Toxicity Evaluation and Biomarker Selection with Validated Reference Gene in Embryonic Zebrafish Exposed to Mitoxantrone

Notwithstanding the widespread use and promising clinical value of chemotherapy, the pharmacokinetics, toxicology, and mechanism of mitoxantrone remains unclear. To promote the clinical value in the treatment of human diseases and the exploration of potential subtle effects of mitoxantrone, zebrafish embryos were employed to evaluate toxicity with validated reference genes based on independent stability evaluation programs. The most stable and recommended reference gene was gapdh, followed by tubα1b, for the 48 h post fertilization (hpf) zebrafish embryo mitoxantrone test, while both eef1a1l1 and rpl13α were recommended as reference genes for the 96 hpf zebrafish embryo mitoxantrone test. With gapdh as an internal control, we analyzed the mRNA levels of representative hepatotoxicity biomarkers, including fabp10a, gclc, gsr, nqo1, cardiotoxicity biomarker erg, and neurotoxicity biomarker gfap in the 48 hpf embryo mitoxantrone test. The mRNA levels of gclc, gsr, and gfap increased significantly in 10 and 50 μg/L mitoxantrone-treated 48 hpf embryos, while the transcript levels of fabp10a decreased in a dose-dependent manner, indicating that mitoxantrone induced hepatotoxicity and neurotoxicity. Liver hematoxylin–eosin staining and the spontaneous movement of embryos confirmed the results. Thus, the present research suggests that mitoxantrone induces toxicity during the development of the liver and nervous system in zebrafish embryos and that fabp10a is recommended as a potential biomarker for hepatotoxicity in zebrafish embryos. Additionally, gapdh is proposed as a reference gene for the 48 hpf zebrafish embryo mitoxantrone toxicity test, while eef1a1l1 and rpl13α are proposed as that for the 96 hpf test.

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Reference Gene Selection for Quantitative Real-Time PCR of Mycelia fromLentinula edodesunder High-Temperature Stress

BioMed Research International ◽

10.1155/2018/1670328 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Xu Zhao ◽

Huanling Yang ◽

Mingjie Chen ◽

Xiaoxia Song ◽

Changxia Yu ◽

...

Keyword(s):

High Temperature ◽

Real Time ◽

Temperature Stress ◽

Reference Gene ◽

Reference Genes ◽

Candidate Reference Gene ◽

Housekeeping Genes ◽

High Temperature Stress ◽

Stable Gene ◽

Mrna Levels

Housekeeping genes are important for measuring the transcription expression of functional genes; 10 traditional reference genes,TUB, TUA, GADPH, EF1, 18S, GTP, ACT, UBI, UBC,andH2A, were tested for their adequacy inLentinula edodes(L. edodes). Using specific primers, mRNA levels of these candidate housekeeping genes were evaluated in mycelia ofL. edodes, which were treated with high-temperature stress at 37°C for 0, 4, 8, 12, 18, and 24 hours. After treatment, expression stability of candidate genes was evaluated using three statistical software programs: geNorm, NormFinder, and BestKeeper. According to geNorm,TUBhad the lowest M values inL. edodesstrains 18 and 18N44. Using NormFinder, the best candidate reference gene in strain 18 wasTUB(0.030), and the best candidate reference gene in strain 18N44 wasUBI(0.047). In BestKeeper analysis, the standard deviation (SD) values ofUBC,TUA,H2A,EF1,ACT,18S, andGTPin strain 18 and those ofGADPHandGTPin strain 18N44 were greater than 1; thus, these genes were disqualified as reference genes. Taken together, onlyUBIandTUBwere found to be desirable reference genes by BestKeeper software. Based on the results of three software analyses,TUBwas the most stable gene under all conditions and was verified as an appropriate reference gene for quantitative real-time polymerase chain reaction inL. edodesmycelia under high-temperature stress.

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Validation of Reference Genes for Quantitative Real-time PCR in Diaphanosoma Celebensis: For Chemical Exposure Conditions and Different Ages

10.21203/rs.3.rs-847536/v1 ◽

2021 ◽

Author(s):

Young-Mi Lee ◽

Soyeon In ◽

Se-Joo Kim ◽

Eun-Ji Won ◽

Hayoung Cho ◽

...

Keyword(s):

Gene Expression ◽

Real Time ◽

Reference Gene ◽

Reference Genes ◽

Expression Profiles ◽

Chemical Exposure ◽

Mrna Levels ◽

Qrt Pcr ◽

Different Ages ◽

Diaphanosoma Celebensis

Abstract Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), a primary approach for evaluating gene expression, requires an appropriate normalization strategy to rule out variations in gene expression among samples. The best option is to use a reference gene whose expression level is stable across various experimental conditions to compare the mRNA levels of a target gene. However, there is limited information on how the reference gene is differentially expressed at different ages (growth) in small invertebrates with notable changes such as molting. In this study, expression profiles of nine candidate reference genes from the brackish water flea, Diaphanosoma celebensis, were evaluated under diverse exposure to toxicants and according to growth. As a result, four different algorithms showed similar stabilities of genes for chemical exposures in the case of limited conditions using the same developmental stage (e.g., adult), while the results according to age showed a significantly different pattern in suite of candidate reference genes. This affected the results of genes EcRA and GST, which are involved in development and detoxification mechanisms, respectively. Our finding is the first step towards establishing a standardized real-time qRT-PCR analysis of this environmentally important invertebrate that has potential for aquatic ecotoxicology, particularly in estuarine environments.

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Validation of Reference Genes for RT-qPCR in Marine Bivalve Ecotoxicology: Systematic Review and Case Study

10.1101/074542 ◽

2016 ◽

Cited By ~ 1

Author(s):

Moritz Volland ◽

Julián Blasco ◽

Miriam Hampel

Keyword(s):

Reference Gene ◽

Reference Genes ◽

Good Practice ◽

Optimal Number ◽

Suitable Reference Gene ◽

Marine Bivalve ◽

Mrna Levels ◽

Experimental Conditions

AbstractReverse transcription real-time quantitative PCR (RT-qPCR) is the predominant method of choice for the quantification of mRNA transcripts of a selected gene of interest. Here reference genes are commonly used to normalize non-biological variation in mRNA levels and their appropriate selection is therefore essential for the accurate interpretation the collected data. In recent years the use of multiple validated references genes has been shown to substantially increase the robustness of the normalization. It is therefore considered good practice to experimentally validate putative reference genes under specific experimental conditions, determine the optimal number of reference genes to be employed, and report the method or methods used.Under this premise, we assessed the current state of reference gene base normalization in RT-qPCR bivalve ecotoxicology studies (post 2011), employing a systematic quantitative literature review. A total of 52 papers published met our criteria and were analysed for the gene or genes used, whether they employed multiple reference genes, as well as the validation method employed. In addition we performed a case study using primary hemocytes from the marine bivalve Ruditapes philippinarum after in vitro copper exposure. Herein we further critically discuss methods for reference gene validation, including the established algorithms geNorm, NormFinder and BestKeeper, as well as the popular online tool RefFinder.We identified that RT-qPCR normalization in bivalve ecotoxicology studies is largely performed using single reference genes, while less than 40% of the studies attempted to experimentally validate the expression stability of the reference genes used. 18s rRNA and β-Actin were the most popular genes, yet their un-validated use did introduce artefactual variance that altered the interpretation of the resulting data, while the use of appropriately validated reference genes did substantially improve normalization. Our findings further suggest that combining the results from multiple individual algorithms and calculating the overall best-ranked gene, as e.g. computed by the RefFinder tool, does not by default lead to the identification of the most suitable reference gene or combination of reference genes.

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Validation of reference genes for quantitative real-time PCR in chemical exposed and at different age’s brackish water flea Diaphanosoma celebensis

Scientific Reports ◽

10.1038/s41598-021-03098-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Young-Mi Lee ◽

Hayoung Cho ◽

Ryeo-Ok Kim ◽

Soyeon In ◽

Se-Joo Kim ◽

...

Keyword(s):

Gene Expression ◽

Real Time ◽

Reference Gene ◽

Brackish Water ◽

Reference Genes ◽

Expression Profiles ◽

Mrna Levels ◽

Water Flea ◽

Qrt Pcr ◽

Diaphanosoma Celebensis

AbstractReal-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), a primary approach for evaluating gene expression, requires an appropriate normalization strategy to confirm relative gene expression levels by comparison, and rule out variations that might occur in analytical procedures. The best option is to use a reference gene whose expression level is stable across various experimental conditions to compare the mRNA levels of a target gene. However, there is limited information on how the reference gene is differentially expressed at different ages (growth) in small invertebrates with notable changes such as molting. In this study, expression profiles of nine candidate reference genes from the brackish water flea, Diaphanosoma celebensis, were evaluated under diverse exposure to toxicants and according to growth. As a result, four different algorithms showed similar stabilities of genes for chemical exposures in the case of limited conditions using the same developmental stage (H2A was stable, whereas Act was fairly unstable in adults), while the results according to age showed a significantly different pattern in suite of candidate reference genes. This affected the results of genes EcRA and GST, which are involved in development and detoxification mechanisms, respectively. Our finding is the first step towards establishing a standardized real-time qRT-PCR analysis of this environmentally important invertebrate that has potential for aquatic ecotoxicology, particularly in estuarine environments.

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The Importance of the Selection of Appropriate Reference Genes for Gene Expression Profiling in Adrenal Medulla or Sympathetic Ganglia of Spontaneously Hypertensive Rat

Physiological Research ◽

10.33549/physiolres.933351 ◽

2016 ◽

pp. 401-411 ◽

Cited By ~ 4

Author(s):

A. VAVŘÍNOVÁ ◽

M. BEHULIAK ◽

J. ZICHA

Keyword(s):

Mrna Expression ◽

Adrenal Medulla ◽

Reference Gene ◽

Internal Control ◽

Reference Genes ◽

Sympathetic Ganglia ◽

Stable Reference Gene ◽

Spontaneously Hypertensive ◽

Wky Rats ◽

Catecholaminergic System

Catecholaminergic system plays an important role in hypertension development. The available results on mRNA expression of catecholaminergic system genes in spontaneously hypertensive rats (SHR) are often contradictory. One of the possible causes might be the use of various reference genes as internal controls. In the present study, we searched for suitable reference genes in adrenal medulla or sympathetic ganglia of SHR and Wistar-Kyoto (WKY) rats, which would enable reliable comparison of mRNA expression between these two strains. The mRNA expression was measured by quantitative real-time PCR in adrenal medulla and superior cervical ganglia of 4-week-old or 24-week-old SHR and WKY rats. We evaluated 12 reference genes by three software tools (Normfinder, BestKeeper, geNorm) and compared them for the standardization of mRNA expression. Combination of reference genes Hprt1 and Ywhaz in adrenal medulla and Gapdh and 18S in sympathetic ganglia were chosen as the best ones. 18S was found as applicable reference gene in both tissues. We found many alterations in expression of catecholaminergic system genes in adrenal medulla and sympathetic ganglia of SHR. The usage of the most or the least stable reference gene as internal control changed results moderately in sympathetic ganglia but seriously in adrenal medulla. For example, tyrosine hydroxylase (Th) gene was underexpressed in adrenal medulla of adult SHR using the appropriate reference gene but unchanged after the standardization to the least stable reference gene. Our results indicate the importance of appropriate internal control. The suitability of reference genes should be checked again in the case of change in experimental conditions.

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Anti-Melanogenesis Activity of 6-O-Isobutyrylbritannilactone from Inula britannica on B16F10 Melanocytes and In Vivo Zebrafish Models

Molecules ◽

10.3390/molecules25173887 ◽

2020 ◽

Vol 25 (17) ◽

pp. 3887

Author(s):

Dae Kil Jang ◽

Chau Ha Pham ◽

Ik Soo Lee ◽

Seung-Hyun Jung ◽

Ji Hye Jeong ◽

...

Keyword(s):

Zebrafish Embryos ◽

Mrna Levels ◽

Dependent Manner ◽

B16f10 Cells ◽

Inula Britannica ◽

Phosphoinositide 3 Kinase ◽

Related Proteins ◽

Dose Dependent ◽

Tyrosinase Expression

A potential natural melanogenesis inhibitor was discovered in the form of a sesquiterpene isolated from the flowers of Inula britannica, specifically 6-O-isobutyrylbritannilactone (IBL). We evaluated the antimelanogenesis effects of IBL on B16F10 melanocytes and zebrafish embryos. As a result, we found that 3-isobutyl-1-methylxanthine (IBMX)-induced melanin production was reduced in a dose-dependent manner in B16F10 cells by IBL. We also analyzed B16F10 cells that were and were not treated with IBMX, investigating the melanin concentration, tyrosinase activity, mRNA levels. We also studied the protein expressions of microphthalmia-associated transcription factor (MITF), tyrosinase, and tyrosinase-related proteins (TRP1, and TRP2). Furthermore, we found that melanin synthesis and tyrosinase expression were also inhibited by IBL through the modulation of the following signaling pathways: ERK, phosphoinositide 3-kinase (PI3K)/AKT, and CREB. In addition, we studied antimelanogenic activity using zebrafish embryos and found that the embryos had significantly reduced pigmentation in the IBL-treated specimens compared to the untreated controls.

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The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue

F1000Research ◽

10.12688/f1000research.7656.2 ◽

2016 ◽

Vol 5 ◽

pp. 99 ◽

Cited By ~ 6

Author(s):

Catríona M. Dowling ◽

Dara Walsh ◽

John C. Coffey ◽

Patrick A. Kiely

Keyword(s):

Real Time ◽

Internal Control ◽

Reference Genes ◽

Mrna Levels ◽

Colon Tissue ◽

3 Dimensional ◽

Polymerase Chain ◽

Number Of Publications ◽

Accurate Quantification ◽

Selection Of

Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) remains the most sensitive technique for nucleic acid quantification. Its popularity is reflected in the remarkable number of publications reporting RT-qPCR data. Careful normalisation within RT-qPCR studies is imperative to ensure accurate quantification of mRNA levels. This is commonly achieved through the use of reference genes as an internal control to normalise the mRNA levels between different samples. The selection of appropriate reference genes can be a challenge as transcript levels vary with physiology, pathology and development, making the information within the transcriptome flexible and variable. In this study, we examined the variation in expression of a panel of nine candidate reference genes in HCT116 and HT29 2-dimensional and 3-dimensional cultures, as well as in normal and cancerous colon tissue. Using normfinder we identified the top three most stable genes for all conditions. Further to this we compared the change in expression of a selection of PKC coding genes when the data was normalised to one reference gene and three reference genes. Here we demonstrated that there is a variation in the fold changes obtained dependent on the number of reference genes used. As well as this, we highlight important considerations namely; assay efficiency tests, inhibition tests and RNA assessment which should also be implemented into all RT-qPCR studies. All this data combined demonstrates the need for careful experimental design in RT-qPCR studies to help eliminate false interpretation and reporting of results.

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The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue

F1000Research ◽

10.12688/f1000research.7656.1 ◽

2016 ◽

Vol 5 ◽

pp. 99 ◽

Cited By ~ 4

Author(s):

Catríona M. Dowling ◽

Dara Walsh ◽

John C. Coffey ◽

Patrick A. Kiely

Keyword(s):

Real Time ◽

Internal Control ◽

Reference Genes ◽

Mrna Levels ◽

Colon Tissue ◽

3 Dimensional ◽

Polymerase Chain ◽

Number Of Publications ◽

Accurate Quantification ◽

Selection Of

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A new set of reference genes for RT-qPCR assays in the yeast Dekkera bruxellensis

Canadian Journal of Microbiology ◽

10.1139/cjm-2012-0457 ◽

2012 ◽

Vol 58 (12) ◽

pp. 1362-1367 ◽

Cited By ~ 10

Author(s):

Will de Barros Pita ◽

Fernanda Cristina Bezerra Leite ◽

Anna Theresa de Souza Liberal ◽

Luciana Filgueira Pereira ◽

Marcelo Falsarella Carazzolle ◽

...

Keyword(s):

Gene Expression ◽

Reference Gene ◽

Reference Genes ◽

Gene Expression Analysis ◽

Regulation Of Gene Expression ◽

Culture Conditions ◽

Mrna Levels ◽

Dekkera Bruxellensis ◽

Expression Of Genes ◽

Normalization Factors

The yeast Dekkera bruxellensis has been recently regarded as an important microorganism for bioethanol production owing to its ability to convert glucose, sucrose, and cellobiose to ethanol. The aim of this work was to validate a new set of reference genes for gene expression analysis by quantitative real-time PCR in D. bruxellensis and compare the influence of the method of choice for quantification of mRNA levels with the reliability of our data. Three candidate reference genes, DbEFA1, DbEFB1, and DbYNA1, were used in a quantitative analysis of 4 genes of interest, DbYNR1, DbTPS1, DbADH7, and DbUBA4, based on an approach for calculating the normalization factors by means of the geNorm applet. Each reference gene was also individually used for a [Formula: see text] (comparative Cq method) calculation of the relative expression of genes of interest. Our results showed that the 3 reference genes provided enough stability and were complementary to the normalization factors method in different culture conditions. This work was able to confirm the usefulness of a previously reported reference gene, EFA1/TEF1, and increased the set of possible reference genes in D. bruxellensis to 4. Moreover, this can improve the reliability of the analysis of the regulation of gene expression in the industrial yeast D. bruxellensis.

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Endotoxin-Induced Tissue Factor in Human Monocytes is Dependent upon Protein Kinase C Activation

Thrombosis and Haemostasis ◽

10.1055/s-0038-1649673 ◽

1993 ◽

Vol 70 (05) ◽

pp. 800-806 ◽

Cited By ~ 29

Author(s):

C Ternisien ◽

M Ramani ◽

V Ollivier ◽

F Khechai ◽

T Vu ◽

...

Keyword(s):

Protein Kinase C ◽

Protein Kinase ◽

Tissue Factor ◽

Factor Ix ◽

Transcriptional Level ◽

Mrna Levels ◽

Dependent Manner ◽

Human Monocytes ◽

Kinase C ◽

Pkc Activation

SummaryTissue factor (TF) is a transmembrane receptor which, in association with factors VII and Vila, activates factor IX and X, thereby activating the coagulation protease cascades. In response to bacterial lipopolysaccharide (LPS) monocytes transcribe, synthesize and express TF on their surface. We investigated whether LPS-induced TF in human monocytes is mediated by protein kinase C (PKC) activation. The PKC agonists phorbol 12- myristate 13-acetate (PMA) and phorbol 12, 13 dibutyrate (PdBu) were both potent inducers of TF in human monocytes, whereas 4 alpha-12, 13 didecanoate (4 a-Pdd) had no such effect. Both LPS- and PMA-induced TF activity were inhibited, in a concentration dependent manner, by three different PKC inhibitors: H7, staurosporine and calphostin C. TF antigen determination confirmed that LPS-induced cell-surface TF protein levels decreased in parallel to TF functional activity under staurosporine treatment. Moreover, Northern blot analysis of total RNA from LPS- or PMA-stimulated monocytes showed a concentration-dependent decrease in TF mRNA levels in response to H7 and staurosporine. The decay rate of LPS-induced TF mRNA evaluated after the arrest of transcription by actinomycin D was not affected by the addition of staurosporine, suggesting that its inhibitory effect occurred at a transcriptional level. We conclude that LPS-induced production of TF and its mRNA by human monocytes are dependent on PKC activation.

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