Identification of suitable reference genes for quantitative gene expression analysis in rat adipose stromal cells induced to trilineage differentiation

Development of a membrane and a bilayer of chitosan, gelatin, and polyhydroxybutyrate to be used as wound dressing for the regeneration of rat excisional wounds

The skin is the largest organ in the human body that acts as a protective barrier from the outside environment. Certain dermatological pathologies or significant skin lesions can result in serious complications. Several studies have focused on the development of tissue-engineered skin substitutes. In this study, a new bilayer scaffold composed of a chitosan-gelatin membrane and a chitosan-polyhydroxybutyrate (PHB) porous matrix was synthesized and populated with human adipose-derived mesenchymal stem cells (hASCs) to be potentially used for wound dressing applications. By combining this membrane and porous matrix with the stem cells, we aimed to provide immunomodulation and differentiation capabilities for the wound environment, as well as mechanical strength and biocompatibility for the underlying tissue. The membrane was prepared from the mixture of chitosan and gelatin in a 2:1 ratio and the porous matrix was prepared from the mixture of chitosan and PHB, in equal proportions to form a final solution at 2.5% (m/v). Fourier transform infrared spectroscopy analysis showed the formation of blends, and micro-computed tomography, scanning electron microscopy and atomic force microscopy images demonstrated membrane roughness and matrix porosity. The MTT assay showed that the scaffolds were biocompatible with hASC. The membrane and the bilayer were used as dressing and support for cell migration in the dorsal excisional wound model in Wistar rats. Histological and gene transcriptional analyses showed that the animals that received the scaffolds regenerated the hair follicles in the deep dermis in the central region of the wound. Our results demonstrate the potential of these new biomaterials as dressings in wound healing studies, favoring tissue regeneration.

Reference gene expression stability within the rat brain under mild intermittent ketosis induced by supplementation with medium-chain triglycerides

Reverse transcription followed by quantitative (real-time) polymerase chain reaction (RT-qPCR) has become the gold standard in mRNA expression analysis. However, it requires an accurate choice of reference genes for adequate normalization. The aim of this study was to validate the reference genes for qPCR experiments in the brain of rats in the model of mild ketosis established through supplementation with medium-chain triglycerides (MCT) and intermittent fasting. This approach allows to reproduce certain neuroprotective effects of the classical ketogenic diet while avoiding its adverse effects. Ketogenic treatment targets multiple metabolic pathways, which may affect the reference gene expression. The standard chow of adult Wistar rats was supplemented with MCT (2 ml/kg orogastrically, during 6 h of fasting) or water (equivolume) for 1 month. The mRNA expression of 9 housekeeping genes (Actb, B2m, Gapdh, Hprt1, Pgk1, Ppia, Rpl13a, Sdha, Ywhaz) in the medial prefrontal cortex, dorsal and ventral hippocampus was measured by RT-qPCR. Using the RefFinder® online tool, we have found that the reference gene stability ranking strongly depended on the analyzed brain region. The most stably expressed reference genes were found to be Ppia, Actb, and Rpl13a in the medial prefrontal cortex; Rpl13a, Ywhaz, and Pgk1 in the dorsal hippocampus; Ywhaz, Sdha, and Ppia in the ventral hippocampus. The B2m was identified as an invalid reference gene in the ventral hippocampus, while Sdha, Actb, and Gapdh were unstable in the dorsal hippocampus. The stabilities of the examined reference genes were lower in the dorsal hippocampus compared to the ventral hippocampus and the medial prefrontal cortex. When normalized to the three most stably expressed reference genes, the Gapdh mRNA was upregulated, while the Sdha mRNA was downregulated in the medial prefrontal cortex of MCT-fed animals. Thus, the expression stability of reference genes strongly depends on the examined brain regions. The dorsal and ventral hippocampal areas differ in reference genes stability rankings, which should be taken into account in the RT-qPCR experimental design.

Tyrosol retards induction of fibrosis in rats

Liver fibrosis, which still does not have a standard treatment due to its complex pathogenesis, is an important cause of mortality and morbidity. In this study, it was aimed to examine the possible protective and antifibrotic effects of tyrosol on the liver through histopathologic, immunohistochemical, biochemical, and molecular methods in rats with chronic liver damage induced by thioacetamide (TAA). The study was carried out in four groups with eight rats in each group. Created groups are, respectively, control, TAA, tyrosol and TAA +tyrosol. Chronic liver damage was induced in the TAA and TAA +tyrosol groups by the addition of TAA (200 mg/L) to drinking water. Tyrosol (20 mg/kg/b.w./daily) was administered by oral gavage to tyrosol and TAA +tyrosol groups for 10 weeks. The results of this study demonstrate that the consumption of tyrosol alleviated the histopathologic changes such as inflammation, degeneration, and especially fibrosis induced by TAA in the liver. In addition, administration of tyrosol significantly attenuated alpha-smooth muscle actin (α-SMA) expression and apoptosis expression. Biochemically, it was determined that tyrosol increased glutathione (GSH) level, glutathione peroxidase (GSH.Px), and catalase (CAT) activities and showed antioxidant efficacy by reducing malondialdehyde (MDA) level. Moreover, it reduced inflammation and fibrosis by decreasing gene expression levels of tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and transforming growth factor-beta (TGF-β1). Western blot analysis also revealed similar results in TGF-β1 expression. As a result, tyrosol suppressed fibrogenesis thanks to its antioxidant, anti-inflammatory, and anti-apoptotic effects and showed an antifibrotic effect in the liver. PRACTICAL APPLICATIONS: It is stated that tyrosol, a natural phenolic antioxidant found in olive oil, has neuroprotective, cardioprotective, anti-inflammatory, and anticancer properties. In this study, tyrosol suppressed fibrogenesis thanks to its antioxidant, anti-inflammatory, and anti-apoptotic effects and showed an antifibrotic effect in the liver. Olive oil has an important place in the Mediterranean diet, which reduces the incidence of chronic diseases. It is thought that the anti-fibrotic effect of tyrosol plays a role in this feature. As a result, it is thought that tyrosol can be used to prevent or slow down chronic liver diseases.

Dietary high calories from sunflower oil, sucrose and fructose sources alters lipogenic genes expression levels in liver and skeletal muscle in rats

INTRODUCTION AND OBJECTIVES

The objectives of this study were to investigate the underlying mechanism of PPARα, LXRα, ChREBP, and SREBP-1c at the level of gene and protein expression with high-energy diets in liver and skeletal muscle.

MATERIALS AND METHODS

Metabolic changes with consumption of high fat (Hfat), high sucrose (Hsuc) and high fructose (Hfru) diets were assessed. Levels of mRNA and protein of PPARα, LXRα, ChREBP, and SREBP-1c were investigated. Body weight changes, histological structure of liver and plasma levels of some parameters were also examined.

RESULTS

In Hfru group, body weights were higher than other groups (P<0.05). In liver, LXRα levels of Hsuc and Hfru groups were upregulated as 1.87±0.30 (P<0.05) and 2.01±0.29 (P<0.01). SREBP-1c levels were upregulated as 4.52±1.25 (P<0.05); 4.05±1.11 (P<0.05) and 3.85±1.04 (P<0.05) in Hfat, Hsuc, and Hfru groups, respectively. In skeletal muscle, LXRα and SREBP-1c were upregulated as 1.77±0.30 (P<0.05) and 2.71±0.56 (P<0.05), in the Hfru group. Protein levels of ChREBP (33.92±8.84ng/mg protein (P<0.05)) and SREBP-1c (135.16±15.57ng/mg protein (P<0.001)) in liver were higher in Hfru group. In skeletal muscle, LXRα, ChREBP and SREBP-1c in Hfru group were 6.67±0.60, 7.11±1.29 and 43.17±6.37ng/mg, respectively (P<0.05; P<0.01; P<0.05). The rats in Hfru group had the most damaged livers.

CONCLUSION

Besides liver, fructose consumption significantly effects skeletal muscle and leads to weight gain, triggers lipogenesis and metabolic disorders.

Comparative Evaluation of RNAlater Solution and Snap Frozen Methods for Gene Expression Studies in Different Tissues

Introduction: Freezing of tissues with liquid nitrogen is the most common method in studies performed at the RNA level. However, the use of RNA stabilization solutions has become a popular alternative method. The aim of this study is to investigate the effectiveness of RNAlater on RNA stabilization in different tissues.

Material and Methods: In this study, RNA were isolated from the lung, heart, liver and skeletal muscle tissues of rats that were frozen with liquid nitrogen (snap frozen, SF group) or stored in RNAlater solution (RL group), and the changes in concentration, purity, reference genes expression, and fold-change levels between groups were analyzed.

Results: In the RL group, the concentration of RNA isolated from the liver tissues was higher (P<0.05), whereas the A260/280 ratio was lower in the heart and liver tissues (P<0.05). PPIA and SRP72 genes were found to have lower Ct values in the heart tissues of rats in the RL group (P<0.05 and P<0.001, respectively) than the SF group. Expression levels of PPIA, ACTB, and SRP72 genes across the tissues were found to be different between the groups (P<0.05). The gene expression level examined in terms of fold-change was significantly different in the RL group (upregulated up to 4 folds and downregulated about 0.5 fold) (P< 0.05).

Conclusions: The results showed that RNAlater can maintain the RNA integrity and can also change the results of gene expression because it does not inhibit biological activity. The snap freezing method is more reliable because gene expression is more stable in tissues frozen with liquid nitrogen.

Reference Gene Validation in the Brain Regions of Young Rats after Pentylenetetrazole-Induced Seizures

Reverse transcription followed by quantitative polymerase chain reaction (qRT-PCR) is a powerful and commonly used tool for gene expression analysis. It requires the right choice of stably expressed reference genes for accurate normalization. In this work, we aimed to select the optimal reference genes for qRT-PCR normalization within different brain areas during the first week following pentylenetetrazole-induced seizures in immature (P20–22) Wistar rats. We have tested the expression stability of a panel of nine housekeeping genes: Actb, Gapdh, B2m, Rpl13a, Sdha, Ppia, Hprt1, Pgk1, and Ywhaz. Based on geometric averaging of ranks obtained by four common algorithms (geNorm, NormFinder, BestKeeper, Comparative Delta-Ct), we found that the stability of tested reference genes varied significantly between different brain regions. The expression of the tested panel of genes was very stable within the medial prefrontal and temporal cortex, and the dorsal hippocampus. However, within the ventral hippocampus, the entorhinal cortex and amygdala expression levels of most of the tested genes were not steady. The data revealed that in the pentylenetetrazole-induced seizure model in juvenile rats, Pgk1, Ppia, and B2m expression are the most stable within the medial prefrontal cortex; Ppia, Rpl13a, and Sdha within the temporal cortex; Pgk1, Ppia, and Rpl13a within the entorhinal cortex; Gapdh, Ppia, and Pgk1 within the dorsal hippocampus; Rpl13a, Sdha, and Ppia within the ventral hippocampus; and Sdha, Pgk1, and Ppia within the amygdala. Our data indicate the need for a differential selection of reference genes across brain regions, including the dorsal and ventral hippocampus.

Reporting Guidelines, Review of Methodological Standards, and Challenges Toward Harmonization in Bone Marrow Adiposity Research. Report of the Methodologies Working Group of the International Bone Marrow Adiposity Society

The interest in bone marrow adiposity (BMA) has increased over the last decade due to its association with, and potential role, in a range of diseases (osteoporosis, diabetes, anorexia, cancer) as well as treatments (corticosteroid, radiation, chemotherapy, thiazolidinediones). However, to advance the field of BMA research, standardization of methods is desirable to increase comparability of study outcomes and foster collaboration. Therefore, at the 2017 annual BMA meeting, the International Bone Marrow Adiposity Society (BMAS) founded a working group to evaluate methodologies in BMA research. All BMAS members could volunteer to participate. The working group members, who are all active preclinical or clinical BMA researchers, searched the literature for articles investigating BMA and discussed the results during personal and telephone conferences. According to the consensus opinion, both based on the review of the literature and on expert opinion, we describe existing methodologies and discuss the challenges and future directions for (1) histomorphometry of bone marrow adipocytes, (2) ex vivo BMA imaging, (3) in vivo BMA imaging, (4) cell isolation, culture, differentiation and in vitro modulation of primary bone marrow adipocytes and bone marrow stromal cell precursors, (5) lineage tracing and in vivo BMA modulation, and (6) BMA biobanking. We identify as accepted standards in BMA research: manual histomorphometry and osmium tetroxide 3D contrast-enhanced μCT for ex vivo quantification, specific MRI sequences (WFI and H-MRS) for in vivo studies, and RT-qPCR with a minimal four gene panel or lipid-based assays for in vitro quantification of bone marrow adipogenesis. Emerging techniques are described which may soon come to complement or substitute these gold standards. Known confounding factors and minimal reporting standards are presented, and their use is encouraged to facilitate comparison across studies. In conclusion, specific BMA methodologies have been developed. However, important challenges remain. In particular, we advocate for the harmonization of methodologies, the precise reporting of known confounding factors, and the identification of methods to modulate BMA independently from other tissues. Wider use of existing animal models with impaired BMA production (e.g., Pfrt^-/-, Kit^W/W-v) and development of specific BMA deletion models would be highly desirable for this purpose.

Identification of Suitable Reference Genes for Quantitative Gene Expression Analysis in Innervated and Denervated Adipose Tissue from Cafeteria Diet-Fed Rats

Our previous studies show that cafeteria diet increases body adiposity, plasma insulin levels, and sympathetic activity to brown adipose tissue (BAT) and white adipose tissue (WAT) of Wistar rats, leading to rapid and progressive changes in the metabolic profile. The identification of suitable reference genes that are not affected by the experimental conditions is a critical step in accurate normalization of the reverse transcription quantitative real-time PCR (qRT-PCR), a commonly used assay to elucidate changes in the gene expression profile. In the present study, the effects of the cafeteria diet and sympathetic innervation on the gene expression of adrenoceptor beta 3 (Adrb3) from BAT and WAT were assessed using one of the most stable and one of the least stable genes as normalizers. Rats were fed the cafeteria diet and on the 17th day, interscapular BAT or retroperitoneal WAT was denervated and, 7 days after surgery, the contralateral innervated tissue was used as control. Ten reference genes were evaluated (18S, B2m, Actb, CypA, Gapdh, Hprt1, Rpl32, Tbp, Ubc, and Ywhaz) and ranked according to their stability using the following algorithms: geNorm, NormFinder, BestKeeper, and comparative delta threshold cycle (ΔC _t ) method. According to the algorithms employed, the normalization of Adrb3 expression by the least stable genes produced opposite results compared with the most stable genes and literature data. In cafeteria and control diet-fed rats, the three most stable genes were Hprt1, Tbp, and Rpl32 for interscapular BAT and Tbp, B2m, and Hprt1 for retroperitoneal WAT, while the least stable genes were 18S, Actb, and Gapdh for both tissues.

Reliable reference genes for expression analysis of proliferating and adipogenically differentiating human adipose stromal cells

Background

The proliferation and adipogenic differentiation of adipose stromal cells (ASCs) are complex processes comprising major phenotypical alterations driven by up- and downregulation of hundreds of genes. Quantitative RT-PCR can be employed to measure relative changes in the expression of a gene of interest. This approach requires constitutively expressed reference genes for normalization to counteract inter-sample variations due to differences in RNA quality and quantity. Thus, a careful validation of quantitative RT-PCR reference genes is needed to accurately measure fluctuations in the expression of genes. Here, we evaluated candidate reference genes applicable for quantitative RT-PCR analysis of gene expression during proliferation and adipogenesis of human ASCs with the immunophenotype DLK1⁺/CD34⁺/CD90⁺/CD105⁺/CD45⁻/CD31⁻.

Methods

We evaluated the applicability of 10 candidate reference genes (GAPDH, TBP, RPS18, EF1A, TFRC, GUSB, PSMD5, CCNA2, LMNA and MRPL19) using NormFinder, geNorm and BestKeeper software.

Results

The results indicate that EF1A and MRPL19 are the most reliable reference genes for quantitative RT-PCR analysis of proliferating ASCs. PSMD5 serves as the most reliable endogenous control in adipogenesis. CCNA2 and LMNA were among the least consistent genes.

Conclusions

Applying these findings for future gene expression analyses will help elucidate ASC biology.

Electronic supplementary material

The online version of this article (10.1186/s11658-019-0140-6) contains supplementary material, which is available to authorized users.