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Teixeira LFS, Gigliotti R, da Silva Ferreira L, Bellini MH. Identification of appropriate housekeeping genes for gene expression studies in human renal cell carcinoma under hypoxic conditions. Mol Biol Rep 2022. [PMID: 35277789 DOI: 10.1007/s11033-022-07236-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Hypoxia pathways are deregulated in clear renal cell carcinoma (ccRCC) because of the loss of the von Hippel-Lindau tumor suppressor function. Quantitative PCR is a powerful tool for quantifying differential expression between normal and cancer cells. Reliable gene expression analysis requires the use of genes encoding housekeeping genes. Therefore, in this study, eight reference candidate genes were evaluated to determine their stability in 786-0 cells under normoxic and hypoxic conditions. METHODS AND RESULTS Four different tools were used to rank the most stable genes-geNorm, NormFinder, BestKeeper, and Comparative Ct (ΔCt), and a general ranking was performed using RankAggreg. According to the four algorithms, the TFRC reference gene was identified as the most stable. There was no agreement among the results from the algorithms for the 2nd and 3rd positions. A general classification was then established using the RankAggreg tool. Finally, the three most suitable reference genes for use in 786-0 cells under normoxic and hypoxic conditions were TFRC, RPLP0, and SDHA. CONCLUSIONS To the best of our knowledge, this is the first study to identify reliable genes that can be used for gene expression analysis in ccRCC in a hypoxic environment.
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Salata C, Monteil V, Leijon M, Bell-Sakyi L, Mirazimi A. Identification and validation of internal reference genes for real-time quantitative polymerase chain reaction-based studies in Hyalomma anatolicum ticks. Ticks Tick Borne Dis 2020; 11:101417. [PMID: 32222359 PMCID: PMC7284302 DOI: 10.1016/j.ttbdis.2020.101417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/10/2020] [Accepted: 03/17/2020] [Indexed: 12/18/2022]
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is an emerging tick-borne viral disease caused by the orthonairovirus CCHF virus (CCHFV). Ticks of the genus Hyalomma are the viral reservoir and they represent the main vector transmitting the virus to their hosts during blood feeding. However, how CCHFV replicates in its natural arthropod host cells and the nature of virus/host interactions are still largely unknown. With the aim of developing tools for use in this field, we identified and validated expression of four candidate endogenous control tick genes in a Hyalomma anatolicum-derived cell line. These genes will be useful for normalization of viral/cellular transcripts in infection/expression studies or as internal controls in molecular epidemiology surveys of pathogens transmitted by Hyalomma ticks.
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Affiliation(s)
- Cristiano Salata
- Department of Molecular Medicine, University of Padova, Via Gabelli, 63, IT-35121 Padova, Italy; Department of Microbiology, The Public Health Agency of Sweden, Nobels Väg 18, SE-171 82 Solna, Sweden.
| | - Vanessa Monteil
- Department of Microbiology, The Public Health Agency of Sweden, Nobels Väg 18, SE-171 82 Solna, Sweden; Department for Laboratory Medicine, Karolinska University Hospital and KI, SE-14186 Huddinge, Sweden.
| | - Mikael Leijon
- National Veterinary Institute, SE-756 51 Uppsala, Sweden.
| | - Lesley Bell-Sakyi
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, Science Park IC2, 146 Brownlow Hill, Liverpool L3 5RF, United Kingdom.
| | - Ali Mirazimi
- Department of Microbiology, The Public Health Agency of Sweden, Nobels Väg 18, SE-171 82 Solna, Sweden; Department for Laboratory Medicine, Karolinska University Hospital and KI, SE-14186 Huddinge, Sweden; National Veterinary Institute, SE-756 51 Uppsala, Sweden.
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Marciano CMM, Ibelli AMG, Peixoto JDO, Savoldi IR, do Carmo KB, Fernandes LT, Ledur MC. Stable reference genes for expression studies in breast muscle of normal and white striping-affected chickens. Mol Biol Rep 2019; 47:45-53. [PMID: 31583571 DOI: 10.1007/s11033-019-05103-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/24/2019] [Indexed: 02/08/2023]
Abstract
The normalization with proper reference genes is a crucial step to obtain accurate mRNA expression levels in quantitative PCR (qPCR) studies. Therefore, in this study, 10 reference candidate genes were evaluated to determine their stability in normal pectoralis major muscle of broilers and those counterparts affected with White Striping (WS) myopathy at 42 days age. Four different tools were used for ranking the most stable genes: GeNorm, NormFinder, BestKeeper and Comparative Ct (ΔCt), and a general ranking was performed using the RankAggreg tool to select the best reference genes among all tools. From the 10 genes evaluated in the breast muscle of broilers, 8 were amplified. Most of the algorithms/tools indicated the same two genes, RPL30 and RPL5, as the most stable in the broilers breast muscle. In addition, there was agreement among the tools for the least stable genes: MRPS27, GAPDH and RPLP1 in the broilers breast muscle. Therefore, it is interesting to note that even with different tools for evaluating gene expression, there was consensus on the most and least stable genes. These results indicate that the Ribosomal protein L30 (RPL30) and Ribosomal protein L5 (RPL5) can be recommended for accurate normalization in qPCR studies with chicken pectoralis major muscle affected with White Striping and other myopathies.
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Affiliation(s)
- Caroline Michele Marinho Marciano
- Programa de Pós-Graduação em Zootecnia, Universidade do Estado de Santa Catarina, UDESC-Oeste, Rua Beloni Trombeta Zanin 680E, Chapecó, Santa Catarina, 89815-630, Brazil
| | - Adriana Mércia Guaratini Ibelli
- Embrapa Suínos e Aves, Rodovia BR-153, Km 110, Distrito de Tamanduá, Caixa Postal: 321, Concórdia, Santa Catarina, 89715-899, Brazil.,Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Alameda Élio Antonio Dalla Vecchia, 838, Guarapuava-Paraná, 85040-167, Brazil
| | - Jane de Oliveira Peixoto
- Embrapa Suínos e Aves, Rodovia BR-153, Km 110, Distrito de Tamanduá, Caixa Postal: 321, Concórdia, Santa Catarina, 89715-899, Brazil.,Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Alameda Élio Antonio Dalla Vecchia, 838, Guarapuava-Paraná, 85040-167, Brazil
| | - Igor Ricardo Savoldi
- Programa de Pós-Graduação em Zootecnia, Universidade do Estado de Santa Catarina, UDESC-Oeste, Rua Beloni Trombeta Zanin 680E, Chapecó, Santa Catarina, 89815-630, Brazil
| | - Kamilla Bleil do Carmo
- Universidade do Contestado, Rua Victor Sopelsa, 3000, Concórdia, Santa Catarina, 89711-330, Brazil
| | - Lana Teixeira Fernandes
- Centro de Diagnóstico de Sanidade Animal, Rodovia BR-153, Km 110, Distrito de Tamanduá, Caixa Postal: 321, Concórdia, Santa Catarina, 89715-899, Brazil
| | - Mônica Corrêa Ledur
- Programa de Pós-Graduação em Zootecnia, Universidade do Estado de Santa Catarina, UDESC-Oeste, Rua Beloni Trombeta Zanin 680E, Chapecó, Santa Catarina, 89815-630, Brazil. .,Embrapa Suínos e Aves, Rodovia BR-153, Km 110, Distrito de Tamanduá, Caixa Postal: 321, Concórdia, Santa Catarina, 89715-899, Brazil.
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Moreira VS, Soares VLF, Silva RJS, Sousa AO, Otoni WC, Costa MGC. Selection and validation of reference genes for quantitative gene expression analyses in various tissues and seeds at different developmental stages in Bixa orellana L. Physiol Mol Biol Plants 2018; 24:369-378. [PMID: 29692545 PMCID: PMC5911269 DOI: 10.1007/s12298-018-0528-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/16/2018] [Accepted: 03/26/2018] [Indexed: 06/07/2023]
Abstract
Bixa orellana L., popularly known as annatto, produces several secondary metabolites of pharmaceutical and industrial interest, including bixin, whose molecular basis of biosynthesis remain to be determined. Gene expression analysis by quantitative real-time PCR (qPCR) is an important tool to advance such knowledge. However, correct interpretation of qPCR data requires the use of suitable reference genes in order to reduce experimental variations. In the present study, we have selected four different candidates for reference genes in B. orellana, coding for 40S ribosomal protein S9 (RPS9), histone H4 (H4), 60S ribosomal protein L38 (RPL38) and 18S ribosomal RNA (18SrRNA). Their expression stabilities in different tissues (e.g. flower buds, flowers, leaves and seeds at different developmental stages) were analyzed using five statistical tools (NormFinder, geNorm, BestKeeper, ΔCt method and RefFinder). The results indicated that RPL38 is the most stable gene in different tissues and stages of seed development and 18SrRNA is the most unstable among the analyzed genes. In order to validate the candidate reference genes, we have analyzed the relative expression of a target gene coding for carotenoid cleavage dioxygenase 1 (CCD1) using the stable RPL38 and the least stable gene, 18SrRNA, for normalization of the qPCR data. The results demonstrated significant differences in the interpretation of the CCD1 gene expression data, depending on the reference gene used, reinforcing the importance of the correct selection of reference genes for normalization.
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Affiliation(s)
- Viviane S. Moreira
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia 45662-900 Brazil
| | - Virgínia L. F. Soares
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia 45662-900 Brazil
| | - Raner J. S. Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia 45662-900 Brazil
| | - Aurizangela O. Sousa
- Departamento de Tecnologia e Ciências Sociais, Universidade do Estado da Bahia, Juazeiro, Bahia 48905-680 Brazil
| | - Wagner C. Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900 Brazil
| | - Marcio G. C. Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia 45662-900 Brazil
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