN) Laboratory, 53000 Laval, France;
- Mixed Research Unit 1280 Pathophysiology of Nutritional adaptations (UMR 1280 PhAN) Nantes University, Research Center in Human Nutrition-West (CRNH-O), Institute of Digestive Tract Diseases (IMAD), French National Research Institute for Agriculture, Food and Environment (INRAE), F-44000 Nantes, France; (C.-Y.B.); (A.G.); (I.G.); (P.d.C.); (D.D.)
| | - Clair-Yves Boquien
- Mixed Research Unit 1280 Pathophysiology of Nutritional adaptations (UMR 1280 PhAN) Nantes University, Research Center in Human Nutrition-West (CRNH-O), Institute of Digestive Tract Diseases (IMAD), French National Research Institute for Agriculture, Food and Environment (INRAE), F-44000 Nantes, France; (C.-Y.B.); (A.G.); (I.G.); (P.d.C.); (D.D.)
| | - Alexis Gandon
- Mixed Research Unit 1280 Pathophysiology of Nutritional adaptations (UMR 1280 PhAN) Nantes University, Research Center in Human Nutrition-West (CRNH-O), Institute of Digestive Tract Diseases (IMAD), French National Research Institute for Agriculture, Food and Environment (INRAE), F-44000 Nantes, France; (C.-Y.B.); (A.G.); (I.G.); (P.d.C.); (D.D.)
| | - Isabelle Grit
- Mixed Research Unit 1280 Pathophysiology of Nutritional adaptations (UMR 1280 PhAN) Nantes University, Research Center in Human Nutrition-West (CRNH-O), Institute of Digestive Tract Diseases (IMAD), French National Research Institute for Agriculture, Food and Environment (INRAE), F-44000 Nantes, France; (C.-Y.B.); (A.G.); (I.G.); (P.d.C.); (D.D.)
| | - Pierre de Coppet
- Mixed Research Unit 1280 Pathophysiology of Nutritional adaptations (UMR 1280 PhAN) Nantes University, Research Center in Human Nutrition-West (CRNH-O), Institute of Digestive Tract Diseases (IMAD), French National Research Institute for Agriculture, Food and Environment (INRAE), F-44000 Nantes, France; (C.-Y.B.); (A.G.); (I.G.); (P.d.C.); (D.D.)
| | - Dominique Darmaun
- Mixed Research Unit 1280 Pathophysiology of Nutritional adaptations (UMR 1280 PhAN) Nantes University, Research Center in Human Nutrition-West (CRNH-O), Institute of Digestive Tract Diseases (IMAD), French National Research Institute for Agriculture, Food and Environment (INRAE), F-44000 Nantes, France; (C.-Y.B.); (A.G.); (I.G.); (P.d.C.); (D.D.)
- Nantes University Hospital (CHU) Nantes, F-44000 Nantes, France
| | - Marie-Cécile Alexandre-Gouabau
- Mixed Research Unit 1280 Pathophysiology of Nutritional adaptations (UMR 1280 PhAN) Nantes University, Research Center in Human Nutrition-West (CRNH-O), Institute of Digestive Tract Diseases (IMAD), French National Research Institute for Agriculture, Food and Environment (INRAE), F-44000 Nantes, France; (C.-Y.B.); (A.G.); (I.G.); (P.d.C.); (D.D.)
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18
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Huang J, Feng X, Zhu R, Guo D, Wei Y, Cao X, Ma Y, Shi D. Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo. BMC Genomics 2020; 21:710. [PMID: 33045988 PMCID: PMC7552535 DOI: 10.1186/s12864-020-07120-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important driver that affects IMF deposition. RESULTS To reveal the intrinsic factors responsible for the low IMF content of buffalo, mRNA expression patterns in muscle and adipose tissue between buffalo and cattle were characterized by RNA sequencing analysis. The IMF content in Nanyang cattle was higher than that in Xinyang buffalo. A total of 1566 mRNAs expressed in adipose tissue showed differential expression between the longissimus dorsi muscles of buffalo and cattle. Functional annotation suggested a difference in the glycolysis/gluconeogenesis pathway between the two species. The results of RT-qPCR analysis and gain-of-function experiments confirmed the positive association between the IMF content and phosphoenolpyruvate carboxykinase 1 (PCK1) expression in buffalo. In both mouse C2C12 cells and cultured bovine myocytes, the activity of the PCK1 promoter in buffalo is lower than that in cattle. However, in mouse 3T3-L1 adipocytes and cultured bovine adipocytes, the activity of PCK1 in buffalo promoter is higher than that in cattle. CONCLUSIONS These results indicate the important role of PCK1 in buffalo IMF deposition and illustrate the differences between buffalo and cattle promoter activity that drive PCK1 expression. This research helps to establish a foundation for further studies investigating IMF deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China. .,College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.
| | - Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Duo Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Yutong Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Xiaodan Cao
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.,School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
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19
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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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20
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Catalogue of stage-specific transcripts in Ixodes ricinus and their potential functions during the tick life-cycle. Parasit Vectors 2020; 13:311. [PMID: 32546252 PMCID: PMC7296661 DOI: 10.1186/s13071-020-04173-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/05/2020] [Indexed: 12/15/2022] Open
Abstract
Background The castor bean tick Ixodes ricinus is an important vector of several clinically important diseases, whose prevalence increases with accelerating global climate changes. Characterization of a tick life-cycle is thus of great importance. However, researchers mainly focus on specific organs of fed life stages, while early development of this tick species is largely neglected. Methods In an attempt to better understand the life-cycle of this widespread arthropod parasite, we sequenced the transcriptomes of four life stages (egg, larva, nymph and adult female), including unfed and partially blood-fed individuals. To enable a more reliable identification of transcripts and their comparison in all five transcriptome libraries, we validated an improved-fit set of five I. ricinus-specific reference genes for internal standard normalization of our transcriptomes. Then, we mapped biological functions to transcripts identified in different life stages (clusters) to elucidate life stage-specific processes. Finally, we drew conclusions from the functional enrichment of these clusters specifically assigned to each transcriptome, also in the context of recently published transcriptomic studies in ticks. Results We found that reproduction-related transcripts are present in both fed nymphs and fed females, underlining the poorly documented importance of ovaries as moulting regulators in ticks. Additionally, we identified transposase transcripts in tick eggs suggesting elevated transposition during embryogenesis, co-activated with factors driving developmental regulation of gene expression. Our findings also highlight the importance of the regulation of energetic metabolism in tick eggs during embryonic development and glutamate metabolism in nymphs. Conclusions Our study presents novel insights into stage-specific transcriptomes of I. ricinus and extends the current knowledge of this medically important pathogen, especially in the early phases of its development.![]()
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Wu X, Zhou X, Ding X, Chu M, Liang C, Pei J, Xiong L, Bao P, Guo X, Yan P. Reference gene selection and myosin heavy chain (MyHC) isoform expression in muscle tissues of domestic yak (Bos grunniens). PLoS One 2020; 15:e0228493. [PMID: 32027673 PMCID: PMC7004298 DOI: 10.1371/journal.pone.0228493] [Citation(s) in RCA: 10] [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: 08/11/2019] [Accepted: 01/16/2020] [Indexed: 01/04/2023] Open
Abstract
Domestic yak (Bos grunniens) is the most crucial livestock in the Qinghai-Tibetan Plateau, providing meat and other necessities for local people. The skeletal muscle of adult livestock is composed of muscle fibers, and fiber composition in muscle has influence on meat qualities, such as tenderness, pH, and color. Real-time quantitative polymerase chain reaction (RT-qPCR) is a powerful tool to evaluate the gene expression of muscle fiber, but the normalization of the data depends on the stability of expressed reference genes. Unfortunately, there is no consensus for an ideal reference gene for data normalization in muscle tissues of yak. In this study, we aimed to assess the stability of 14 commonly used candidate reference genes by using five algorithms (GeNorm, NormFinder, BestKeeper, Delat Ct and Refinder). Our results suggested UXT and PRL13A were the most stable reference genes, while the most commonly used reference gene, GAPDH, was most variably expressed across different muscle tissues. We also found that the extensor digitorum lateralis (EDL), trapezius pars thoracica (TPT), and psoas major (PM) muscle had the higher content of type I muscle fibers and the lowest content of type IIB muscle fibers, while gluteobiceps (GB) muscle had the highest content of type IIB muscle fibers. Our study provides the suitable reference genes for accurate analysis of yak muscle fiber composition.
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Affiliation(s)
- Xiaoyun Wu
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuelan Zhou
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuezhi Ding
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunnian Liang
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jie Pei
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lin Xiong
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- * E-mail: (PY); (XG)
| | - Ping Yan
- Key Lab of Yak Breeding Engineering, Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- * E-mail: (PY); (XG)
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Salemi M, Rappazzo G, Ridolfo F, Salluzzo MG, Cannarella R, Castiglione R, Caniglia S, Tirolo C, Calogero AE, Romano C. Cerebellar degeneration-related protein 1 expression in fibroblasts of patients affected by down syndrome. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1832922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
| | - Giancarlo Rappazzo
- Laboratory of Molecular Genetics, Department of Biological Geological Environmental Sciences, University of Catania, Catania, Italy
| | - Federico Ridolfo
- UOSD of Clinical Pathology, ASUR Marche – AV2, Hospital of Senigallia, Senigallia, Italy
| | | | - Rossella Cannarella
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
| | - Roberto Castiglione
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
| | | | | | - Aldo E. Calogero
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
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Meat Species Identification: Amplification Refractory Mutation System-Polymerase Chain Reaction–Based Assay. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01640-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Moura MT, Silva RLO, Nascimento PS, Ferreira-Silva JC, Cantanhêde LF, Kido EA, Benko-Iseppon AM, Oliveira MAL. Inter-genus gene expression analysis in livestock fibroblasts using reference gene validation based upon a multi-species primer set. PLoS One 2019; 14:e0221170. [PMID: 31412093 PMCID: PMC6693880 DOI: 10.1371/journal.pone.0221170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Quantitative reverse transcription PCR (RT-qPCR) remains as an accurate approach for gene expression analysis but requires labor-intensive validation of reference genes using species-specific primers. To ease such demand, the aim was to design and test a multi-species primer set to validate reference genes for inter-genus RT-qPCR gene expression analysis. Primers were designed for ten housekeeping genes using transcript sequences of various livestock species. All ten gene transcripts were detected by RT-PCR in Bos taurus (cattle), Bubalus bubalis (buffaloes), Capra hircus (goats), and Ovis aries (sheep) cDNA. Primer efficiency was attained for eight reference genes using B. taurus—O. aries fibroblast cDNA (95.54–98.39%). The RT-qPCR data normalization was carried out for B. taurus vs. O. aries relative gene expression using Bestkeeper, GeNorm, Norm-finder, Delta CT method, and RefFinder algorithms. Validation of inter-genus RT-qPCR showed up-regulation of TLR4 and ZFX gene transcripts in B. taurus fibroblasts, irrespectively of normalization conditions (two, three, or four reference genes). In silico search in mammalian transcriptomes showed that the multi-species primer set is expected to amplify transcripts of at least two distinct loci in 114 species, and 79 species would be covered by six or more primers. Hence, a multi-species primer set allows for inter-genus gene expression analysis between O. aries and B. taurus fibroblasts and further reveals species-specific gene transcript abundance of key transcription factors.
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Affiliation(s)
- Marcelo T. Moura
- Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Pernambuco, Brazil
- * E-mail:
| | - Roberta L. O. Silva
- Departamento de Genética, Universidade Federal de Pernambuco, Pernambuco, Brazil
| | - Pábola S. Nascimento
- Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Pernambuco, Brazil
| | - José C. Ferreira-Silva
- Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Pernambuco, Brazil
| | - Ludymila F. Cantanhêde
- Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Pernambuco, Brazil
| | - Ederson A. Kido
- Departamento de Genética, Universidade Federal de Pernambuco, Pernambuco, Brazil
| | - Ana M. Benko-Iseppon
- Departamento de Genética, Universidade Federal de Pernambuco, Pernambuco, Brazil
| | - Marcos A. L. Oliveira
- Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Pernambuco, Brazil
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Identification of qPCR reference genes suitable for normalizing gene expression in the mdx mouse model of Duchenne muscular dystrophy. PLoS One 2019; 14:e0211384. [PMID: 30699165 PMCID: PMC6353192 DOI: 10.1371/journal.pone.0211384] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/11/2019] [Indexed: 12/15/2022] Open
Abstract
The mdx mouse is the most widely-used animal model of the human disease Duchenne muscular dystrophy, and quantitative PCR analysis of gene expression in the muscles of this animal plays a key role in the study of pathogenesis and disease progression and in evaluation of potential therapeutic interventions. Normalization to appropriate stably-expressed reference genes is essential for accurate quantitative measurement, but determination of such genes is challenging: healthy and dystrophic muscles present very different transcriptional environments, further altering with disease progression and muscle use, raising the possibility that no single gene or combination of genes may be stable under all experimental comparative scenarios. Despite the pedigree of this animal model, this problem remains unaddressed. The aim of this work was therefore to comprehensively assess reference gene suitability in the muscles of healthy and dystrophic mice, identifying reference genes appropriate for specific experimental comparisons, and determining whether an essentially universally-applicable set of genes exists. Using a large sample collection comprising multiple muscles (including the tibialis anterior, diaphragm and heart muscles) taken from healthy and mdx mice at three disease-relevant ages, and a panel of sixteen candidate reference genes (FBXO38, FBXW2, MON2, ZFP91, HTATSF1, GAPDH, ACTB, 18S, CDC40, SDHA, RPL13a, CSNK2A2, AP3D1, PAK1IP1, B2M and HPRT1), we used the geNorm, BestKeeper and Normfinder algorithms to identify genes that were stable under multiple possible comparative scenarios. We reveal that no single gene is stable under all conditions, but a normalization factor derived from multiple genes (RPL13a, CSNK2A2, AP3D1 and the widely-used ACTB) appears suitable for normalizing gene expression in both healthy and dystrophic mouse muscle regardless of muscle type or animal age. We further show that other popular reference genes, including GAPDH, are markedly disease- or muscle-type correlated. This study demonstrates the importance of empirical reference gene identification, and should serve as a valuable resource for investigators wishing to study gene expression in mdx mice.
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Zhu X, Zhang L, Hu Y, Zhang J. Identification of suitable reference genes for real-time qPCR in homocysteine-treated human umbilical vein endothelial cells. PLoS One 2018; 13:e0210087. [PMID: 30596787 PMCID: PMC6312244 DOI: 10.1371/journal.pone.0210087] [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: 04/15/2018] [Accepted: 12/17/2018] [Indexed: 12/14/2022] Open
Abstract
The imbalance in homocysteine (Hcy) metabolism has been implicated in the pathogenesis of human diseases, including cardiovascular and neurodegenerative disorders. When attempting to identify gene expression profiles using quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR), the selection of suitable reference genes is important. Here, the expression levels of 10 commonly used reference genes were assessed for normalization of RT-qPCR in Hcy-treated human umbilical vein endothelial cells (HUVECs) and control cells. The suitability of eight selected candidate genes was comparatively analyzed across the tested samples and separately ranked by four programs, geNorm, NormFinder, BestKeeper, and the ΔCt method. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was the most stable gene in the final ranking using the RankAggreg package. Surprisingly, the β-actin (ACTB) levels decreased significantly in Hcy-treated HUVECs compared with control HUVECs (P<0.05), and further study indicated that Hcy suppressed the expression of ACTB by upregulating the miR-145-5p level in Hcy-treated HUVECs. Our data suggest that GAPDH can be used as a reliable reference gene, while ACTB cannot; normalization of gene expression in RT-qPCR experiments in Hcy-treated HUVECs. The data, which identifies a suitable reference gene in Hcy-treated HUVECs, will contribute to the design of an effective and accurate method for quantitation of gene expression.
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Affiliation(s)
- Xia Zhu
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Cardiology, Urumqi Friendship Hospital, Urumqi, China
| | - Lujun Zhang
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
- * E-mail: (LZ); (JZ)
| | - Yangxi Hu
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jianliang Zhang
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
- * E-mail: (LZ); (JZ)
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