Differences In Gene Expression Levels Research Articles

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein coexpression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship.

Physiological and transcriptomic strategies related to photosynthesis of rice in response to vanadium stress

Vanadium (V) is recognized as an environmental contaminant that affects plant growth and development. However, the photosynthetic response of plants to V stress at molecular level remains unclear. In this study, we examined the photosynthetic responses of two rice varieties (Oryza sativa L.) with diverse V tolerance under various V levels (0, 10, 20, 30, and 40 mg L−1) using physiological, cytological, and transcriptomic approaches. Our findings indicated that V stress significantly reduced the photosynthetic rate and chlorophyll content in both genotypes, with the V-sensitive rice displaying a more pronounced reduction. Furthermore, we observed numerous plastoglobuli, deformed stroma, and ruptured thylakoid membranes in the chloroplasts of the V-sensitive rice. In transcriptome analysis, we found 34 differentially expressed genes of 21 enzymes potentially affect chlorophyll metabolism. Among them, most of the genes involved in chlorophyll biosynthesis and phototoxic intermediate degradation were down-regulated under V stress, while chlorophyll degradation-related genes exhibited up-regulation. In addition, the different expression levels of genes encoding uroporphyrinogen III synthase (UROS), protoporphyrinogen oxidase (PPO), chlorophyllase (CLH), pheophorbide a oxygenase (PAO), and red chlorophyll catabolite reductase (RCCR) between the two rice varieties may indicate a potential tolerance mechanism in rice plants in response to V stress. Overall, this study contributes to our understanding of the molecular mechanisms underlying plant tolerance to V toxicity, while also highlighting potential targets for improving plant tolerance in V-contaminated soils.

298 Differential Gene Expression Underlying Glioma Related Epilepsy

INTRODUCTION: Seizures are a common sequalae for patients suffering from gliomas. There are several factors, such as molecular characteristics, known to influence the initiation of seizures that may ultimately drive tumor growth. However, different levels of gene expression associated with seizures for gliomas remain unclear. Here, we review current literature and analyze RNA sequencing of gliomas to further probe these differences. METHODS: Utilizing total RNA sequencing obtained from The Cancer Genome Atlas - Lower Grade Glioma to identify and characterize differential expression in patients that do and do not experience seizures. Utilizing QIAGEN Ingenuity Pathways Analysis (IPA), we identified canonical and functional pathways to further characterize differential expression. RESULTS: From 289 patients with gliomas, 83 (28.7%) had available information regarding seizures and other variables of interest. Of these, 50 (60.2%) were allocated to the seizure group and the remaining 33 (39.8%) to the non-seizure group. There were no statistically significant differences in age (p = 0.4661), sex (p = -0.1338), race/ethnicity (p = 0.7331), molecular subtype (0.8656), tumor grade (p = 0.2260), or anatomical location. When comparing the level of RNA expression from these tumors between the seizure and non-seizure groups, we identified 52 genes that were significantly differentially regulated. Critical canonical pathways were identified, most significantly RHOGDI and Semaphorin Neuronal Repulsive signaling.Finally, in the functional analysis, tumors that promoted seizures had gene sets that were significantly increased involving neuronal differentiation and synaptogenesis. CONCLUSIONS: In the setting of gliomas, differences in tumor gene expression exist between individuals with seizures and without seizures despite similarities in patient demographics and other tumor characteristics. There was significant difference in gene expression that were most associated with neuron development and synaptogenesis, ultimately suggesting a mechanistic role of a tumor-neuron synapse in seizure initiation and potentially tumor growth.

Anti-Obesity Effect of a Tea Mixture Nano-Formulation on Rats Occurs via the Upregulation of AMP-Activated Protein Kinase/Sirtuin-1/Glucose Transporter Type 4 and Peroxisome Proliferator-Activated Receptor Gamma Pathways.

White, green, and oolong teas are produced from the tea plant (Camellia sinensis (L.) Kuntze) and are reported to have anti-obesity and hypolipidemic effects. The current study aims to investigate the anti-obesity effects of a tea mixture nano-formulation by targeting the AMPK/Sirt-1/GLUT-4 axis in rats. In vitro lipase and α-amylase inhibition assays were used to determine the active sample, which was then incorporated into a nanoparticle formulation subjected to in vivo anti-obesity testing in rats by measuring the expression level of different genes implicated in adipogenesis and inflammation using qRT-PCR. Moreover, metabolomic analysis was performed for each tea extract using LC/ESI MS/MS coupled to chemometrics in an attempt to find a correlation between the constituents of the extracts and their biological activity. The in vitro pancreatic lipase and α-amylase inhibition assays demonstrated more effective activity in the tea mixture than the standards, orlistat and acarbose, respectively, and each tea alone. Thus, the herbal tea mixture and its nanoparticle formulation were evaluated for their in vivo anti-obesity activity. Intriguingly, the tea mixture significantly decreased the serum levels of glucose and triglycerides and increased the mRNA expression of GLUT-4, P-AMPK, Sirt-1, and PPAR-γ, which induce lipolysis while also decreasing the mRNA expression of TNF-α and ADD1/SREBP-1c, thereby inhibiting the inflammation associated with obesity. Our study suggests that the tea mixture nano-formulation is a promising therapeutic agent in the treatment of obesity and may also be beneficial in other metabolic disorders by targeting the AMPK/Sirt-1/Glut-4 pathway.

Differential sense and antisense expression profiles of Syrista parreyssi (Hymenoptera: Cephidae) mitochondrial transcripts.

The transcription of the mitogenome shows a unique pattern that is both similar to and different from the nuclear and bacterial patterns. Mitochondrial transcription generates five polycistronic units from three promoters in Drosophila melanogaster, and different expression levels of genes were observed in both different and, interestingly, the same polycistronic units in D. melanogaster. This study was conducted to test this phenomenon in the mitogenome of Syrista parreyssi (Hymenoptera: Cephidae). RNA isolation and DNase digestion were performed using only one whole individual, and real-time polymerase chain reaction analyses were performed with complementary DNAs of 11 gene regions using gene-specific primers. It was found that the expression level of each gene exhibited differences from each other, and some genes (e.g., cox genes, and rrnS) were interestingly expressed at significant levels in the corresponding antisense chain. Additionally, the mitogenome of S. parreyssi was found to have the capacity to encode 169 additional peptides from 13 known protein-coding genes, most of which were encoded in antisense transcript units. One of the unique findings was a potential open reading frame sequence that was potentially encoded in the antisense rrnL gene and included a conserved cox3 domain.

Analysis of Changes in the Expression of Selected Genes from the ABC Family in Patients with Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) is characterized by a lack of expression of hormone receptors (estrogen and progesterone), as cancer cells also do not overexpress the HER2 receptor. Due to their molecular profile, treatments for this type of breast cancer are limited. In some cases, the pharmacotherapy of patients with TNBC is hindered by the occurrence of multidrug resistance, which is largely conditioned by proteins encoded by genes from the ABC family. The aim of our study was to determine the expression profile of 14 selected genes from the ABC family using real-time PCR in 68 patients with TNBC by comparing the obtained results with clinical data and additionally using bioinformatics tools (Ualcan and The Breast Cancer Gene Expression Miner v4.8 (bc -GenExMiner v4.8)), as well as by comparing experimental data with data in the Cancer Genome Atlas (TCGA) database. Based on the conducted studies, we found different levels of gene expression depending on the age of patients, tumor sizes, metastases to lymph nodes, cell infiltration into adipose tissue, tumor stages, or lymphovascularinvasion. The results of the presented studies demonstrate the effect of the expression level of the studied genes on the clinical course and prognosis of patients with TNBC, and suggest how profiling the expression level of genes from the ABC family may be a useful tool in determining personalized TNBC treatment.

CircROBO1 promotes prostate cancer growth and enzalutamide resistance via accelerating glycolysis.

Background and aim: As non-coding RNAs, circular RNAs (circRNAs) contribute to the progression of malignancies by regulating various biological processes. In prostate cancer, however, there is still a lack of understanding regarding the potential molecular pathways and roles of circRNAs. Methods: Loss-off function experiments were performed to investigate the potential biological function of circRNA in the progression of prostate cancer. Western blot, qRT-PCR, and IHC assay were used to examine the expression level of different genes or circRNAs. Further molecular biology experiments were conducted to uncover the molecular mechanism underlying circRNA in prostate cancer using dual luciferase reporter and RNA immunoprecipitation (RIP) assays. Results: A novel circRNA (hsa_circ_0124696, named circROBO1) was identified as a significantly upregulated circRNA in both prostate cancer cells and tissues. Suppression of circROBO1 significantly attenuated the proliferation of prostate cancer cells. In addition, we found that the knockdown of circROBO1 remarkably increased the sensitivity of prostate cancer to enzalutamide treatment. A deceleration in glycolysis rate was observed after inhibition of circROBO1, which could suppress prostate cancer growth and overcome resistance to enzalutamide. Our results revealed that circROBO1 promotes prostate cancer growth and enzalutamide resistance via accelerating glycolysis. Conclusion: Our study identified the biological role of the circROBO1-miR-556-5p-PGK1 axis in the growth and enzalutamide resistance of prostate cancer, which is the potential therapeutic target of prostate cancer.

MICALL2 as a substrate of ubiquitinase TRIM21 regulates tumorigenesis of colorectal cancer

BackgroundMolecule interacting with CasL-like protein 2 (MICALL2) is believed to regulate cytoskeleton dynamics, tight junction formation, and neurite outgrowth. However, its biological role and the underlying mechanism in colorectal cancer (CRC) remain largely elusive.MethodsqRT-PCR, Western blotting and immunohistochemistry assays were used to detect the expression levels of different genes. Next, mass spectrometry, co-immunoprecipitation and immunofluorescence staining were used to detect the interactions of proteins. Furthermore, MTT assay, colony formation assay, wound-healing assays and xenograft tumor models were performed to demonstrate the functions of MICALL2 in CRC. In addition, transcriptome sequencing and Western blotting were conducted to verify the mechanism of MICALL2 in CRC.ResultsWe found that both mRNA and protein levels of MICALL2 are up-regulated in colorectal cancer tissues compared with non-tumor tissues and that its overexpression is closely correlated with poor prognosis. Ubiquitin E3 ligase Tripartite motif-containing protein 21 (TRIM21) mediated MICALL2 ubiquitination and proteasome-dependent degradation, negatively correlated with MICALL2 levels, and reversely regulated the tumorigenic activity of MICALL2 in CRC. Functional studies confirmed that MICALL2 promoted colorectal cancer cell growth and migration via the Wnt/β-catenin signaling pathway.ConclusionsAs a substrate of ubiquitinase TRIM21, MICALL2 enhances the growth and migration of colorectal cancer cells and activates the Wnt/β-catenin signaling pathway.ETVfCpwrPH62REPkpszJSTVideo abstract

Combined Effects of Temperature and Salinity on Antioxidants in the Immune System of the Pearl Oyster Pinctada fucata

A water environment can impact many physiological processes of aquatic animals. The antioxidant response of immune system of the pearl oyster to temperature and salinity is of great significance to health. This study analyzed the physiological changes and immune responses under different temperature and salinity levels (temperature: 20, 25, and 30 °C; salinity: 23, 28, and 33‰) in the short term (7 d) in the hepatopancreas and other tissues of 405 pearl oysters. The combined effects of temperature and salinity on antioxidants in the immune system of the pearl oyster were evaluated via response surface methodology and Box–Benhnken design (BBD) under laboratory conditions. The secondary effects of salinity on the activities of glutathione peroxidase (GSH-PX), catalase (CAT), and superoxide dismutase (SOD) were significant, and CAT and SOD showed an inverted U-shaped trend with the increase in salinity. Temperature significantly impacted GSH-PX, CAT, glutathione (GSH), and SOD in primary and secondary effects, and the maximum values of CAT, GSH, and SOD were observed. The phenoloxidase (POX) and alkaline phosphatase (AKP) activities increased with the increasing temperatures. The interaction of temperature and salinity was significant on CAT and SOD, but was not significant on GSH-PX. The interaction between salinity and temperature on AKP was significant, which was contrary to the results of AKP in the hemolymph. The expression levels of antioxidant genes varied between tissues, and the expression levels of different genes in the same tissue were different. Appropriate immunity and antioxidant index models were established under the combined temperature and salinity conditions. The optimal combination of temperature and salinity was 24.95 °C and 28.11‰, respectively, and the desirability was 0.803. This study provides theoretical reference points for the pearl oyster to respond to temperature and salinity changes and can be used to establish an index model for shellfish aquaculture.

The Static Magnetic Field Regulates the Structure, Biochemical Activity, and Gene Expression of Plants.

The purpose of this paper is to review the scientific results and summarise the emerging topic of the effects of statistic magnetic field on the structure, biochemical activity, and gene expression of plants. The literature on the subject reports a wide range of possibilities regarding the use of the magnetic field to modify the properties of plant cells. MFs have a significant impact on the photosynthesis efficiency of the biomass and vigour accumulation indexes. Treating plants with SMFs accelerates the formation and accumulation of reactive oxygen species. At the same time, the influence of MFs causes the high activity of antioxidant enzymes, which reduces oxidative stress. SMFs have a strong influence on the shape of the cell and the structure of the cell membrane, thus increasing their permeability and influencing the various activities of the metabolic pathways. The use of magnetic treatments on plants causes a higher content of proteins, carbohydrates, soluble and reducing sugars, and in some cases, lipids and fatty acid composition and influences the uptake of macro- and microelements and different levels of gene expression. In this study, the effect of MFs was considered as a combination of MF intensity and time exposure, for different varieties and plant species. The following article shows the wide-ranging possibilities of applying magnetic fields to the dynamics of changes in the life processes and structures of plants. Thus far, the magnetic field is not widely used in agricultural practice. The current knowledge about the influence of MFs on plant cells is still insufficient. It is, therefore, necessary to carry out detailed research for a more in-depth understanding of the possibilities of modifying the properties of plant cells and achieving the desired effects by means of a magnetic field.

The hyaluronan-related genes HAS2, HYAL1-4, PH20 and HYALP1 are associated with prognosis, cell viability and spheroid formation capacity in ovarian cancer

PurposeHyaluronan modulates tumour progression, including cell adhesion, cohesion, proliferation and invasion, and the cancer stem cell phenotype. In ovarian cancer, high levels of stromal hyaluronan are associated with poor prognosis. In this work, hyaluronan synthases (HAS1-3) and hyaluronidases (HYAL1-4, PH-20, HYALP1) were examined with regard to different levels of gene expression and its influence on ovarian cancer patients’ survival. The impact of a siRNA depletion of HAS2 was investigated in vitro.MethodsUsing the Kaplan–Meier Plotter tool, we investigated the influence of hyaluronic synthases and hyaluronidases on the survival of a collective of 1435 ovarian cancer patients. Differences in gene expression between normal (n = 46) and cancerous (n = 744) ovarian tissue were examined using the TNMplot database. Following an evaluation of hyaluronan-related gene expression in the ATCC ovarian cancer panel, we studied SKOV3 and SW 626 ovarian cancer cells subjected to HAS2 siRNA or control siRNA treatment in terms of HAS1-3, HYAL2 and HYAL3 mRNA expression. We investigated the ability to form spheroids using the Hanging Drop method and the response to chemotherapy at different concentrations using the MTT Assay. By STRING analysis, interactions within the enzymes of the hyaluronic acid system and with binding partners were visualized.ResultsHAS1, HYAL1 and HYAL4 mRNA expression is significantly upregulated, whereas HAS2, HYAL2 and HYAL3 mRNA expression is significantly downregulated in ovarian cancer tissue compared to controls. HAS2 improves cell viability, the capability to form tumour spheroids and has a negative prognostic value regarding overall survival. Lower HAS2 expression and high expression of HYAL2 and HYAL3 favours the survival of ovarian cancer patients. HAS2 knockdown cells and control cells showed a moderate response to combinatorial in vitro chemotherapy with taxol and cisplatin.ConclusionIn conclusion, our study shows that the hyaluronic acid system has a relevant influence on the survival of ovarian cancer patients and could therefore be considered as a possible prognostic factor.

Long noncoding RNA ST8SIA6-AS1 promotes cell proliferation and metastasis in triple-negative breast cancer by targeting miR-145-5p/CDCA3 to inactivate the p53/p21 signaling pathway.

Triple-negative breast cancer (TNBC), the most aggressive subtype of breast cancer, always exhibits a poor prognosis due to high risk of early recurrence and distant metastasis. Long noncoding RNAs (lncRNAs) have been reported as crucial regulators in breast cancer. However, the functions and action mechanisms of lncRNA ST8SIA6-AS1 in TNBC are largely unknown. Quantitative real-time PCR and western blot assays were used to measure the expression levels of different genes and proteins. Cell proliferation ability was monitored by CCK-8, colony forming and flow cytometry assays. Wound healing and transwell assays were performed to evaluate cell migration and invasion. The regulatory mechanisms of ST8SIA6-AS1 in TNBC were confirmed by dual luciferase reporter and RIP assays. A mouse xenograft model was established to investigate the role of ST8SIA6-AS1 in TNBC tumor growth. ST8SIA6-AS1 displayed a higher expression in TNBC cells. Silencing ST8SIA6-AS1 impaired cell proliferation, cell cycle progression, migration, and invasion in vitro, and slowed tumor growth in vivo. Mechanistically, ST8SIA6-AS1 could facilitate the expression of its target CDCA3 (cell division cycle associated protein 3) and inactivate the p53/p21 signaling by inhibiting miR-145-5p. Moreover, miR-145-5p exerted a tumor-suppressive activity by targeting CDCA3. The tumor-suppressive effects induced by ST8SIA6-AS1 knockdown were abated by the down-regulation of miR-145-5p or the up-regulation of CDCA3. ST8SIA6-AS1 exerts an oncogenic role in TNBC by interacting with miR-145-5p to up-regulate CDCA3 expression and inactivate the p53/p21 signaling, highlighting ST8SIA6-AS1 as a promising molecular target to combat TNBC.

Breast Cancer Genomics: Primary and Most Common Metastases.

Simple SummaryBreast cancer is a heterogeneous disease, and numerous associated genetic alterations have been identified. Knowledge of driver and other associated mutations has progressed significantly in recent years, secondarily to advances in gene sequencing. This manuscript provides an overview of genetic alterations in both primary and metastatic breast cancer.Specific genomic alterations have been found in primary breast cancer involving driver mutations that result in tumorigenesis. Metastatic breast cancer, which is uncommon at the time of disease onset, variably impacts patients throughout the course of their disease. Both the molecular profiles and diverse genomic pathways vary in the development and progression of metastatic breast cancer. From the most common metastatic site (bone), to the rare sites such as orbital, gynecologic, or pancreatic metastases, different levels of gene expression indicate the potential involvement of numerous genes in the development and spread of breast cancer. Knowledge of these alterations can, not only help predict future disease, but also lead to advancement in breast cancer treatments. This review discusses the somatic landscape of breast primary and metastatic tumors.

Canonical, and Multistranded, Alternative and Transitional Helical (C‐MATH) Nucleic Acid Microarrays: Next Generation Double‐, and Four‐Stranded DNA and RNA Microarrays

Many different types of nucleic acids, with unique structures, play important roles in prokaryotic and eukaryotic regulation of an organisms genome, e.g., canonical double‐stranded (ds‐) right‐handed B‐DNA, alternative left‐handed ds‐Z‐DNA, triplex DNA, G4‐quadruplex DNA, i‐motif DNA, slipped‐strand DNA and cruciform DNA. These canonical and exotic (e.g., Z‐DNA, and four‐stranded G4‐quadruplex DNA) nucleic acid structures also regulate many different pathological conditions. The application of exotic nucleic acids, based on its structure, has not been applied to commercial, conventional DNA microarrays. Conventional DNA microarrays are powerful tools that allow for gene expression studies, however, they have severe limitations. The basic principle behind conventional DNA microarrays is that complementary sequences of DNA molecules will bind to each other. Commercial DNA microarrays measure the relative abundance of mRNA sequences isolated from cells by taking advantage of complementary DNA base pairing. Researchers employ DNA microarrays to quantify the different levels of gene expression involving very large numbers of genes simultaneously, or to genotype numerous areas of an organisms genomic makeup. DNA microarrays needs to evolve beyond these limitations. The novel, next generation DNA and RNA microarrays, i.e., Canonical, and Multistranded, Alternative and Transitional Helical (C‐MATH) Nucleic Acid Microarrays, allow for a completely different approach to studying gene expression [e.g., genes (B‐DNA, Z‐DNA) and telomers (G4‐quadruplex DNA)], based on the different structure of ds‐DNA and RNA, and multi‐stranded DNA and RNA molecules. It also allows for the characterization of different drugs and biologics that can directly bind to nucleic acids and inhibit gene expression (or enhance it). C‐MATH DNA microarrays can enhance the “drug discovery” part of “drug discovery and development”, resulting in new drugs, new uses for old drugs and lower coast for drug‐based research. Recent advances in the novel C‐MATH nucleic acid microarrays allow for more precise quantification of multiple fluorescent signals coming from a single immobilized DNA molecule (fluorescently labelled), i.e., B‐DNA, Z‐DNA and G4‐quadruplex DNA. Fluorescent and colorimetric DNA microarrays scanners were employed. The C‐MATH microarrays allow for superior analysis of colocalization, and permits competitive binding assays involving two or more fluorescently labelled drugs or biologicals binding to a gene sequence. Positive and negative controls involve direct binding by DNA‐binding chemicals and anti‐DNA antibodies. Conventional image analysis software was used, along with the development of novel algorithms to differentiate multiple fluorescence signals and intensity. The C‐MATH DNA and RNA microarrays will allow for development of new classes of DNA and RNA structure‐based drugs, and biologics (e.g., antibody, transcription factors), i.e., sequence‐specific and non‐sequence‐specific DNA and RNA binding therapeutics. Additionally, it will also allow for characterization of nucleic acids under different environmental conditions similar to a cell.

Mechanisms underlying DMARD inefficacy in difficult-to-treat rheumatoid arthritis: a narrative review with systematic literature search.

Management of RA patients has significantly improved over the past decades. However, a substantial proportion of patients is difficult-to-treat (D2T), remaining symptomatic after failing biological and/or targeted synthetic DMARDs. Multiple factors can contribute to D2T RA, including treatment non-adherence, comorbidities and co-existing mimicking diseases (e.g. fibromyalgia). Additionally, currently available biological and/or targeted synthetic DMARDs may be truly ineffective (‘true’ refractory RA) and/or lead to unacceptable side effects. In this narrative review based on a systematic literature search, an overview of underlying (immune) mechanisms is presented. Potential scenarios are discussed including the influence of different levels of gene expression and clinical characteristics. Although the exact underlying mechanisms remain largely unknown, the heterogeneity between individual patients supports the assumption that D2T RA is a syndrome involving different pathogenic mechanisms.

NEIL3-deficient bone marrow displays decreased hematopoietic capacity and reduced telomere length

Deficiency of NEIL3, a DNA repair enzyme, has significant impact on mouse physiology, including vascular biology and gut health, processes related to aging. Leukocyte telomere length (LTL) is suggested as a marker of biological aging, and shortened LTL is associated with increased risk of cardiovascular disease. NEIL3 has been shown to repair DNA damage in telomere regions in vitro. Herein, we explored the role of NEIL3 in telomere maintenance in vivo by studying bone marrow cells from atherosclerosis-prone NEIL3-deficient mice. We found shortened telomeres and decreased activity of the telomerase enzyme in bone marrow cells derived from Apoe−/−Neil3−/− as compared to Apoe−/− mice. Furthermore, Apoe−/−Neil3−/− mice had decreased leukocyte levels as compared to Apoe−/− mice, both in bone marrow and in peripheral blood. Finally, RNA sequencing of bone marrow cells from Apoe−/−Neil3−/− and Apoe−/− mice revealed different expression levels of genes involved in cell cycle regulation, cellular senescence and telomere protection. This study points to NEIL3 as a telomere-protecting protein in murine bone marrow in vivo.

Comparative expression of genes implicated in lipid metabolism in different tissues of Barbari goats

The expression of genes linked to lipid metabolism mainly in lipogenesis, lipid transport and deposition contributes to the quality and composition of fat/lipids in the tissues. The present study investigated the expression changes in genes implicated in lipid biosynthesis (AGPAT2, DGAT2, FASN and GPAM), transport of fatty acids (FABP3) and lipid deposition (PLIN4) in muscles, liver, pancreas and kidney of Barbari goats. Real time quantitative PCR (polymerase chain reaction) analysis was used to estimate the expression level of different genes in the tissue samples. The expression of AGPAT2, DGAT2 and GPAM genes was higher in the liver while FASN was significantly (p<0.01) higher in skeletal muscles. FABP3 gene that coordinates transportation and signalling of lipids, as well as PLIN4 associated with fat deposition were mainly expressed in the muscles. The present study offers insight into the differential expression of genes involved in lipid metabolism in different tissues of Barbari goat.

Control of Gene Expression With Quercetin-Responsive Modular Circuits.

Control of gene expression is crucial for several biotechnological applications, especially for implementing predictable and controllable genetic circuits. Such circuits are often implemented with a transcriptional regulator activated by a specific signal. These regulators should work independently of the host machinery, with low gratuitous induction or crosstalk with host components. Moreover, the signal should also be orthogonal, recognized only by the regulator with minimal interference with the host operation. In this context, transcriptional regulators activated by plant metabolites as flavonoids emerge as candidates to control gene expression in bacteria. However, engineering novel circuits requires the characterization of the genetic parts (e.g., genes, promoters, ribosome binding sites, and terminators) in the host of interest. Therefore, we decomposed the QdoR regulatory system of B. subtilis, responsive to the flavonoid quercetin, and reassembled its parts into genetic circuits programmed to have different levels of gene expression and noise dependent on the concentration of quercetin. We showed that only one of the promoters regulated by QdoR worked well in E. coli, enabling the construction of other circuits induced by quercetin. The QdoR expression was modulated with constitutive promoters of different transcriptional strengths, leading to low expression levels when QdoR was highly expressed and vice versa. E. coli strains expressing high and low levels of QdoR were mixed and induced with the same quercetin concentration, resulting in two stable populations expressing different levels of their gene reporters. Besides, we demonstrated that the level of QdoR repression generated different noise levels in gene expression dependent on the concentration of quercetin. The circuits presented here can be exploited in applications requiring adjustment of gene expression and noise using a highly available and natural inducer as quercetin.

Genetic and Epigenetic Alterations Induced by Pesticide Exposure: Integrated Analysis of Gene Expression, microRNA Expression, and DNA Methylation Datasets

Environmental or occupational exposure to pesticides is considered one of the main risk factors for the development of various diseases. Behind the development of pesticide-associated pathologies, there are both genetic and epigenetic alterations, where these latter are mainly represented by the alteration in the expression levels of microRNAs and by the change in the methylation status of the DNA. At present, no studies have comprehensively evaluated the genetic and epigenetic alterations induced by pesticides; therefore, the aim of the present study was to identify modifications in gene miRNA expression and DNA methylation useful for the prediction of pesticide exposure. For this purpose, an integrated analysis of gene expression, microRNA expression, and DNA methylation datasets obtained from the GEO DataSets database was performed to identify putative genes, microRNAs, and DNA methylation hotspots associated with pesticide exposure and responsible for the development of different diseases. In addition, DIANA-miRPath, STRING, and GO Panther prediction tools were used to establish the functional role of the putative biomarkers identified. The results obtained demonstrated that pesticides can modulate the expression levels of different genes and induce different epigenetic alterations in the expression levels of miRNAs and in the modulation of DNA methylation status.

Effective and Ineffective Samples of Mesenchymal Multipotent Stromal Cells Used for Acute Graft-Versus-Host Disease Prophylaxis after Allogeneic Bone Marrow Transplantation Differ in the Expression Level of HLA-DR When Co-Cultured with Activated Lymphocytes

IntroductionMultipotent mesenchymal stromal cells (MSCs) are widely used for the prevention and treatment of acute graft versus host disease (aGVHD) after allogeneic bone marrow transplantation (allo-BMT). In some cases prophylaxis of aGVHD failed. The reasons of the failure could be either the result of particular qualities of donor-recipient interaction, patient status or differences in MSC samples. In order to discriminate effective and ineffective for aGVHD prophylaxis MSCs the growth and differentiation characteristics, relative expression levels of different genes and changes in the expression of surface MSC molecules during co-cultivation with activated lymphocytes were investigated in all MSC samples.MethodsMSCs from the bone marrow of corresponding hematopoietic stem cells donor were injected into 59 patients after allo-BMT at the moment of blood count recovery. MSCs from the bone marrow of those donors were analyzed by cultivation in standard conditions (aMEM, 10% fetal calf serum) for 3 passages. Relative expression level (REL) of 30 genes involved in proliferation, differentiation and immunomodulation was estimated by RT-qPCR in all MSC samples. MSCs were seeded 105 cells per T25 flask, and then 106 allogeneic lymphocytes from single donor were added to all MSCs cultures. For lymphocytes activation 5 mg/ml phytohemagglutinin (PHA) was added to half of these cultures. Lymphocytes were removed from MSCs on 1st and 4th days of co-cultivation. Than trypsinized MSCs were collected from the bottom of the flask and expression of HLA-DR, HLA-ABC, CD73, PD-L1, CD54, CD80, CD86, CD105, CD146 and FAS-L on their surface was measured by flow cytometry. p<0.05 was considered statistically significant, all data is present as medium ± SEM.ResultsThe injection of MSCs reduced the incidence of aGVHD 2 times and increased the 5 years overall survival of patients (p=0.047). Eight of 51 MSC samples had been ineffective for preventing aGVHD. Analysis of individual donor characteristics (gender, age, body mass index) found no significant differences between the MSCs, effective and ineffective for preventing aGVHD. REL analysis of 30 genes involved in proliferation, differentiation and immunomodulation in MSCs reviled only 4 genes differs significantly between effective and ineffective MSC samples (table). During 4 days of cultivation the MFI of HLA-DR did not change on MSCs. When MSCs co-cultivated with non-activated lymphocytes for 4 days MFI of HLA-DR increased only in 1.3 fold (p=0.03). Co-cultivation of MSCs with activated lymphocytes led to 7 fold increases in HLA-DR expression between 1st and 4th days (p≤0,001). On 4th day of co-cultivation MSCs with activated lymphocytes the MFI of HLA-DR was 3 fold lower in ineffective MSC samples than in effective (table). These data indicate that the effectiveness of MSCs used depends on the degree of their immunogenicity and, accordingly, on the immunomodulating potential. Among studied molecules only Fas L was significantly lower in effective MSC samples than in ineffective (table). It is possible that such MSC samples survived in the organism better than ineffective and their immunomodulating function lasts longer in the organism.ConclusionsIn summary, this study showed that MSC injections resulted in a significant 2-fold decrease in aGvHD development compared with the standard prophylaxis treatment. When compared with ineffective MSC, effective MSC samples are characterized by higher total cell production and REL of CFH, FGFR1, PDGFRa, and ICAM1. ExpressionofHLA-DR increased significantly in MSCs co-cultivated with lymphocytes, so these cells became immunogenic in organism. It is evident that the level of HLA-DR expression on MSCs important for MSCs efficiency in aGVHD prophylaxis. It is possible to predict efficiency of MSCs injection by simple test of co-cultivation of these cells with activated lymphocytes and measuring the expression level of HLA-DR on them.The materials are supported by grant from the Russian Science Foundation, Project № 16-15-00102 [Display omitted] DisclosuresShipounova:Russian Foundation for Basic Research, Project № 15-04-02514: Research Funding.