The dilution effect and the importance of selecting the right internal control genes for RT-qPCR: a paradigmatic approach in fetal sheep

Innovative graph analysis method to assess gene expression modulation after fine particles exposures of 3D human airway epithelia

Environmental particles have dramatic consequences for health, especially for the most vulnerable people, such as asthmatics. To better understand the impact on gene expression modulation of fine particles (PM2.5-0.3) from different emission sources, a 3D-airway model, a human bronchial epithelium (MucilAir-HF™) reconstructed from primary cells from healthy (EpiH) or asthmatic (EpiA) donors, was used. Repeated air-liquid exposures were performed, and epithelia were sacrificed to extract RNAs and assess gene expression. Data were analyzed according to the emission sources, physiological status, and exposure doses using a recent model consisting in a graph analysis on pairwise expression ratio. The results were compared with those from the classical ΔΔCt method. The graph analysis method proved to have better statistical properties than the classical ΔΔCt method and demonstrated that repeated PM2.5-0.3 exposures induced a dose-dependent up-regulation of the metabolic gene (CYP1B1) and a down-regulation of the inflammation gene (CXCL10). These modulations were greater for "industrial" than for "urban traffic" fine particles, and the effects were found to be greater after exposure of EpiA than EpiH, thus emphasizing the importance of the epithelium's physiological status in sensitivity to particles. Our study is original in terms of the experimental conditions and the graphical statistical analysis model established. The results highlight the importance of particle chemistry on the modulation of cellular and molecular responses, which may vary according to the individual's vulnerability.

Impacts of Time-Fed Concentrate-Based Diets on Plasma Metabolites, Rumen Histology, and mRNA Expression of Hepatic Enzymes of Wethers

Simple Summary

In modern ruminant meat production systems, wethers and steers are commonly fed diets containing 80% grain, or more. These diets are commonly fed to increase fat deposition in meat-producing ruminants. However, when wethers and steers are not appropriately transitioned to grain-based diets, they can experience metabolic and inflammatory conditions that negatively affect health and production. It is still unclear how meat-producing ruminants adapt to grain-based diets over time. This study evaluated the effects of an abrupt dietary change, from 80% forage to 80% grain, on rumen, plasma, and liver metabolism in growing wethers and monitored their ability to adapt over time. The results of the study suggest that wethers fed an 80% grain diet adapt over time by altering the expression of key enzymes involved in the systemic inflammation, iron metabolism, and cholesterol and glucose synthesis. This study provides novel insight into the physiology of fattening ruminants that have been abruptly fed grain-based diets and highlights the fact that meat-producing animals can be fed grain-based diets to meet increasing human meat requirements.

Abstract

Transition to grain increases inflammation and causes parakeratosis, which can decrease growth performance in fattening animals. It is unknown if ruminants adapt to these inflammatory responses over time. In a three-phase, 49-day experiment, all wethers (n = 13, BW = 50.6 ± 4.7 kg; 4.9 ± 0.3 months of age) were fed an 80% forage diet during P1(day 0 to 21). On day 21, 4 wethers were slaughtered to obtain baseline liver and rumen tissue. During P2 (day 22 to 25), the remaining wethers were fed an 80% concentrate diet. Four wethers were slaughtered on day 25 to obtain P2 liver and rumen tissue. During P3 (day 22 to 49), the remaining five wethers were fed 80% concentrate diets and were slaughtered on day 49 to obtain P3 liver and rumen tissue. Rumen parakeratosis was greater (p ≤ 0.02) in wethers sampled in P2 and P3 when compared to those sampled in P1. Among positive acute phase reactants, expression of serum α-amyloid (SAA) and haptoglobin (HPT) tended (p ≤ 0.12) to be 6- and 10-fold greater, respectively, in wethers sampled in P2 compared to wethers sampled in P1; however, SAA and HPT expression was not different between wethers sampled in P3 and P1. Plasma glucose and β-hydroxybutyric acid (BHBA) increased (p ≤ 0.03) in wethers sampled in both P2 and P3 compared to the wethers sampled in P1, while total protein and cholesterol decreased (p ≤ 0.06) only in wethers sampled from P2 compared to those sampled in P1. Hepatic acute phase responses suggest that the wethers adapted to an 80% concentrate diet over time.

What's the norm in normalization? A frightening note on the use of RT-qPCR in the livestock science

Reverse-Transcription quantitative PCR (RT-qPCR) provides a valuable tool to study gene expression with exquisite sensitivity. To retain its inferential power, user-introduced technical variability must be reduced and accounted for. Selecting a set of stably expressed internal control genes (ICG), validated for each experimental condition/sample set, is widely accepted as a reliable way to normalize RT-qPCR data and account for said variability. Despite significant efforts in establishing standardized and resource-efficient normalization approaches, numerous recent reports have underlined deficiencies in the state of RT-qPCR normalization. Livestock science has benefitted tremendously from the use of RT-qPCR; however, the issue of lack of proper normalization likely affects this discipline as well. We thus decided to determine whether this is true, and to which extent. We conducted an in-depth analysis of all (225) RT-qPCR articles published in the six most prominent livestock journals in the field from 2013 to 2017. A quantitative scale was constructed, and values were assigned to each article based on the number of ICG used, the use of a publicly available algorithm to assess the reliability of ICG, and the reporting of pertinent information related to ICG (ranges from 0 = total noncompliance - to 100 = total compliance). Out of the surveyed group, only 10.7% of the publications obtained a score of 100, while the largest group (n = 158) was represented by articles that scored 0. Subdividing articles based on whether an algorithm to validate ICG was used (YAL) or not (NAL) revealed the use of a larger number of ICG to normalize RT-qPCR in the YAL group compared to NAL (1.4-fold more, 95% C.I.: 1.11–1.84) and was closer to the “gold standard” of three ICG. Using an algorithm also increased the diversity of ICG and significantly reduced the use of RNA18S, whose suitability as ICG has been thoroughly debated. These remarkably low normalization standards are likely to generate questionable results that can severely hinder the advance of transcriptomic studies in livestock science and related fields.

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Subpar normalization of reverse transcription qPCR was reported for the five major livestock journals over the period 2013-2017

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The use of algorithms for validation led to a greater number of ICG used, and greater variety of ICGs

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The issue could be solved by editors by enforcing the use of the standardized MIQE guidelines for RT-qPCR

Effects of Red Ginseng Extract on the Pharmacokinetics and Elimination of Methotrexate via Mrp2 Regulation

We aimed to investigate the effects of red ginseng extract (RGE) on the expression of efflux transporters and to study the pharmacokinetics of representative substrate. For this, rats received single or repeated administration of RGE (1.5 g/kg/day) for 1 and 2 weeks via oral gavage. mRNA and protein levels of multidrug resistance-associated protein2 (Mrp2), bile salt export pump (Bsep), and P-glycoprotein (P-gp) in the rat liver were measured via real-time polymerase chain reaction and Western blot analysis. Ginsenosides concentrations from the rat plasma were also monitored using a liquid chromatography–tandem mass spectrometry (LC–MS/MS) system. Plasma concentrations of ginsenoside Rb1, Rb2, Rc, and Rd following repeated administration of RGE for 1 and 2 weeks were comparable but significantly higher than those after single administration of RGE. These dosing regimens did not induce significant biochemical abnormalities in the liver, kidneys, and lipid homeostasis. In the RGE repeated oral administration groups, the mRNA and protein levels of Mrp2 significantly decreased. Accordingly, we investigated the changes in the pharmacokinetics of methotrexate, a probe substrate for Mrp2, following intravenous administration of 3 mg/kg methotrexate to rats in the RGE 1-week repeated oral administration group, compared to that in the control group. Biliary excretion, but not urinary excretion, of methotrexate decreased in the RGE repeated administration group, compared to that in the control group. Consequently, the plasma concentrations of methotrexate slightly increased in the RGE repeated administration group. In conclusion, repeated administration of RGE for 1 week resulted in a decrease in Mrp2 expression without inducing significant liver or kidney damage. Pharmacokinetic herb–drug interaction between RGE and methotrexate might occur owing to the decrease in the mRNA and protein levels of Mrp2.

Ursodeoxycholate Restores Biliary Excretion of Methotrexate in Rats with Ethinyl Estradiol Induced-Cholestasis by Restoring Canalicular Mrp2 Expression

The in vivo relevance of ursodeoxycholate (UDCA) treatment (100 mg/kg/day, per oral tid for 5 days before cholestasis induction followed by the same dosing for 5 days) on hepatic function was investigated in rats with 17α-ethinylestradiol (EE, 10 mg/kg, subcutaneous for 5 days)-induced experimental cholestasis. The bile flow rate and the expression level of hepatic multidrug resistance-associated protein 2 (Mrp 2) that were decreased in cholestasis were restored after UDCA treatment. Consistent with this, the biliary excretion clearance (CL_exc,bile) of a representative Mrp2 substrate—methotrexate (MTX)—was decreased in cholestatic rats but was restored after UDCA treatment. Consequently, the plasma concentrations of MTX, which were increased by cholestasis, were decreased to control levels by UDCA treatment. Thus, the restoration of CL_exc,bile appears to be associated with the increase in Mrp2 expression on the canalicular membrane by UDCA treatment followed by Mrp2-mediated biliary excretion of MTX. On the other hand, the hepatic uptake clearance (CL_up,liver) of MTX was unchanged by cholestasis or UDCA treatment, suggestive of the absence of any association between the uptake process and the overall biliary excretion of MTX. Since UDCA has been known to induce the expression of canalicular MRP2 in humans, UDCA treatment might be effective in humans to maintain or accelerate the hepatobiliary elimination of xenobiotics or metabolic conjugates that are MRP2 substrates.

Aquaporin expression in the fetal porcine urinary tract changes during gestation

The expression of aquaporins (AQPs) in the fetal porcine urinary tract and its relation to gestational age has not been established. Tissue samples from the renal pelvis, ureter, bladder and urethra were obtained from porcine fetuses. Samples were examined by RT-PCR (AQPs 1-11), QPCR (AQPs positive on RT-PCR), and immunohistochemistry. Bladder samples were additionally examined by Western blotting. RNA was extracted from 76 tissue samples obtained from 19 fetuses. Gestational age was 60 (n=11) or 100 days (n=8). PCR showed that AQP1, 3, 9 and 11 mRNA was expressed in all locations. The expression of AQP3 increased significantly at all four locations with gestational age, whereas AQP11 significantly decreased. AQP1 expression increased in the ureter, bladder and urethra. AQP9 mRNA expression increased in the urethra and bladder, but decreased in the ureter. AQP5 was expressed only in the urethra. Immunohistochemistry showed AQP1 staining in sub-urothelial vessels at all locations. Western blotting analysis confirmed increased AQP1 protein levels in bladder samples during gestation. Expression levels of AQP1, 3, 5, 9 and 11 in the urinary tract change during gestation, and further studies are needed to provide insights into normal and pathophysiological water handling mechanisms in the fetus.

Selection of internal references for qRT-PCR assays of human hepatocellular carcinoma cell lines

Selecting internal references is important for normalizing the loading quantity of samples in quantitative reverse-transcription PCR (qRT-PCR). In the present study, a systematic evaluation of reference genes among nine hepatocellular carcinoma (HCC) cell lines was conducted. After screening the microarray assay data of ten HCC cell lines, 19 candidate reference genes were preselected and then evaluated by qRT-PCR, together with ACTB, GAPDH, HPRT1 and TUBB The expression evenness of these candidate genes was evaluated using RefFinder. The stabilities of the reference genes were further evaluated under different experimental perturbations in Huh-7 and MHCC-97L, and the applicability of the reference genes was assessed by measuring the mRNA expression of CCND1, CCND3, CDK4 and CDK6 under sorafenib treatment in Huh-7. Results showed that TFG and SFRS4 are among the most reliable reference genes, and ACTB ranks third and acts quite well as a classical choice, whereas GAPDH, HPRT1 and TUBB are not proper reference genes in qRT-PCR assays among the HCC cell lines. SFRS4, YWHAB, SFRS4 and CNPY3 are the most stable reference genes of the MHCC-97L under the perturbations of chemotherapy, oxidative stress, starvation and hypoxia respectively, whereas YWHAB is the most stable one of Huh-7 under all perturbations. GAPDH is recommended as a reference gene under chemotherapy perturbations. YWHAB and UBE2B, TMED2 and TSFM, and GAPDH and TSFM are the two best reference genes under oxidative stress, starvation and hypoxia perturbations respectively. TSFM is stable in both cell lines across all the perturbations.

Analysis of Different Approaches for the Selection of Reference Genes in RT-qPCR Experiments: A Case Study in Skeletal Muscle of Growing Mice

The reliability of reverse transcription-quantitative PCR (RT-qPCR) results in gene expression studies depends on the approaches used to account for non-biological variations. In order to find a proper normalization strategy for the study of genes related to growth hormone signaling in skeletal muscle of growing mice, nine unrelated genes were evaluated as internal controls. According to the most used algorithms–geNorm, the Comparative ΔCq method, NormFinder and BestKeeper–GSK3B, YWHAZ, RPL13A and RN18S were found as the most stable. However, the relative expression levels of eight of the potential reference genes assessed decreased with age in cDNA samples obtained from the same amount of total RNA. In a different approach to analyze this apparent discrepancy, experiments were performed with cDNA obtained from equal amounts of purified mRNA. Since the decline was still observed, the hypothesis of an age-related change in mRNA to total RNA ratio that could account for the systematic decrease was rejected. Differences among experimental groups could be due to a substantial increase with age in highly expressed mRNAs, which would bias the quantitation of the remaining genes. Consequently, those reference genes reflecting this dilution effect, which would have been discarded considering their variable relative expression levels, arose as suitable internal controls.

Whole-Transcriptome Selection and Evaluation of Internal Reference Genes for Expression Analysis in Protocorm Development of Dendrobium officinale Kimura et Migo

Dendrobium officinale Kimu et Migo has increased many researchers' interest for its high medical and horticultural values and the molecular mechanism of its protocorm development remains unclear. In this study, 19 genes from 26 most stably expressed genes in whole transcriptome of protocorms and 5 housekeeping genes were used as candidate reference genes and screened with 4 application softwares (geNorm, NormFinder, BestKeeper and RefFinder). The results showed that a few reference genes could effectively normalize expression level of specific genes in protocorm development and the optimal top 2 reference genes were ASS and APH1L. Meanwhile, validation of GNOM, AP2 and temperature induced gene (TIL) for normalization demonstrates the usefulness of the validated candidate reference genes. The expression profiles of these genes varied under protocorms and temperature stress according to the stablest and unstablest reference genes, which proved the importance of the choice of appropriate reference genes. The first systematic evaluation of stably expressed genes will be very useful in the future analysis of specific genes expression in D. officinale.

The importance of selecting the right internal control gene to study the effects of antenatal glucocorticoid administration in human placenta

RT-qPCR requires a suitable set of internal control genes (ICGs) for an accurate normalization. The usefulness of 7 previously published ICGs in the human placenta was analyzed according to the effects of betamethasone treatment, sex and fetal age. Raw RT-qPCR data of the ICGs were evaluated using published algorithms. The algorithms revealed that a reliable normalization was achieved using the geometrical mean of PPIA, RPL19, HMBS and SDHA. The use of a different subset ICGs out of the 7 investigated, although not statistically affected by the conditions, biased the results, as demonstrated through changes in expression of glucocorticoid receptor (NR3C1) mRNA as a target gene.

A Panel of Stably Expressed Reference Genes for Real-Time qPCR Gene Expression Studies of Mallards (Anas platyrhynchos)

Determining which reference genes have the highest stability, and are therefore appropriate for normalising data, is a crucial step in the design of real-time quantitative PCR (qPCR) gene expression studies. This is particularly warranted in non-model and ecologically important species for which appropriate reference genes are lacking, such as the mallard--a key reservoir of many diseases with relevance for human and livestock health. Previous studies assessing gene expression changes as a consequence of infection in mallards have nearly universally used β-actin and/or GAPDH as reference genes without confirming their suitability as normalisers. The use of reference genes at random, without regard for stability of expression across treatment groups, can result in erroneous interpretation of data. Here, eleven putative reference genes for use in gene expression studies of the mallard were evaluated, across six different tissues, using a low pathogenic avian influenza A virus infection model. Tissue type influenced the selection of reference genes, whereby different genes were stable in blood, spleen, lung, gastrointestinal tract and colon. β-actin and GAPDH generally displayed low stability and are therefore inappropriate reference genes in many cases. The use of different algorithms (GeNorm and NormFinder) affected stability rankings, but for both algorithms it was possible to find a combination of two stable reference genes with which to normalise qPCR data in mallards. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies in ducks. The fact that nearly all previous studies of the influence of pathogen infection on mallard gene expression have used a single, non-validated reference gene is problematic. The toolkit of putative reference genes provided here offers a solid foundation for future studies of gene expression in mallards and other waterfowl.

Whole-Transcriptome Selection and Evaluation of Internal Reference Genes for Expression Analysis in Protocorm Development of Dendrobium officinale Kimura et Migo

Dendrobium officinale Kimu et Migo has increased many researchers' interest for its high medical and horticultural values and the molecular mechanism of its protocorm development remains unclear. In this study, 19 genes from 26 most stably expressed genes in whole transcriptome of protocorms and 5 housekeeping genes were used as candidate reference genes and screened with 4 application softwares (geNorm, NormFinder, BestKeeper and RefFinder). The results showed that a few reference genes could effectively normalize expression level of specific genes in protocorm development and the optimal top 2 reference genes were ASS and APH1L. Meanwhile, validation of GNOM, AP2 and temperature induced gene (TIL) for normalization demonstrates the usefulness of the validated candidate reference genes. The expression profiles of these genes varied under protocorms and temperature stress according to the stablest and unstablest reference genes, which proved the importance of the choice of appropriate reference genes. The first systematic evaluation of stably expressed genes will be very useful in the future analysis of specific genes expression in D. officinale.