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Li W, LiLi, Wang X. Transcriptomic analysis of different intramuscular fat contents on the flavor of the longissimus dorsi tissues from Guangling donkey. Genomics 2024; 116:110905. [PMID: 39084475 DOI: 10.1016/j.ygeno.2024.110905] [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: 01/23/2024] [Revised: 07/14/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND In this study, researchers aimed to explore the impact of intramuscular fat (IMF) concentration on the flavor of donkey meat, specifically in the longissimus dorsi muscle of Guangling donkeys. The internal volatile organic compounds that cause the flavor differences between donkey muscles are not clear at present. Transcriptomic technologies were utilized to analyze gene expression and its relationship to donkey meat flavor. METHOD Thirty Guangling donkeys had their IMF content evaluated in the longissimus dorsi muscle. Based on IMF content, 16 donkeys of similar ages were divided into two groups: low-fat (L) and high-fat (H). Headspace solid-phase microextraction Gas chromatography-mass spectrometry (HS-SPME-GC-MS) and headspace solid phase microextraction mass spectrometry were used to identify potential flavor components that differed between the two groups. RESULTS Five key volatile substances were identified, and WGCNA and KEGG analysis was conducted to analyze the genes associated with these substances. The results showed that pathways like PPAR signaling, nucleotide excision repair, glucagon signaling, arachidonic acid metabolism, and glycolysis/glycogenesis were involved in lipid deposition. Additionally, a gene-gene interaction network map was constructed, highlighting the importance of hub genes such as EEF2, DDX49, GAP43, SNAP25, NDUFS8, MRPS11, RNASEH2A, POLR2E, POLR2C and ALB in regulating key flavor substances. CONCLUSION This study provided valuable insights into the regulation of genes and protein expression related to flavor substances in donkey meat. It also deepened understanding of the influence of IMF on flavor and laid a foundation for future molecular breeding improvements in Guangling donkeys.
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Affiliation(s)
- Wufeng Li
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801. China.
| | - LiLi
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801. China
| | - Xi Wang
- Institute of Ecological Agriculture and Animal Husbandry, Shanxi Agricultural University, Youyu 037200, China.
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2
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Serum artemin is not correlated with sensitivity within dogs with naturally occurring osteoarthritis pain. Sci Rep 2021; 11:6682. [PMID: 33758254 PMCID: PMC7988108 DOI: 10.1038/s41598-021-85976-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/03/2021] [Indexed: 11/14/2022] Open
Abstract
Osteoarthritis (OA) pain is associated with peripheral and central sensitization in humans and results in widespread increased sensitivity across the body. Sensitization contributes to the OA-associated pain (OAP) state. We recently identified increased levels of an endogenous neurotrophic factor, artemin (ARTN), in dogs with OAP compared to healthy pain-free controls. Circulating ARTN released from damaged tissues in OA, may play a central role in widespread sensitivity and pain. However, the relationship between ARTN and somatosensory sensitivity remains unknown. The study aimed to assess the relationship between serum ARTN concentrations and measures of sensitivity in dogs with OAP using quantitative sensory testing. We hypothesized that there would be a positive association between circulating ARTN and increased sensitivity to mechanical and thermal stimuli in dogs with OAP. We used linear and logistic regression models to assess the relationship between ARTN, sensitization, and pain within a cohort of 43 dogs with spontaneous OAP. Serum ARTN was not associated with the degree of sensitization within dogs with OAP. Further, across dogs with varying OAP severity, we did not find any association between ARTN, and clinical measures of joint pain and disability. Although a relationship between ARTN and joint pain was not ruled out.
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Gerber N, Brunner MAT, Jagannathan V, Leeb T, Gerhards NM, Welle MM, Dettwiler M. Transcriptional Differences between Canine Cutaneous Epitheliotropic Lymphoma and Immune-Mediated Dermatoses. Genes (Basel) 2021; 12:160. [PMID: 33504055 PMCID: PMC7912288 DOI: 10.3390/genes12020160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
Canine cutaneous epitheliotropic T-cell lymphoma (CETL) and immune-mediated T-cell predominant dermatoses (IMD) share several clinical and histopathological features, but differ substantially in prognosis. The discrimination of ambiguous cases may be challenging, as diagnostic tests are limited and may prove equivocal. This study aimed to investigate transcriptional differences between CETL and IMD, as a basis for further research on discriminating diagnostic biomarkers. We performed 100bp single-end sequencing on RNA extracted from formalin-fixed and paraffin-embedded skin biopsies from dogs with CETL and IMD, respectively. DESeq2 was used for principal component analysis (PCA) and differential gene expression analysis. Genes with significantly different expression were analyzed for enriched pathways using two different tools. The expression of selected genes and their proteins was validated by RT-qPCR and immunohistochemistry. PCA demonstrated the distinct gene expression profiles of CETL and IMD. In total, 503 genes were upregulated, while 4986 were downregulated in CETL compared to IMD. RT-qPCR confirmed the sequencing results for 5/6 selected genes tested, while the protein expression detected by immunohistochemistry was not entirely consistent. Our study revealed transcriptional differences between canine CETL and IMD, with similarities to human cutaneous lymphoma. Differentially expressed genes are potential discriminatory markers, but require further validation on larger sample collections.
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Affiliation(s)
- Nadja Gerber
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland; (N.G.); (M.A.T.B.); (N.M.G.); (M.M.W.)
- Dermfocus, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (V.J.); (T.L.)
- Grosstierpraxis Weibel + Werner, Oberdorfstrasse 15, 3438 Lauperswil, Switzerland
| | - Magdalena A. T. Brunner
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland; (N.G.); (M.A.T.B.); (N.M.G.); (M.M.W.)
- Dermfocus, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (V.J.); (T.L.)
| | - Vidhya Jagannathan
- Dermfocus, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (V.J.); (T.L.)
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109A, 3001 Bern, Switzerland
| | - Tosso Leeb
- Dermfocus, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (V.J.); (T.L.)
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109A, 3001 Bern, Switzerland
| | - Nora M. Gerhards
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland; (N.G.); (M.A.T.B.); (N.M.G.); (M.M.W.)
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Monika M. Welle
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland; (N.G.); (M.A.T.B.); (N.M.G.); (M.M.W.)
- Dermfocus, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (V.J.); (T.L.)
| | - Martina Dettwiler
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland; (N.G.); (M.A.T.B.); (N.M.G.); (M.M.W.)
- Dermfocus, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (V.J.); (T.L.)
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Henderson E, Clements DN, Johnson CI. An in vitro study of the effect of the optimal irrigation solution conditions during canine articular surgery. Vet Res Commun 2019; 44:1-7. [PMID: 31788728 DOI: 10.1007/s11259-019-09765-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 09/13/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To establish whether chondrocyte viability, matrix degradation and the induction of proteolytic gene expression in canine cartilage is independent of irrigation fluid osmolality and time following exposure to the irrigation fluid. METHODS Canine cartilage explants were exposed to one of three different solution types i) Culture medium (270-280 mOsmol/kg) ii) NaCl 0.9% (302 mOsmol/kg) iii) NaCl 0.9% with sucrose (600 mOsmol/kg). Chondrocyte viability and selected proteolytic gene expression were measured at two time points; immediately following exposure and 24 h following exposure. The media samples at 24 h following exposure were assessed for sulphated glycosaminoglycan (sGAG) release. RESULTS In all samples, no cell death was observed across the superficial or deeper layers of the cartilage. When adjusting for time, gene expression was not shown to be dependent on solution type. However for all solution types, Matrix Metalloproteinase 13 (MMP13) and A Disintegrin and Metalloproteinase with Thrombospondin Motifs 5 (ADAMTS5) expression was significantly decreased in cartilage samples at 24 h post exposure comparatively to samples tested immediately post exposure. No significant differences were identified in the relative sGAG release between the solution types. CLINICAL SIGNIFCANCE Arthroscopic solution irrigation of cartilage explants had no effect on cell viability or proteinase production. At present there is no indication to optimise irrigation fluid osmolarity, as conventional arthroscopic solution was not deleterious to healthy cartilage in this model.
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Affiliation(s)
- E Henderson
- Lumbry Park Veterinary Specialists, Selborne Road, Alton, Hampshire, GU34 3HL, UK.
| | - D N Clements
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, UK
| | - C I Johnson
- Centre for Applied Anatomy, University of Bristol, Southwell Street, Bristol, BS2 8EJ, UK
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Yan L, Toohey-Kurth KL, Crossley BM, Bai J, Glaser AL, Tallmadge RL, Goodman LB. Inhibition monitoring in veterinary molecular testing. J Vet Diagn Invest 2019; 32:758-766. [PMID: 31735123 DOI: 10.1177/1040638719889315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many of the sample matrices typically used for veterinary molecular testing contain inhibitory factors that can potentially reduce analytic sensitivity or produce false-negative results by masking the signal produced by the nucleic acid target. Inclusion of internal controls in PCR-based assays is a valuable strategy not only for monitoring for PCR inhibitors, but also for monitoring nucleic acid extraction efficiency, and for identifying technology errors that may interfere with the ability of an assay to detect the intended target. The Laboratory Technology Committee of the American Association of Veterinary Laboratory Diagnosticians reviewed the different types of internal controls related to monitoring inhibition of PCR-based assays, and provides information here to encourage veterinary diagnostic laboratories to incorporate PCR internal control strategies as a routine quality management component of their molecular testing.
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Affiliation(s)
- Lifang Yan
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Kathy L Toohey-Kurth
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Beate M Crossley
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Jianfa Bai
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Amy L Glaser
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Rebecca L Tallmadge
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Laura B Goodman
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
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6
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He T, Huang Y, Chak JC, Klar RM. Recommendations for improving accuracy of gene expression data in bone and cartilage tissue engineering. Sci Rep 2018; 8:14874. [PMID: 30291289 PMCID: PMC6173755 DOI: 10.1038/s41598-018-33242-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/26/2018] [Indexed: 12/15/2022] Open
Abstract
Autogenous tissue grafting remains the gold standard in the treatment of critical sized bone and certain cartilage defects, while the translation of tissue engineered osteogenesis or chondrogenesis from the lab bench into clinical practice, utilizing natural or synthetic biomimetic devices, remains challenging. One of the crucial underestimated reasons for non-translatability could be the imprecision and inconsistency of generated gene expression profiles, utilizing improperly optimized and standardized quantitative gene assays. Utilizing GeNorm for downstream qRT-PCR applications, the stability of reference genes in relation to optimal cDNA amounts was assessed on human bone marrow-derived mesenchymal and adipose-derived stem cells neat and made to differentiate into chondrocytes including normal human derived chondrocytes and muscle tissue from rats. Results showed that reference genes can vary substantially across separately and/or combined cell lines and/or tissue types including treatment parameters. The recommendations to all bone and cartilage tissue engineers utilizing qRT-PCR is not to assume that reference gene stability and quantity remain conserved across cell lines or tissue types but to always determine, for each new experiment, the stability and normalization quantity of reference genes anew.
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Affiliation(s)
- Tao He
- Laboratory of Biomechanics and Experimental Orthopaedics, Department of Orthopaedic Surgery, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany.,Department of Orthopaedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yijiang Huang
- Laboratory of Biomechanics and Experimental Orthopaedics, Department of Orthopaedic Surgery, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany
| | - Juy Chi Chak
- Laboratory of Biomechanics and Experimental Orthopaedics, Department of Orthopaedic Surgery, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany
| | - Roland Manfred Klar
- Laboratory of Biomechanics and Experimental Orthopaedics, Department of Orthopaedic Surgery, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany.
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7
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Gao D, Kong F, Sun P, Bi G, Mao Y. Transcriptome-wide identification of optimal reference genes for expression analysis of Pyropia yezoensis responses to abiotic stress. BMC Genomics 2018; 19:251. [PMID: 29653512 PMCID: PMC5899324 DOI: 10.1186/s12864-018-4643-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/03/2018] [Indexed: 01/03/2023] Open
Abstract
Background Pyropia yezoensis, a marine red alga, is an ideal research model for studying the mechanisms of abiotic stress tolerance in intertidal seaweed. Real-time quantitative polymerase chain reaction (RT-qPCR) is the most commonly used method to analyze gene expression levels. To accurately quantify gene expression, selection and validation of stable reference genes is required. Results We used transcriptome profiling data from different abiotic stress treatments to identify six genes with relatively stable expression levels: MAP, ATPase, CGS1, PPK, DPE2, and FHP. These six genes and three conventional reference genes, UBC, EF1-α, and eif4A, were chosen as candidates for optimal reference gene selection. Five common statistical approaches (geNorm, ΔCt method, NormFinder, BestKeeper, and ReFinder) were used to identify the stability of each reference gene. Our results show that: MAP, UBC, and FHP are stably expressed in all analyzed conditions; CGS1 and UBC are stably expressed under conditions of dehydration stress; and MAP, UBC, and CGS1 are stably expressed under conditions of temperature stress. Conclusion We have identified appropriate reference genes for RT-qPCR in P. yezoensis under different abiotic stress conditions which will facilitate studies of gene expression under these conditions. Electronic supplementary material The online version of this article (10.1186/s12864-018-4643-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dong Gao
- Ministry of Education, Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Qingdao, 266003, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Fanna Kong
- Ministry of Education, Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Qingdao, 266003, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Peipei Sun
- Ministry of Education, Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Qingdao, 266003, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guiqi Bi
- Ministry of Education, Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Qingdao, 266003, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yunxiang Mao
- Ministry of Education, Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Qingdao, 266003, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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8
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Marchant TW, Johnson EJ, McTeir L, Johnson CI, Gow A, Liuti T, Kuehn D, Svenson K, Bermingham ML, Drögemüller M, Nussbaumer M, Davey MG, Argyle DJ, Powell RM, Guilherme S, Lang J, Ter Haar G, Leeb T, Schwarz T, Mellanby RJ, Clements DN, Schoenebeck JJ. Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2. Curr Biol 2017; 27:1573-1584.e6. [PMID: 28552356 PMCID: PMC5462623 DOI: 10.1016/j.cub.2017.04.057] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/14/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022]
Abstract
In morphological terms, “form” is used to describe an object’s shape and size. In dogs, facial form is stunningly diverse. Facial retrusion, the proximodistal shortening of the snout and widening of the hard palate is common to brachycephalic dogs and is a welfare concern, as the incidence of respiratory distress and ocular trauma observed in this class of dogs is highly correlated with their skull form. Progress to identify the molecular underpinnings of facial retrusion is limited to association of a missense mutation in BMP3 among small brachycephalic dogs. Here, we used morphometrics of skull isosurfaces derived from 374 pedigree and mixed-breed dogs to dissect the genetics of skull form. Through deconvolution of facial forms, we identified quantitative trait loci that are responsible for canine facial shapes and sizes. Our novel insights include recognition that the FGF4 retrogene insertion, previously associated with appendicular chondrodysplasia, also reduces neurocranium size. Focusing on facial shape, we resolved a quantitative trait locus on canine chromosome 1 to a 188-kb critical interval that encompasses SMOC2. An intronic, transposable element within SMOC2 promotes the utilization of cryptic splice sites, causing its incorporation into transcripts, and drastically reduces SMOC2 gene expression in brachycephalic dogs. SMOC2 disruption affects the facial skeleton in a dose-dependent manner. The size effects of the associated SMOC2 haplotype are profound, accounting for 36% of facial length variation in the dogs we tested. Our data bring new focus to SMOC2 by highlighting its clinical implications in both human and veterinary medicine. A population-based genetics study of dogs that required diagnostic imaging Resolution of a QTL associated with face length reduction (brachycephaly) Association of brachycephaly with a retrotransposon that disrupts SMOC2 splicing The SMOC2 locus explains up to 36% of face length variation in dogs
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Affiliation(s)
- Thomas W Marchant
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Edward J Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Lynn McTeir
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Craig I Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Adam Gow
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tiziana Liuti
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dana Kuehn
- Friendship Hospital for Animals, Washington, DC 20016, USA
| | | | - Mairead L Bermingham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Marc Nussbaumer
- Naturhistorisches Museum, Bernastrasse 15, 3005 Bern, Switzerland
| | - Megan G Davey
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - David J Argyle
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Roger M Powell
- Powell Torrance Diagnostic Services, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Sérgio Guilherme
- Davies Veterinary Specialists, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Johann Lang
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, University of Bern, 3001 Bern, Switzerland
| | - Gert Ter Haar
- Department of Clinical Sciences and Services, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Tobias Schwarz
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Richard J Mellanby
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dylan N Clements
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Jeffrey J Schoenebeck
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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9
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Al-Sabah A, Stadnik P, Gilbert S, Duance V, Blain E. Importance of reference gene selection for articular cartilage mechanobiology studies. Osteoarthritis Cartilage 2016; 24:719-30. [PMID: 26585242 PMCID: PMC4819451 DOI: 10.1016/j.joca.2015.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/30/2015] [Accepted: 11/06/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Identification of genes differentially expressed in mechano-biological pathways in articular cartilage provides insight into the molecular mechanisms behind initiation and/or progression of osteoarthritis (OA). Quantitative PCR (qPCR) is commonly used to measure gene expression, and is reliant on the use of reference genes for normalisation. Appropriate validation of reference gene stability is imperative for accurate data analysis and interpretation. This study determined in vitro reference gene stability in articular cartilage explants and primary chondrocytes subjected to different compressive loads and tensile strain, respectively. DESIGN The expression of eight commonly used reference genes (18s, ACTB, GAPDH, HPRT1, PPIA, RPL4, SDHA and YWHAZ) was determined by qPCR and data compared using four software packages (comparative delta-Ct method, geNorm, NormFinder and BestKeeper). Calculation of geometric means of the ranked weightings was carried out using RefFinder. RESULTS Appropriate reference gene(s) for normalisation of mechanically-regulated transcript levels in articular cartilage tissue or isolated chondrocytes were dependent on experimental set-up. SDHA, YWHAZ and RPL4 were the most stable genes whilst glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and to a lesser extent Hypoxanthine-guanine phosphoribosyltransferase (HPRT), showed variable expression in response to load, demonstrating their unsuitability in such in vitro studies. The effect of using unstable reference genes to normalise the expression of aggrecan (ACAN) and matrix metalloproteinase 3 (MMP3) resulted in inaccurate quantification of these mechano-sensitive genes and erroneous interpretation/conclusions. CONCLUSION This study demonstrates that commonly used 'reference genes' may be unsuitable for in vitro cartilage chondrocyte mechanobiology studies, reinforcing the principle that careful validation of reference genes is essential prior to each experiment to obtain robust and reproducible qPCR data for analysis/interpretation.
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Affiliation(s)
| | | | | | | | - E.J. Blain
- Address correspondence and reprint requests to: E.J. Blain, Arthritis Research UK Biomechanics and Bioengineering Centre, Sir Martin Evans Building, School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK. Tel: 44-(0)2920875171.
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10
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He Y, Yan H, Hua W, Huang Y, Wang Z. Selection and Validation of Reference Genes for Quantitative Real-time PCR in Gentiana macrophylla. FRONTIERS IN PLANT SCIENCE 2016; 7:945. [PMID: 27446172 PMCID: PMC4925707 DOI: 10.3389/fpls.2016.00945] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/14/2016] [Indexed: 05/03/2023]
Abstract
Real time quantitative PCR (RT-qPCR or qPCR) has been extensively applied for analyzing gene expression because of its accuracy, sensitivity, and high throughput. However, the unsuitable choice of reference gene(s) can lead to a misinterpretation of results. We evaluated the stability of 10 candidates - five traditional housekeeping genes (UBC21, GAPC2, EF-1α4, UBQ10, and UBC10) and five novel genes (SAND1, FBOX, PTB1, ARP, and Expressed1) - using the transcriptome data of Gentiana macrophylla. Common statistical algorithms ΔC t, GeNorm, NormFinder, and BestKeeper were run with samples collected from plants under various experimental conditions. For normalizing expression levels from tissues at different developmental stages, GAPC2 and UBC21 had the highest rankings. Both SAND1 and GAPC2 proved to be the optimal reference genes for roots from plants exposed to abiotic stresses while EF-1α4 and SAND1 were optimal when examining expression data from the leaves of stressed plants. Based on a comprehensive ranking of stability under different experimental conditions, we recommend that SAND1 and EF-1α4 are the most suitable overall. In this study, to find a suitable reference gene and its real-time PCR assay for G. macrophylla DNA content quantification, we evaluated three target genes including WRKY30, G10H, and SLS, through qualitative and absolute quantitative PCR with leaves under elicitors stressed experimental conditions. Arbitrary use of reference genes without previous evaluation can lead to a misinterpretation of the data. Our results will benefit future research on the expression of genes related to secoiridoid biosynthesis in this species under different experimental conditions.
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Affiliation(s)
- Yihan He
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal UniversityXi’an, China
- School of Geography and Life Science, Qinghai Normal UniversityXining, China
| | - Hailing Yan
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal UniversityXi’an, China
| | - Wenping Hua
- Department of Life Sciences, Shaanxi XueQian Normal UniversityXi’an, China
| | - Yaya Huang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal UniversityXi’an, China
| | - Zhezhi Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal UniversityXi’an, China
- *Correspondence: Zhezhi Wang,
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11
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Piron Prunier F, Chouteau M, Whibley A, Joron M, Llaurens V. Selection of Valid Reference Genes for Reverse Transcription Quantitative PCR Analysis in Heliconius numata (Lepidoptera: Nymphalidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew034. [PMID: 27271971 PMCID: PMC4896466 DOI: 10.1093/jisesa/iew034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/07/2016] [Indexed: 05/03/2023]
Abstract
Identifying the genetic basis of adaptive variation is challenging in non-model organisms and quantitative real time PCR. is a useful tool for validating predictions regarding the expression of candidate genes. However, comparing expression levels in different conditions requires rigorous experimental design and statistical analyses. Here, we focused on the neotropical passion-vine butterflies Heliconius, non-model species studied in evolutionary biology for their adaptive variation in wing color patterns involved in mimicry and in the signaling of their toxicity to predators. We aimed at selecting stable reference genes to be used for normalization of gene expression data in RT-qPCR analyses from developing wing discs according to the minimal guidelines described in Minimum Information for publication of Quantitative Real-Time PCR Experiments (MIQE). To design internal RT-qPCR controls, we studied the stability of expression of nine candidate reference genes (actin, annexin, eF1α, FK506BP, PolyABP, PolyUBQ, RpL3, RPS3A, and tubulin) at two developmental stages (prepupal and pupal) using three widely used programs (GeNorm, NormFinder and BestKeeper). Results showed that, despite differences in statistical methods, genes RpL3, eF1α, polyABP, and annexin were stably expressed in wing discs in late larval and pupal stages of Heliconius numata This combination of genes may be used as a reference for a reliable study of differential expression in wings for instance for genes involved in important phenotypic variation, such as wing color pattern variation. Through this example, we provide general useful technical recommendations as well as relevant statistical strategies for evolutionary biologists aiming to identify candidate-genes involved adaptive variation in non-model organisms.
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Affiliation(s)
- Florence Piron Prunier
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205, CNRS - Muséum National d'Histoire Naturelle - UPMC - EPHE, Sorbonne Universités, Paris, France, Corresponding author, e-mail: , and Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier 5, France Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205, CNRS - Muséum National d'Histoire Naturelle - UPMC - EPHE, Sorbonne Universités, Paris, France, Corresponding author, e-mail: , and Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier 5, France
| | - Mathieu Chouteau
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205, CNRS - Muséum National d'Histoire Naturelle - UPMC - EPHE, Sorbonne Universités, Paris, France, Corresponding author, e-mail: , and Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier 5, France Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205, CNRS - Muséum National d'Histoire Naturelle - UPMC - EPHE, Sorbonne Universités, Paris, France, Corresponding author, e-mail: , and Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier 5, France
| | - Annabel Whibley
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205, CNRS - Muséum National d'Histoire Naturelle - UPMC - EPHE, Sorbonne Universités, Paris, France, Corresponding author, e-mail: , and Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier 5, France
| | - Mathieu Joron
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205, CNRS - Muséum National d'Histoire Naturelle - UPMC - EPHE, Sorbonne Universités, Paris, France, Corresponding author, e-mail: , and Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier 5, France Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205, CNRS - Muséum National d'Histoire Naturelle - UPMC - EPHE, Sorbonne Universités, Paris, France, Corresponding author, e-mail: , and Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier 5, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205, CNRS - Muséum National d'Histoire Naturelle - UPMC - EPHE, Sorbonne Universités, Paris, France, Corresponding author, e-mail: , and Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier 5, France
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12
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Igarashi H, Ohno K, Fujiwara-Igarashi A, Kanemoto H, Fukushima K, Goto-Koshino Y, Uchida K, Tsujimoto H. Functional analysis of pattern recognition receptors in miniature dachshunds with inflammatory colorectal polyps. J Vet Med Sci 2014; 77:439-47. [PMID: 25650150 PMCID: PMC4427745 DOI: 10.1292/jvms.14-0505] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Inflammatory colorectal polyps (ICRPs) frequently occur in miniature dachshunds (MDs) in
Japan. MDs with ICRPs develop multiple polyps with severe neutrophil infiltration that
respond to immunosuppressive therapy. Therefore, ICRPs are thought to constitute a novel,
breed-specific form of canine inflammatory bowel disease (IBD). Pattern recognition
receptors (PRRs) play a key role in the distinction of pathogens from commensal bacteria
and food antigens. Dysfunction resulting from genetic disorders of PRRs have been linked
to human and canine IBD. Therefore, we analyzed the reactivity of PRRs in MDs with ICRPs.
Twenty-six MDs with ICRPs and 16 control MDs were recruited. Peripheral blood-derived
monocytes were obtained from each dog and then stimulated with PRR ligands for 6 and 24
hr; subsequently, messenger RNA (mRNA) expression levels and protein secretion of IL-1β
were quantified using quantitative real-time PCR and ELISA, respectively. The levels of
IL-1β mRNA and protein secretion after stimulation with a nucleotide-binding
oligomerization domain 2 (NOD2) ligand were significantly greater in monocytes from
ICRP-affected MDs than in those from control MDs. In addition, IL-1β protein secretion
induced by toll-like receptor (TLR) 1/2, TLR2 and TLR2/6 stimulation was also
significantly greater in ICRP-affected MDs. These results suggest that reactivity against
NOD2, TLR1/2, TLR2 and TLR2/6 signals is enhanced in ICRP-affected MDs and may play a role
in the pathogenesis of ICRPs in MDs. Additional studies of the genetic background of these
PRRs should be performed.
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Affiliation(s)
- Hirotaka Igarashi
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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13
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Zornhagen KW, Kristensen AT, Hansen AE, Oxboel J, Kjaer A. Selection of suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using quantitative real-time polymerase chain reaction. Vet Comp Oncol 2014; 13:485-93. [PMID: 24995963 DOI: 10.1111/vco.12108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/04/2014] [Indexed: 12/13/2022]
Abstract
Quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) is a sensitive technique for quantifying gene expression. Stably expressed reference genes are necessary for normalization of RT-qPCR data. Only a few articles have been published on reference genes in canine tumours. The objective of this study was to demonstrate how to identify suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using RT-qPCR. Primer pairs for 17 potential reference genes were designed and tested in archival tumour biopsies from six dogs. The geNorm algorithm was used to analyse the most suitable reference genes. Eight potential reference genes were excluded from this final analysis because of their dissociation curves. β-Glucuronidase (GUSB) and proteasome subunit, beta type, 6 (PSMB6) were most stably expressed with an M value of 0.154 and a CV of 0.053 describing their average stability. We suggest that choice of reference genes should be based on specific testing in every new experimental set-up.
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Affiliation(s)
- K W Zornhagen
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital and Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - A T Kristensen
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - A E Hansen
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital and Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark.,Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J Oxboel
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital and Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - A Kjaer
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital and Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
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14
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Igarashi H, Ohno K, Maeda S, Kanemoto H, Fukushima K, Uchida K, Tsujimoto H. Expression profiling of pattern recognition receptors and selected cytokines in miniature dachshunds with inflammatory colorectal polyps. Vet Immunol Immunopathol 2014; 159:1-10. [DOI: 10.1016/j.vetimm.2014.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/21/2014] [Accepted: 03/03/2014] [Indexed: 12/16/2022]
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15
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Bai WL, Yin RH, Yin RL, Jiang WQ, Wang JJ, Wang ZY, Zhu YB, Zhao ZH, Yang RJ, Luo GB, He JB. Selection and validation of suitable reference genes in skin tissue of Liaoning cashmere goat during hair follicle cycle. Livest Sci 2014. [DOI: 10.1016/j.livsci.2013.12.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Zhou CF, Lin P, Yao XH, Wang KL, Chang J, Han XJ. Selection of reference genes for quantitative real-time PCR in six oil-tea camellia based on RNA-seq. Mol Biol 2013. [DOI: 10.1134/s0026893313060198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Park SJ, Huh JW, Kim YH, Lee SR, Kim SH, Kim SU, Kim HS, Kim MK, Chang KT. Selection of internal reference genes for normalization of quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis in the canine brain and other organs. Mol Biotechnol 2013; 54:47-57. [PMID: 22531949 DOI: 10.1007/s12033-012-9543-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive technique for quantifying gene expression. To analyze qRT-PCR data accurately, suitable reference genes that show consistent expression patterns across different tissues and experimental conditions should be selected. The objective of this study was to obtain the most stable reference genes in dogs, using samples from 13 different brain tissues and 10 other organs. 16 well-known candidate reference genes were analyzed by the geNorm, NormFinder, and BestKeeper programs. Brain tissues were derived from several different anatomical regions, including the forebrain, cerebrum, diencephalon, hindbrain, and metencephalon, and grouped accordingly. Combination of the three different analyses clearly indicated that the ideal reference genes are ribosomal protien S5 (RPS5) in whole brain, RPL8 and RPS5 in whole body tissues, RPS5 and RPS19 in the forebrain and cerebrum, RPL32 and RPS19 in the diencephalon, GAPDH and RPS19 in the hindbrain, and MRPS7 and RPL13A in the metencephalon. These genes were identified as ideal for the normalization of qRT-PCR results in the respective tissues. These findings indicate more suitable and stable reference genes for future studies of canine gene expression.
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Affiliation(s)
- Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk 363-883, Republic of Korea
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18
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Park SJ, Kim YH, Huh JW, Lee SR, Kim SH, Kim SU, Kim JS, Jeong KJ, Kim KM, Kim HS, Chang KT. Selection of new appropriate reference genes for RT-qPCR analysis via transcriptome sequencing of cynomolgus monkeys (Macaca fascicularis). PLoS One 2013; 8:e60758. [PMID: 23613744 PMCID: PMC3626658 DOI: 10.1371/journal.pone.0060758] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/01/2013] [Indexed: 12/13/2022] Open
Abstract
In the investigation of the expression levels of target genes, reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is the most accurate and widely used method. However, a normalization step is a prerequisite to obtain accurate quantification results from RT-qPCR data. Therefore, many studies regarding the selection of reference genes have been carried out. Recently, these studies have involved large-scale gene analysis methods such as microarray and next generation sequencing. In our previous studies, we analyzed large amounts of transcriptome data from the cynomolgus monkey. Using a modification of this large-scale transcriptome sequencing dataset, we selected and compared 12 novel candidate reference genes (ARFGAP2, ARL1, BMI1, CASC3, DDX3X, MRFAP1, ORMDL1, RSL24D1, SAR1A, USP22, ZC3H11A, and ZRANB2) and 4 traditionally used reference genes (ACTB, GAPDH, RPS19, and YWHAZ) in 13 different whole-body tissues by the 3 well-known programs geNorm, NormFinder, and BestKeeper. Combined analysis by these 3 programs showed that ADP-ribosylation factor GTPase activating protein 2 (ARFGAP2), morf4 family associated protein 1 (MRFAP1), and ADP-ribosylation factor-like 1 (ARL1) are the most appropriate reference genes for accurate normalization. Interestingly, 4 traditionally used reference genes were the least stably expressed in this study. For this reason, selection of appropriate reference genes is vitally important, and large-scale analysis is a good method for finding new candidate reference genes. Our results could provide reliable reference gene lists for future studies on the expression of various target genes in the cynomolgus monkey.
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Affiliation(s)
- Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Sang-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Sun-Uk Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Ji-Su Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Kang-Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Kyoung-Min Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
- * E-mail: (HSK); (KTC)
| | - Kyu-Tae Chang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
- * E-mail: (HSK); (KTC)
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Tsai PC, Breen M. Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs. Am J Vet Res 2013; 73:1335-43. [PMID: 22924713 DOI: 10.2460/ajvr.73.9.1335] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. SAMPLE Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. PROCEDURES Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. RESULTS LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. CONCLUSIONS AND CLINICAL RELEVANCE Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.
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Affiliation(s)
- Pei-Chien Tsai
- Department of Molecular Biomedical Science, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
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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.
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21
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Reference genes for measuring mRNA expression. Theory Biosci 2012; 131:215-23. [PMID: 22588998 DOI: 10.1007/s12064-012-0152-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/26/2012] [Indexed: 12/29/2022]
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22
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Ciclosporin modulates the responses of canine progenitor epidermal keratinocytes (CPEK) to toll-like receptor agonists. Vet Immunol Immunopathol 2012; 147:91-6. [PMID: 22525195 DOI: 10.1016/j.vetimm.2012.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 02/20/2012] [Accepted: 03/12/2012] [Indexed: 11/23/2022]
Abstract
Toll-like receptor (TLR) 2 dependent pathways have an important role in the antimicrobial defense of human keratinocytes, and various factors and compounds have been shown to affect those pathways. Investigating Toll-like receptor function in canine keratinocytes and the potential for their modulation is of similar relevance in dogs due to the frequency of staphylococcal skin infections in this species, particularly in the context of canine atopic dermatitis. This pilot study hypothesized that ciclosporin would have a modulatory effect on the cytokine and TLR mRNA expression of canine progenitor epidermal keratinocytes in response to TLR2 agonists. No detectable up-regulation of TLR2, TLR4, IL-8 and TNF-α mRNA was detected following exposure to FSL-1, Pam3CSK4 and staphylococcal peptidoglycan (PGN). Ciclosporin alone did not alter the expression levels of these transcripts but in the presence of ciclosporin, TNF-α mRNA expression was upregulated in response to all three agonists and both TNF-α and IL-8 transcript abundance was increased in response to Pam3CSK4. The enhanced responsiveness of canine keratinocytes to TLR2 agonists in response to ciclosporin may imply that administration of this drug might enhance the innate immune barrier of skin.
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Schmitz S, Garden OA, Werling D, Allenspach K. Gene expression of selected signature cytokines of T cell subsets in duodenal tissues of dogs with and without inflammatory bowel disease. Vet Immunol Immunopathol 2012; 146:87-91. [DOI: 10.1016/j.vetimm.2012.01.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 01/16/2012] [Accepted: 01/16/2012] [Indexed: 12/21/2022]
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24
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Too IHK, Ling MHT. Signal Peptidase Complex Subunit 1 and Hydroxyacyl-CoA Dehydrogenase Beta Subunit Are Suitable Reference Genes in Human Lungs. ISRN BIOINFORMATICS 2011; 2012:790452. [PMID: 25969744 PMCID: PMC4407196 DOI: 10.5402/2012/790452] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 10/27/2011] [Indexed: 11/24/2022]
Abstract
Lung cancer is a common cancer, and expression profiling can provide an accurate indication to advance the medical intervention. However, this requires the availability of stably expressed genes as reference. Recent studies had shown that genes that are stably expressed in a tissue may not be stably expressed in other tissues suggesting the need to identify stably expressed genes in each tissue for use as reference genes. DNA microarray analysis has been used to identify those reference genes with low fluctuation. Fourteen datasets with different lung conditions were employed in our study. Coefficient of variance, followed by NormFinder, was used to identify stably expressed genes. Our results showed that classical reference genes such as GAPDH and HPRT1 were highly variable; thus, they are unsuitable as reference genes. Signal peptidase complex subunit 1 (SPCS1) and hydroxyacyl-CoA dehydrogenase beta subunit (HADHB), which are involved in fundamental biochemical processes, demonstrated high expression stability suggesting their suitability in human lung cell profiling.
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Affiliation(s)
- Issac H K Too
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Maurice H T Ling
- Department of Zoology, The University of Melbourne, Parkville, Victoria 3010, Australia
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Chimura N, Kondo N, Shibata S, Kimura T, Mori T, Hoshino Y, Murayama N, Nagata M, Ide K, Nishifuji K, Kamishina H, Maeda S. Gene transcription analysis in lesional skin of canine epitheliotropic cutaneous lymphoma using quantitative real-time RT-PCR. Vet Immunol Immunopathol 2011; 144:329-36. [DOI: 10.1016/j.vetimm.2011.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/19/2011] [Accepted: 08/20/2011] [Indexed: 12/22/2022]
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Uddin MJ, Cinar MU, Tesfaye D, Looft C, Tholen E, Schellander K. Age-related changes in relative expression stability of commonly used housekeeping genes in selected porcine tissues. BMC Res Notes 2011; 4:441. [PMID: 22023805 PMCID: PMC3219825 DOI: 10.1186/1756-0500-4-441] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/24/2011] [Indexed: 01/01/2023] Open
Abstract
Background Gene expression analysis using real-time RT-PCR (qRT-PCR) is increasingly important in biological research due to the high-throughput and accuracy of qRT-PCR. For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes or internal control genes is required. The stability of reference genes has a tremendous effect on the results of relative quantification of gene expression by qRT-PCR. The expression stability of reference genes could vary according to tissues, age of individuals and experimental conditions. In the pig however, very little information is available on the expression stability of reference genes. The aim of this research was therefore to develop a new set of reference genes which can be used for normalization of mRNA expression data of genes expressed in varieties of porcine tissues at different ages. Results The mRNA expression stability of nine commonly used reference genes (B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP and YWHAZ) was determined in varieties of tissues collected from newborn, young and adult pigs. geNorm, NormFinder and BestKeeper software were used to rank the genes according to their stability. geNorm software revealed that RPL4, PPIA and YWHAZ showed high stability in newborn and adult pigs, while B2M, YWHAZ and SDHA showed high stability in young pigs. In all cases, GAPDH showed the least stability in geNorm. NormFinder revealed that TBP was the most stable gene in newborn and young pigs, while PPIA was most stable in adult pigs. Moreover, geNorm software suggested that the geometric mean of three most stable gene would be the suitable combination for accurate normalization of gene expression study. Conclusions Although, there was discrepancy in the ranking order of reference genes obtained by different analysing software methods, the geometric mean of the RPL4, PPIA and YWHAZ seems to be the most appropriate combination of housekeeping genes for accurate normalization of gene expression data in different porcine tissues at different ages.
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Affiliation(s)
- Muhammad Jasim Uddin
- Animal Breeding and Husbandry/Genetics group, Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
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p53 inhibits mRNA 3′ processing through its interaction with the CstF/BARD1 complex. Oncogene 2011; 30:3073-83. [DOI: 10.1038/onc.2011.29] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Cheng WC, Chang CW, Chen CR, Tsai ML, Shu WY, Li CY, Hsu IC. Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis. PLoS One 2011; 6:e17347. [PMID: 21390309 PMCID: PMC3044736 DOI: 10.1371/journal.pone.0017347] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/31/2011] [Indexed: 01/11/2023] Open
Abstract
Background The accuracy of quantitative real-time PCR (qRT-PCR) is highly dependent on
reliable reference gene(s). Some housekeeping genes which are commonly used
for normalization are widely recognized as inappropriate in many
experimental conditions. This study aimed to identify reference genes for
clinical studies through microarray meta-analysis of human clinical
samples. Methodology/Principal Findings After uniform data preprocessing and data quality control, 4,804 Affymetrix
HU-133A arrays performed by clinical samples were classified into four
physiological states with 13 organ/tissue types. We identified a list of
reference genes for each organ/tissue types which exhibited stable
expression across physiological states. Furthermore, 102 genes identified as
reference gene candidates in multiple organ/tissue types were selected for
further analysis. These genes have been frequently identified as
housekeeping genes in previous studies, and approximately 71% of them
fall into Gene Expression (GO:0010467) category in Gene Ontology. Conclusions/Significance Based on microarray meta-analysis of human clinical sample arrays, we
identified sets of reference gene candidates for various organ/tissue types
and then examined the functions of these genes. Additionally, we found that
many of the reference genes are functionally related to transcription, RNA
processing and translation. According to our results, researchers could
select single or multiple reference gene(s) for normalization of qRT-PCR in
clinical studies.
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Affiliation(s)
- Wei-Chung Cheng
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
| | - Cheng-Wei Chang
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
| | - Chaang-Ray Chen
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
| | - Min-Lung Tsai
- Institute of Athletics, National Taiwan Sport
University, Taichung, Taiwan
| | - Wun-Yi Shu
- Institute of Statistics, National Tsing Hua
University, Hsinchu, Taiwan
| | - Chia-Yang Li
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
| | - Ian C. Hsu
- Department of Biomedical Engineering and
Environmental Sciences, National Tsing Hua University, Hsinchu,
Taiwan
- * E-mail:
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Giménez MJ, Pistón F, Atienza SG. Identification of suitable reference genes for normalization of qPCR data in comparative transcriptomics analyses in the Triticeae. PLANTA 2011; 233:163-73. [PMID: 20960006 DOI: 10.1007/s00425-010-1290-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 09/22/2010] [Indexed: 05/03/2023]
Abstract
Comparative transcriptomics are useful to determine the role of orthologous genes among Triticeae species. Thus they constitute an interesting tool to improve the use of wild relatives for crop breeding. Reverse transcription quantitative real-time PCR (qPCR) is the most accurate measure of gene expression but efficient normalization is required. The choice and optimal number of reference genes must be experimentally determined and the primers optimized for cross-species amplification. Our goal was to test the utility of wheat-reference genes for qPCR normalization when species carrying the following genomes (A, B, D, R, H ( v ) and H ( ch )) are compared either simultaneously or in smaller subsets of samples. Wheat/barley/rye consensus primers outperformed wheat-specific ones which indicate that consensus primers should be considered for data normalization in comparative transcriptomics. All genes tested were stable but their ranking in terms of stability differed among subsets of samples. CDC (cell division control protein, AAA-superfamily of ATPases, Ta54227) and RLI (68 kDa protein HP68 similar to Arabidopsis thaliana RNase L inhibitor protein, Ta2776) were always among the three most stable genes. The optimal number of reference genes varied between 2 and 3 depending on the subset of samples and the method used (geNorm vs. coefficient of determination between sequential normalization factors). In any case a maximum number of three reference genes would provide adequate normalization independent of the subset of samples considered. This work constitutes a substantial advance towards comparative transcriptomics using qPCR since it provides useful primers/reference genes.
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Affiliation(s)
- María J Giménez
- Departamento de Mejora Genética Vegetal, IAS-Consejo Superior de Investigaciones Cientificas, Córdoba, Spain
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CHIMURA N, SHIBATA S, KIMURA T, KONDO N, MORI T, HOSHINO Y, KAMISHINA H, MAEDA S. Suitable Reference Genes for Quantitative Real-Time RT-PCR in Total RNA Extracted from Canine Whole Blood Using the PAXgene System. J Vet Med Sci 2011; 73:1101-4. [DOI: 10.1292/jvms.11-0050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Naoki CHIMURA
- The United Graduate School of Veterinary Sciences, Gifu University
| | - Sanae SHIBATA
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Tsuyoshi KIMURA
- The United Graduate School of Veterinary Sciences, Gifu University
| | - Naho KONDO
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Takashi MORI
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Yuki HOSHINO
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Hiroaki KAMISHINA
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Sadatoshi MAEDA
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
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Rehrig EM, Appel HM, Schultz JC. Measuring 'normalcy' in plant gene expression after herbivore attack. Mol Ecol Resour 2010; 11:294-304. [PMID: 21429136 DOI: 10.1111/j.1755-0998.2010.02929.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Plants make drastic changes to their transcriptome to appropriately respond to environmental change, and the regulation of genes that are specific to abiotic and biotic stresses is a key to plant survival. The coordination of defence gene transcription is often coupled with significant adjustments in the levels of expression of primary metabolic and structural genes to relocate resources, repair damage and/or induce senescence. This complicates the process of finding suitable 'housekeeping' or reference genes to use in measurements of gene expression by real-time reverse transcription (RT-PCR) in response to herbivore attack. Several software programs have been developed to identify candidate reference genes, but measurement of their expression may still not yield an appropriate gene or suite of genes for normalization. This is especially true in plant-herbivore interactions where tissue damage is immediate and continuous. Here, we show that 12 traditional reference genes customarily used in RT-PCR analysis are not stably expressed after insect attack. We describe the pitfalls of using traditional reference genes and why insect attack may be affecting whole cell metabolism. We propose a method using RNA quantification in combination with an external spike of commercially available mRNA as normalization factors in studies involving herbivory, multiple stress treatments or species where stable reference genes are unknown.
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Affiliation(s)
- Erin MacNeal Rehrig
- Division of Plant Sciences and Christopher Bond Life Sciences Center, The University of Missouri, 105 Bond Life Sciences Center, Columbia, MO 65211, USA.
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Umeda Y, Nakamura S, Fujiki K, Toshida H, Saito A, Murakami A. Distribution of goblet cells and MUC5AC mRNA in the canine nictitating membrane. Exp Eye Res 2010; 91:721-6. [PMID: 20804752 DOI: 10.1016/j.exer.2010.08.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 07/28/2010] [Accepted: 08/19/2010] [Indexed: 11/17/2022]
Abstract
This study evaluated the distribution of goblet cells and the expression of MUC5AC mRNA in the canine nictitating membrane. The distribution of goblet cells in the nictitating membrane and temporal bulbar conjunctiva of beagle dogs was examined by histochemical analysis of impression cytology specimens and frozen sections. MUC5AC mRNA was detected by the reverse transcription polymerase chain reaction (RT-PCR). The distribution of MUC5AC mRNA was also examined by in situ hybridization using digoxigenin-labeled antisense and sense RNA probes. Histochemical analysis showed that the canine nictitating membrane epithelium contained many more periodic acid-Schiff positive goblet cells, particularly on the palpebral side, compared with the temporal bulbar conjunctiva. RT-PCR revealed that MUC5AC was expressed in both the nictitating membrane and in conjunctival tissue. When the distribution of MUC5AC mRNA was assessed by in situ hybridization, its expression was high on the palpebral side of the nictitating membrane and low in the temporal bulbar conjunctiva. MUC5AC mRNA expression corresponded with the distribution of goblet cells by histochemical examination. In conclusion, there were numerous goblet cells in the canine nictitating membrane epithelium, particularly on the palpebral side, and MUC5AC mRNA was expressed in the nictitating membrane epithelium at locations corresponding to the goblet cells.
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Affiliation(s)
- Yasuyoshi Umeda
- Department of Ophthalmology, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
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Ren S, Zhang F, Li C, Jia C, Li S, Xi H, Zhang H, Yang L, Wang Y. Selection of housekeeping genes for use in quantitative reverse transcription PCR assays on the murine cornea. Mol Vis 2010; 16:1076-86. [PMID: 20596249 PMCID: PMC2893048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 06/06/2010] [Indexed: 11/03/2022] Open
Abstract
PURPOSE To evaluate the suitability of common housekeeping genes (HKGs) for use in quantitative reverse transcription PCR (qRT-PCR) assays of the cornea in various murine disease models. METHODS CORNEAL DISEASE MODELS STUDIED WERE: 1) corneal neovascularization (CorNV) induced by suture or chemical burn, 2) corneal infection with Candida albicans or Aspergillus fumigatus by intrastromal injection of live spores, and 3) perforating corneal injury (PCI) in Balb/c mice or C57BL/6 mice. Expression of 8 HKGs (glyceraldehyde-3-phosphate dehydrogenase [GAPDH], beta-actin [ACTB], lactate dehydrogenase A [LDHA], ribosomal protein L5 [RPL5], ubiquitin C [UBC], peptidylprolyl isomerase A [PPIA], TATA-box binding protein [TBP1], and hypoxanthine guanine phosphoribosyl transferase [HPRT1]) in the cornea were measured at various time points by microarray hybridization or qRT-PCR and the data analyzed using geNorm and NormFinder. RESULTS Microarray results showed that under the CorNV condition the expression stability of the 8 HKGs decreased in order of PPIA>RPL5>HPRT1>ACTB>UBC>TBP1>GAPDH>LDHA. qRT-PCR analyses demonstrated that expression of none of the 8 HKGs remained stable under all conditions, while GAPDH and ACTB were among the least stably expressed markers under most conditions. Both geNorm and NormFinder analyses proposed best HKGs or HKG combinations that differ between the various models. NormFinder proposed PPIA as best HKG for three CorNV models and PCI model, as well as UBC for two fungal keratitis models. geNorm analysis demonstrated that a similar model in different mice strains or caused by different stimuli may require different HKGs or HKG pairs for the best normalization. Namely, geNorm proposed PPIA and HRPT1 and PPIA and RPL5 pairs for chemical burn-induced CorNV in Balb/c and C57BL/6 mice, respectively, while UBC and HPRT1 and UBC and LDHA were best for Candida and Aspergillus induced keratitis in Balb/c mice, respectively. CONCLUSIONS When qRT-PCR is designed for studies of gene expression in murine cornea, preselection of situation-specific reference genes is recommended. In the absence of knowledge about situation-specific HKGs, PPIA and UBC, either alone or in combination with HPRT1 or RPL5, can be employed.
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Cevher MA, Kleiman FE. Connections between 3'-end processing and DNA damage response. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:193-9. [PMID: 21956914 DOI: 10.1002/wrna.20] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cellular DNA damage response (DDR) involves changes in the functional and structural properties of a number of nuclear proteins, resulting in a coordinated control of gene expression and DNA repair. This response includes functional interactions of the DNA repair, transcription, and RNA processing machineries. Following DNA damage, cellular levels of polyadenylated transcripts are transiently decreased and normal recovery depends on transcription-coupled repair (TCR). In addition, DNA damage has gene-specific effects regulating the mRNA levels of factors involved in the DDR itself at different times after the damage. The 3'-end processing machinery, which is important in the regulation of mRNA stability, is involved in these general and gene-specific responses to DNA damage. The role of 3'-end processing in DDR supports the idea that the steady-state levels of different mRNAs change upon DNA-damaging conditions as a result of regulation of not only their biosynthesis but also their turnover. Here, we review the mechanistic connections between 3'-end processing and DDR, and discuss the implications of deregulation of this important step of mRNA maturation in the cellular recovery after DNA-damaging treatment. The relevance of these functional connections is illustrated by the increasing number of reports on this relatively unexplored field.
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Affiliation(s)
- Murat A Cevher
- Department of Chemistry, Hunter College, City University of New York, New York, NY 10065, USA
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Nuclear deadenylation/polyadenylation factors regulate 3' processing in response to DNA damage. EMBO J 2010; 29:1674-87. [PMID: 20379136 DOI: 10.1038/emboj.2010.59] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 03/05/2010] [Indexed: 12/23/2022] Open
Abstract
We previously showed that mRNA 3' end cleavage reaction in cell extracts is strongly but transiently inhibited under DNA-damaging conditions. The cleavage stimulation factor-50 (CstF-50) has a role in this response, providing a link between transcription-coupled RNA processing and DNA repair. In this study, we show that CstF-50 interacts with nuclear poly(A)-specific ribonuclease (PARN) using in vitro and in extracts of UV-exposed cells. The CstF-50/PARN complex formation has a role in the inhibition of 3' cleavage and activation of deadenylation upon DNA damage. Extending these results, we found that the tumour suppressor BARD1, which is involved in the UV-induced inhibition of 3' cleavage, strongly activates deadenylation by PARN in the presence of CstF-50, and that CstF-50/BARD1 can revert the cap-binding protein-80 (CBP80)-mediated inhibition of PARN activity. We also provide evidence that PARN along with the CstF/BARD1 complex participates in the regulation of endogenous transcripts under DNA-damaging conditions. We speculate that the interplay between polyadenylation, deadenylation and tumour-suppressor factors might prevent the expression of prematurely terminated messengers, contributing to control of gene expression under different cellular conditions.
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Breshears LA, Cook JL, Stoker AM, Fox DB, Luther JK. The Effect of Uniaxial Cyclic Tensile Load on Gene Expression in Canine Cranial Cruciate Ligamentocytes. Vet Surg 2010; 39:433-43. [DOI: 10.1111/j.1532-950x.2010.00679.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Chia CY, Lim CWX, Leong WT, Ling MHT. High expression stability of microtubule affinity regulating kinase 3 (MARK3) makes it a reliable reference gene. IUBMB Life 2010; 62:200-3. [DOI: 10.1002/iub.295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Cui X, Zhou J, Qiu J, Johnson MR, Mrug M. Validation of endogenous internal real-time PCR controls in renal tissues. Am J Nephrol 2009; 30:413-7. [PMID: 19729889 DOI: 10.1159/000235993] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 07/14/2009] [Indexed: 12/12/2022]
Abstract
BACKGROUND Endogenous internal controls ('reference' or 'housekeeping' genes) are widely used in real-time PCR (RT-PCR) analyses. Their use relies on the premise of consistently stable expression across studied experimental conditions. Unfortunately, none of these controls fulfills this premise across a wide range of experimental conditions; consequently, none of them can be recommended for universal use. METHODS To determine which endogenous RT-PCR controls are suitable for analyses of renal tissues altered by kidney disease, we studied the expression of 16 commonly used 'reference genes' in 7 mildly and 7 severely affected whole kidney tissues from a well-characterized cystic kidney disease model. Expression levels of these 16 genes, determined by TaqMan RT-PCR analyses and Affymetrix GeneChip arrays, were normalized and tested for overall variance and equivalence of the means. RESULTS Both statistical approaches and both TaqMan- and GeneChip-based methods converged on 3 out of the 4 top-ranked genes (Ppia, Gapdh and Pgk1) that had the most constant expression levels across the studied phenotypes. CONCLUSION A combination of the top-ranked genes will provide a suitable endogenous internal control for similar studies of kidney tissues across a wide range of disease severity.
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Affiliation(s)
- Xiangqin Cui
- Department of Medicine, University of Alabama at Birmingham, 1900 University Blvd, Tinsley Harrison Tower 611J, Birmingham, AL 35294, USA
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Shearer PL, Sharp M, Bonne N, Clark P, Raidal SR. A quantitative, real-time polymerase chain reaction assay for beak and feather disease virus. J Virol Methods 2009; 159:98-104. [DOI: 10.1016/j.jviromet.2009.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 03/02/2009] [Accepted: 03/09/2009] [Indexed: 12/20/2022]
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Taylor SE, Vaughan-Thomas A, Clements DN, Pinchbeck G, Macrory LC, Smith RKW, Clegg PD. Gene expression markers of tendon fibroblasts in normal and diseased tissue compared to monolayer and three dimensional culture systems. BMC Musculoskelet Disord 2009; 10:27. [PMID: 19245707 PMCID: PMC2651848 DOI: 10.1186/1471-2474-10-27] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 02/26/2009] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There is a paucity of data regarding molecular markers that identify the phenotype of the tendon cell. This study aims to quantify gene expression markers that distinguish between tendon fibroblasts and other mesenchymal cells which may be used to investigate tenogenesis. METHODS Expression levels for 12 genes representative of musculoskeletal tissues, including the proposed tendon progenitor marker scleraxis, relative to validated reference genes, were evaluated in matched samples of equine tendon (harvested from the superficial digital flexor tendon), cartilage and bone using quantitative PCR (qPCR). Expression levels of genes associated with tendon phenotype were then evaluated in healthy, including developmental, and diseased equine tendon tissue and in tendon fibroblasts maintained in both monolayer culture and in three dimensional (3D) collagen gels. RESULTS Significantly increased expression of scleraxis was found in tendon compared with bone (P = 0.002) but not compared to cartilage. High levels of COL1A2 and scleraxis and low levels of tenascin-C were found to be most representative of adult tensional tendon phenotype. While, relative expression of scleraxis in developing mid-gestational tendon or in acute or chronically diseased tendon did not differ significantly from normal adult tendon, tenascin-C message was significantly upregulated in acutely injured equine tendon (P = 0.001). Relative scleraxis gene expression levels in tendon cell monolayer and 3D cultures were significantly lower than in normal adult tendon (P = 0.002, P = 0.02 respectively). CONCLUSION The findings of this study indicate that high expression of both COL1A2 and scleraxis, and low expression of tenascin-C is representative of a tensional tendon phenotype. The in vitro culture methods used in these experiments however, may not recapitulate the phenotype of normal tensional tendon fibroblasts in tissues as evidenced by gene expression.
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Affiliation(s)
- Sarah E Taylor
- Department of Veterinary Clinical Science, University of Liverpool, Neston, South Wirral, CH64 7TE, UK
| | - Anne Vaughan-Thomas
- Department of Veterinary Clinical Science, University of Liverpool, Neston, South Wirral, CH64 7TE, UK
| | - Dylan N Clements
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Veterinary Centre, Roslin, EH25 9RG, UK
| | - Gina Pinchbeck
- Department of Veterinary Clinical Science, University of Liverpool, Neston, South Wirral, CH64 7TE, UK
| | - Lisa C Macrory
- Department of Veterinary Clinical Science, University of Liverpool, Neston, South Wirral, CH64 7TE, UK
| | - Roger KW Smith
- Royal Veterinary College, Department of Veterinary Clinical Science, North Mymms, Northampton, UK
| | - Peter D Clegg
- Department of Veterinary Clinical Science, University of Liverpool, Neston, South Wirral, CH64 7TE, UK
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Paolacci AR, Tanzarella OA, Porceddu E, Ciaffi M. Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol Biol 2009; 10:11. [PMID: 19232096 PMCID: PMC2667184 DOI: 10.1186/1471-2199-10-11] [Citation(s) in RCA: 432] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 02/20/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Usually the reference genes used in gene expression analysis have been chosen for their known or suspected housekeeping roles, however the variation observed in most of them hinders their effective use. The assessed lack of validated reference genes emphasizes the importance of a systematic study for their identification. For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR. RESULTS The expression stability of 32 genes was assessed by qRT-PCR using a set of cDNAs from 24 different plant samples, which included different tissues, developmental stages and temperature stresses. The selected sequences included 12 well-known HKGs representing different functional classes and 20 genes novel with reference to the normalization issue. The expression stability of the 32 candidate genes was tested by the computer programs geNorm and NormFinder using five different data-sets. Some discrepancies were detected in the ranking of the candidate reference genes, but there was substantial agreement between the groups of genes with the most and least stable expression. Three new identified reference genes appear more effective than the well-known and frequently used HKGs to normalize gene expression in wheat. Finally, the expression study of a gene encoding a PDI-like protein showed that its correct evaluation relies on the adoption of suitable normalization genes and can be negatively affected by the use of traditional HKGs with unstable expression, such as actin and alpha-tubulin. CONCLUSION The present research represents the first wide screening aimed to the identification of reference genes and of the corresponding primer pairs specifically designed for gene expression studies in wheat, in particular for qRT-PCR analyses. Several of the new identified reference genes outperformed the traditional HKGs in terms of expression stability under all the tested conditions. The new reference genes will enable more accurate normalization and quantification of gene expression in wheat and will be helpful for designing primer pairs targeting orthologous genes in other plant species.
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Affiliation(s)
- Anna R Paolacci
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
| | - Oronzo A Tanzarella
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
| | - Enrico Porceddu
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
| | - Mario Ciaffi
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
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Pilbrow AP, Ellmers LJ, Black MA, Moravec CS, Sweet WE, Troughton RW, Richards AM, Frampton CM, Cameron VA. Genomic selection of reference genes for real-time PCR in human myocardium. BMC Med Genomics 2008; 1:64. [PMID: 19114010 PMCID: PMC2632664 DOI: 10.1186/1755-8794-1-64] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 12/29/2008] [Indexed: 11/26/2022] Open
Abstract
Background Reliability of real-time PCR (RT-qPCR) data is dependent on the use of appropriate reference gene(s) for normalization. To date, no validated reference genes have been reported for normalizing gene expression in human myocardium. This study aimed to identify validated reference genes for use in gene expression studies of failed and non-failed human myocardium. Methods Bioinformatic analysis of published human heart gene expression arrays (195 failed hearts, 16 donor hearts) was used to identify 10 stable and abundant genes for further testing. The expression stability of these genes was investigated in 28 failed and 28 non-failed human myocardium samples by RT-qPCR using geNorm software. Results Signal recognition particle 14 kDa (SRP14), tumor protein, translationally-controlled 1 (TPT1) and eukaryotic elongation factor 1A1 (EEF1A1) were ranked the most stable genes. The commonly used reference gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was ranked the least stable of the genes tested. The normalization strategy was tested by comparing RT-qPCR data of both normalized and raw expression levels of brain natriuretic peptide precursor (NPPB), a gene known to be up-regulated in heart failure. Non-normalized levels of NPPB exhibited a marginally significant difference between failed and non-failed samples (p = 0.058). In contrast, normalized NPPB expression levels were significantly higher in heart-failed patients compared with controls (p = 0.023). Conclusion This study used publicly available gene array data to identify a strategy for normalization involving two reference genes in combination that may have broad application for accurate and reliable normalization of RT-qPCR data in failed and non-failed human myocardium.
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Affiliation(s)
- Anna P Pilbrow
- Christchurch Cardioendocrine Research Group, Department of Medicine, University of Otago-Christchurch, PO Box 4345, Christchurch 8014, New Zealand.
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Reference genes for canine skin when using quantitative real-time PCR. Vet Immunol Immunopathol 2008; 126:392-5. [DOI: 10.1016/j.vetimm.2008.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 07/24/2008] [Accepted: 08/13/2008] [Indexed: 12/28/2022]
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Pérez R, Tupac-Yupanqui I, Dunner S. Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue. BMC Mol Biol 2008; 9:79. [PMID: 18786244 PMCID: PMC2561043 DOI: 10.1186/1471-2199-9-79] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 09/11/2008] [Indexed: 11/24/2022] Open
Abstract
Background Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RTqPCR) is a technique used to measure mRNA species copy number as a way to determine key genes involved in different biological processes. However, the expression level of these key genes may vary among tissues or cells not only as a consequence of differential expression but also due to different factors, including choice of reference genes to normalize the expression levels of the target genes; thus the selection of reference genes is critical for expression studies. For this purpose, ten candidate reference genes were investigated in bovine muscular tissue. Results The value of stability of ten candidate reference genes included in three groups was estimated: the so called 'classical housekeeping' genes (18S, GAPDH and ACTB), a second set of genes used in expression studies conducted on other tissues (B2M, RPII, UBC and HMBS) and a third set of novel genes (SF3A1, EEF1A2 and CASC3). Three different statistical algorithms were used to rank the genes by their stability measures as produced by geNorm, NormFinder and Bestkeeper. The three methods tend to agree on the most stably expressed genes and the least in muscular tissue. EEF1A2 and HMBS followed by SF3A1, ACTB, and CASC3 can be considered as stable reference genes, and B2M, RPII, UBC and GAPDH would not be appropriate. Although the rRNA-18S stability measure seems to be within the range of acceptance, its use is not recommended because its synthesis regulation is not representative of mRNA levels. Conclusion Based on geNorm algorithm, we propose the use of three genes SF3A1, EEF1A2 and HMBS as references for normalization of real-time RTqPCR in muscle expression studies.
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Affiliation(s)
- Raquel Pérez
- Dpt. Animal Production, Veterinary Faculty, University Complutense of Madrid, 28040 Madrid, Spain.
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Cappelli K, Felicetti M, Capomaccio S, Spinsanti G, Silvestrelli M, Supplizi AV. Exercise induced stress in horses: selection of the most stable reference genes for quantitative RT-PCR normalization. BMC Mol Biol 2008; 9:49. [PMID: 18489742 PMCID: PMC2412902 DOI: 10.1186/1471-2199-9-49] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 05/19/2008] [Indexed: 11/22/2022] Open
Abstract
Background Adequate stress response is a critical factor during athlete horses' training and is central to our capacity to obtain better performances while safeguarding animal welfare. In order to investigate the molecular mechanisms underlying this process, several studies have been conducted that take advantage of microarray and quantitative real-time PCR (qRT-PCR) technologies to analyse the expression of candidate genes involved in the cellular stress response. Appropriate application of qRT-PCR, however, requires the use of reference genes whose level of expression is not affected by the test, by general physiological conditions or by inter-individual variability. Results The expression of nine potential reference genes was evaluated in lymphocytes of ten endurance horses during strenuous exercise. These genes were tested by qRT-PCR and ranked according to the stability of their expression using three different methods (implemented in geNorm, NormFinder and BestKeeper). Succinate dehydrogenase complex subunit A (SDHA) and hypoxanthine phosphoribosyltransferase (HPRT) always ranked as the two most stably expressed genes. On the other hand, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), transferrin receptor (TFRC) and ribosomal protein L32 (RPL32) were constantly classified as the less reliable controls. Conclusion This study underlines the importance of a careful selection of reference genes for qRT-PCR studies of exercise induced stress in horses. Our results, based on different algorithms and analytical procedures, clearly indicate SDHA and HPRT as the most stable reference genes of our pool.
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Affiliation(s)
- Katia Cappelli
- Department of Pathology, Diagnostic and Veterinary Clinic, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy.
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Using ribosomal protein genes as reference: a tale of caution. PLoS One 2008; 3:e1854. [PMID: 18365009 PMCID: PMC2267211 DOI: 10.1371/journal.pone.0001854] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 02/20/2008] [Indexed: 12/28/2022] Open
Abstract
Background Housekeeping genes are needed in every tissue as their expression is required for survival, integrity or duplication of every cell. Housekeeping genes commonly have been used as reference genes to normalize gene expression data, the underlying assumption being that they are expressed in every cell type at approximately the same level. Often, the terms “reference genes” and “housekeeping genes” are used interchangeably. In this paper, we would like to distinguish between these terms. Consensus is growing that housekeeping genes which have traditionally been used to normalize gene expression data are not good reference genes. Recently, ribosomal protein genes have been suggested as reference genes based on a meta-analysis of publicly available microarray data. Methodology/Principal Findings We have applied several statistical tools on a dataset of 70 microarrays representing 22 different tissues, to assess and visualize expression stability of ribosomal protein genes. We confirmed the housekeeping status of these genes, but further estimated expression stability across tissues in order to assess their potential as reference genes. One- and two-way ANOVA revealed that all ribosomal protein genes have significant expression variation across tissues and exhibit tissue-dependent expression behavior as a group. Via multidimensional unfolding analysis, we visualized this tissue-dependency. In addition, we explored mechanisms that may cause tissue dependent effects of individual ribosomal protein genes. Conclusions/Significance Here we provide statistical and biological evidence that ribosomal protein genes exhibit important tissue-dependent variation in mRNA expression. Though these genes are most stably expressed of all investigated genes in a meta-analysis they cannot be considered true reference genes.
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Mirkin N, Fonseca D, Mohammed S, Cevher MA, Manley JL, Kleiman FE. The 3' processing factor CstF functions in the DNA repair response. Nucleic Acids Res 2008; 36:1792-804. [PMID: 18252771 PMCID: PMC2330234 DOI: 10.1093/nar/gkn005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Following DNA damage, mRNA levels decrease, reflecting a coordinated interaction of the DNA repair, transcription and RNA processing machineries. In this study, we provide evidence that transcription and polyadenylation of mRNA precursors are both affected in vivo by UV treatment. We next show that the polyadenylation factor CstF, plays a direct role in the DNA damage response. Cells with reduced levels of CstF display decreased viability following UV treatment, reduced ability to ubiquitinate RNA polymerase II (RNAP II), and defects in repair of DNA damage. Furthermore, we show that CstF, RNAP II and BARD1 are all found at sites of repaired DNA. Our results indicate that CstF plays an active role in the response to DNA damage, providing a link between transcription-coupled RNA processing and DNA repair.
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Affiliation(s)
- Nurit Mirkin
- Chemistry Department, Hunter College, City University of New York, New York, NY 10027, USA
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