Expression Of Housekeeping Genes Research Articles

New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity.

In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to the chromatin, an interaction that is essential for the functional activity of promoters and insulators. In this study, we describe a new architectural C2H2 protein called Madf and Zinc-Finger Protein 1 (Mzfp1) that interacts with CP190. Mzfp1 has an unusual structure that includes six C2H2 domains organized in a C-terminal cluster and two tandem MADF domains. Mzfp1 predominantly binds to housekeeping gene promoters located in both euchromatin and heterochromatin genome regions. In vivo mutagenesis studies showed that Mzfp1 is an essential protein, and both MADF domains and the CP190 interaction region are required for its functional activity. The C2H2 cluster is sufficient for the specific binding of Mzfp1 to regulatory elements, while the second MADF domain is required for Mzfp1 recruitment to heterochromatin. Mzfp1 binds to the proximal part of the Fub boundary that separates regulatory domains of the Ubx and abd-A genes in the Bithorax complex. Mzfp1 participates in Fub functions in cooperation with the architectural proteins Pita and Su(Hw). Thus, Mzfp1 is a new architectural C2H2 protein involved in the organization of active promoters and insulators in Drosophila.

Genomic context- and H2AK119 ubiquitination-dependent inheritance of human Polycomb silencing.

Polycomb repressive complexes 1 and 2 (PRC1 and 2) are required for heritable repression of developmental genes. The cis- and trans-acting factors that contribute to epigenetic inheritance of mammalian Polycomb repression are not fully understood. Here, we show that, in human cells, ectopically induced Polycomb silencing at initially active developmental genes, but not near ubiquitously expressed housekeeping genes, is inherited for many cell divisions. Unexpectedly, silencing is heritable in cells with mutations in the H3K27me3 binding pocket of the Embryonic Ectoderm Development (EED) subunit of PRC2, which are known to disrupt H3K27me3 recognition and lead to loss of H3K27me3. This mode of inheritance is less stable and requires intact PRC2 and recognition of H2AK119ub1 by PRC1. Our findings suggest that maintenance of Polycomb silencing is sensitive to local genomic context and can be mediated by PRC1-dependent H2AK119ub1 and PRC2 independently of H3K27me3 recognition.

Modified in-vitro AATCC-100 procedure to measure viable bacteria from wound dressings.

Chronic wounds are reoccurring healthcare problems in the United States and cost up to $50 billion annually. Improper wound care results in complications such as wound debridement, surgical amputation, and increased morbidity/ mortality due to opportunistic infections. To eliminate wound infections, many antimicrobial dressings are developed and submitted to FDA for evaluation. AATCC-100 is a standard method widely used to evaluate cloth wound dressings. This method, requires enrichment, followed by culturing to measure the concentration of culturable organisms; a caveat to this method could result in neglected viable but nonculturable (VBNC) bacteria and overestimate the antimicrobial properties of wound dressings. Therefore, the objectives of this study were to assess this accepted protocol with quantitative real-time polymerase chain reaction (qRT-PCR), to measure time dependent antimicrobial efficacy of wound dressing, and to examine for potential viable bacteria but non-culturable as compared with traditional plating methods. The test organisms included opportunistic pathogens: Pseudomonas aeruginosa (ATCC 15692) and Staphylococcus aureus (ATCC 43300). To mimic a wound dressing environment, samples of commercially available wound dressings (McKesson Inc.) with silver ion (positive control) and dressings without silver ion (positive control) were assessed under sterile conditions. All samples were examined by the original protocol (the extended AATCC-100 method) and qRT-PCR. The expression of specific housekeeping genes was measured (proC for P. aeruginosa and 16s rRNA for S. aureus). Based on these tests, log reduction of experimental conditions was compared to identify time dependent and precise antimicrobial properties from wound dressing samples. These results showed antimicrobial properties of wound dressings diminished as incubation days are increased for both methods from day 1 PCR result of 4.31 ± 0.54 and day 1 plating result of 6.31 ± 3.04 to day 3 PCR result of 1.22 ± 0.97 and day 3 plating result of 5.89 ± 2.41. These results show that data from qRT-PCR generally produced lower standard deviation than that of culture methods, hence shown to be more precise. Complementary parallel analysis of samples using both methods better characterized antimicrobial properties of the tested samples.

Reference Gene Validation in the Embryonic and Postnatal Brain in the Rat Hyperhomocysteinemia Model.

Maternal hyperhomocysteinemia (HCY) induced by genetic defects in methionine cycle enzymes or vitamin imbalance is known to be a pathologic factor that can impair embryonal brain development and cause long-term consequences in the postnatal brain development as well as changes in the expression of neuronal genes. Studies of the gene expression on this model requires the selection of optimal housekeeping genes. This work aimed to analyze the expression stability of housekeeping genes in offspring brain. Pregnant female Wistar rats were treated daily with a 0.15% L-methionine solution in the period starting on the 4th day of pregnancy until delivery, to cause the increase in the homocysteine level in fetus blood and brain. Housekeeping gene expression was assessed by RT-qPCR on whole embryonic brain and selected rat brain areas at P20 and P90. The amplification curves were analyzed, and raw means Cq data were imported to the RefFinder online tool to assess the reference genes stability. Most of the analyzed genes showed high stability of mRNA expression in the fetal brain at both periods of analysis (E14 and E20). However, the most stably expressed genes at different age points differed. Actb, Ppia, Rpl13a are the most stably expressed on E14, Ywhaz, Pgk1, Hprt1 - on E20 and P20, Hprt1, Actb, and Pgk1 - on P90. Gapdh gene used as a reference in various studies demonstrates high stability only in the hippocampus and cannot be recommended as the optimal reference gene on HCY model. Hprt1 and Pgk1 genes were found to be the most stably expressed in the brain of rat subjected to HCY. These two genes showed high stability in the brain on E20 and in various areas of the brain on the P20 and P90. On E14, the preferred genes for normalization are Actb, Ppia, Rpl13a.

Differential responses of hepatopancreas transcriptome between fast and slow growth in giant freshwater prawns (Macrobrachium rosenbergii) fed a plant-based diet

Efficient utilisation of plant-based diets in the giant freshwater prawn, Marcrobrachium rosenbergii, varies according to individual, suggesting that it might be associated with differences in physiological and metabolic responses. Therefore, we aimed to investigate the individual differences in the growth response of shrimp fed to a soybean-based diet (SBM). Two hundred shrimp were fed SBM for 90 days, and specific growth rate (SGR) was determined individually. Fast- and slow-growing shrimp (F-shrimp vs. S-shrimp), with the highest and lowest 5% SGRs, respectively, were sampled to determine haemolymph chemistry and carcass composition. The hepatopancreas of these shrimps were used for transcriptome analysis through RNA sequencing (RNA-Seq). The results showed no significant differences in haemolymph chemistry parameters. In terms of carcass proximate composition, F-shrimp exhibited higher protein composition than did S-shrimp, suggesting that F-shrimp have higher protein anabolism. Using RNA-seq and real-time reverse transcription polymerase chain reaction (qRT-PCR), the expression levels of several genes encoding physiologic and metabolic enzymes were found to be upregulated in F-shrimp compared to in S-shrimp, suggesting that these enzymes/proteins mediated the efficient use of SBM-based diets for growth promotion in shrimp. Various DEGs associated with the immune system were observed, indicating a difference in immune processes between F- and S-shrimp. The expression of several housekeeping genes was found to be upregulated in S-shrimp. Collectively, the upregulated expression of several enzymes associated with physiological and/or metabolic processes and increased protein anabolism may be attributed to the efficient use of SBM for maximal growth in shrimp.

Economy of Effort or Sophisticated Programming? The Prevalence of Bidirectional Promoter Complexes in the Human Genome.

An abundance of antisense promoters in the vicinity of the transcriptional start site of coding genes suggests that they play an important role in gene regulation. The divergent transcription of housekeeping genes by a common central promoter region allows for coordinated regulation of genes in related pathways and is also linked to higher promoter activity. However, closely positioned transcription start sites can also result in competition between overlapping promoter elements and generate a binary switch element. Furthermore, the direct competition resulting from the presence of an antisense promoter immediately downstream of the transcription start site of the gene produces an element that can exist in only one of two stable transcriptional states: sense or antisense. In this review, we summarize analyses of the prevalence of antisense transcription in higher eukaryotes and viruses, with a focus on the antisense promoters competing with the promoters of coding genes. The structures of bidirectional promoters driving the simultaneous expression of housekeeping genes are compared with examples of human bidirectional elements that have been shown to act as switches. Since many bidirectional elements contain a noncoding RNA as the divergent transcript, we describe examples of functional noncoding antisense transcripts that affect the epigenetic landscape and alter the expression of their host gene. Finally, we discuss opportunities for additional research on competing sense/antisense promoters, uncovering their potential role in programming cell differentiation.

Interaction and Collaboration of SP1, HIF-1, and MYC in Regulating the Expression of Cancer-Related Genes to Further Enhance Anticancer Drug Development.

Specificity protein 1 (SP1), hypoxia-inducible factor 1 (HIF-1), and MYC are important transcription factors (TFs). SP1, a constitutively expressed housekeeping gene, regulates diverse yet distinct biological activities; MYC is a master regulator of all key cellular activities including cell metabolism and proliferation; and HIF-1, whose protein level is rapidly increased when the local tissue oxygen concentration decreases, functions as a mediator of hypoxic signals. Systems analyses of the regulatory networks in cancer have shown that SP1, HIF-1, and MYC belong to a group of TFs that function as master regulators of cancer. Therefore, the contributions of these TFs are crucial to the development of cancer. SP1, HIF-1, and MYC are often overexpressed in tumors, which indicates the importance of their roles in the development of cancer. Thus, proper manipulation of SP1, HIF-1, and MYC by appropriate agents could have a strong negative impact on cancer development. Under these circumstances, these TFs have naturally become major targets for anticancer drug development. Accordingly, there are currently many SP1 or HIF-1 inhibitors available; however, designing efficient MYC inhibitors has been extremely difficult. Studies have shown that SP1, HIF-1, and MYC modulate the expression of each other and collaborate to regulate the expression of numerous genes. In this review, we provide an overview of the interactions and collaborations of SP1, HIF1A, and MYC in the regulation of various cancer-related genes, and their potential implications in the development of anticancer therapy.

DOT1L is a barrier to histone acetylation during reprogramming to pluripotency.

Embryonic stem cells (ESCs) have transcriptionally permissive chromatin enriched for gene activation-associated histone modifications. A striking exception is DOT1L-mediated H3K79 dimethylation (H3K79me2) that is considered a positive regulator of transcription. We find that ESCs are depleted for H3K79me2 at shared locations of enrichment with somatic cells, which are highly and ubiquitously expressed housekeeping genes, and have lower RNA polymerase II (RNAPII) at the transcription start site (TSS) despite greater nascent transcription. Inhibiting DOT1L increases the efficiency of reprogramming of somatic to induced pluripotent stem cells, enables an ESC-like RNAPII pattern at the TSS, and functionally compensates for enforced RNAPII pausing. DOT1L inhibition increases H3K27 methylation and RNAPII elongation-enhancing histone acetylation without changing the expression of the causal histone-modifying enzymes. Only the maintenance of elevated histone acetylation is essential for enhanced reprogramming and occurs at loci that are depleted for H3K79me2. Thus, DOT1L inhibition promotes the hyperacetylation and hypertranscription pluripotent properties.

S-SCAM is essential for synapse formation.

Synapse formation is critical for the wiring of neural circuits in the developing brain. The synaptic scaffolding protein S-SCAM/MAGI-2 has important roles in the assembly of signaling complexes at post-synaptic densities. However, the role of S-SCAM in establishing the entire synapse is not known. Here, we report significant effects of RNAi-induced S-SCAM knockdown on the number of synapses in early stages of network development in vitro. In vivo knockdown during the first three postnatal weeks reduced the number of dendritic spines in the rat brain neocortex. Knockdown of S-SCAM in cultured hippocampal neurons severely reduced the clustering of both pre- and post-synaptic components. This included synaptic vesicle proteins, pre- and post-synaptic scaffolding proteins, and cell adhesion molecules, suggesting that entire synapses fail to form. Correspondingly, functional and morphological characteristics of developing neurons were affected by reducing S-SCAM protein levels; neurons displayed severely impaired synaptic transmission and reduced dendritic arborization. A next-generation sequencing approach showed normal expression of housekeeping genes but changes in expression levels in 39 synaptic signaling molecules in cultured neurons. These results indicate that S-SCAM mediates the recruitment of all key classes of synaptic molecules during synapse assembly and is critical for the development of neural circuits in the developing brain.

Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression.

Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman-Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named "translational readthrough" and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins' (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs.

Expression of <i>TSPO</i> and <i>HIF-1α</i> genes as predictors of the organism’s resistance to hyperthermia

BACKGROUND: One of the key transcriptional regulators that determine the bodys resistance to hypoxia is the hypoxia-inducible factor HIF-1, the study of the role of which in the bodys resistance to extreme influences can justify new directions in medical technologies for its increase. The bodys resistance to hypoxia largely determines the resistance to other critically significant influences (hyperthermia, hypothermia, hyperbaria, ionizing radiation, chemicals, etc.). However, it was not possible to find a quantitative assessment of this effect in the literature studied by us, which served as the basis for this study.
 AIM: To assess the role of the level of expression of the hypoxia-inducible factor HIF-1 in various tissues of laboratory animals in increasing the resistance of animals to the effects of extreme hyperthermia.
 MATERIALS AND METHODS: The study was carried out on outbred white laboratory rats obtained from the Rappolovo nursery weighing 180220 g. For the study, preliminary laboratory animals were tested for an individual level of resistance to hyperthermia (40 animals), which made it possible to form experimental groups from highly resistant and low resistant to extreme animal influences. The definition of resistance to hyperthermia was carried out by the rate of increase in rectal temperature in animals during 20-minute air hyperthermia (40C). 4 groups of laboratory animals were formed (2 each with high and low resistance), half of which were exposed to a pronounced adverse effect of hyperthermia. Biological material was taken from all animals (whole blood, plasma, tissues of the heart, liver, kidneys, brain), in which the expression of the HIF-1 and TSPO genes (housekeeping gene) was determined by the Real-Time-PCR method. Statistical processing of the obtained data was carried out using the ANOVA analysis of variance.
 RESULTS: It has been established that the level of resistance of animals to hyperthermia is largely determined by their genetic characteristics. Even under thermocomfort conditions, the expression of the TSPO housekeeping gene in animals with a high level of resistance to hyperthermia differed with a high degree of reliability from low-resistant animals (in the kidneys, liver, and brain, on average, by 4060%; in the heart, by 25%). The expression values of this gene, determined in whole blood or plasma, make it possible to differentiate groups of animals according to the level of resistance to hyperthermia. A similar relationship between animals with high and low resistance is also observed in tissues obtained immediately after thermal exposure.
 CONCLUSIONS: The main organ that provides a high level of resistance to both hypoxia and hyperthermia associated with the basic (under thermal comfort conditions) expression of HIF-1 is the brain. The expression of the hypoxia-inducible factor in it is more than 300 times higher than the expression of the housekeeping genes. The second most important organ is the liver, in which HIF-1 expression activity is more than 15 times higher than the expression of housekeeping genes. Under conditions of hyperthermia, low-resistant animals show a compensatory-adaptive reaction associated with the activation of hypoxic defense mechanisms in blood cells, kidneys, and liver, in the absence of such a reaction in the tissues of the heart and brain. Animals highly resistant to hyperthermia were characterized by a significant (30 times) increase in the relative activity of HIF-1 expression mechanisms in blood cells, 2.5 times in liver cells, and a decrease in expression by 25% in the kidneys and almost 2 times in brain tissues. A high level of basal expression of the transcription factor HIF-1 under everyday (thermocomfortable) conditions may be a predictor of a high level of resistance to hyperthermia in a given animal. Probably, to increase the bodys resistance to extreme impacts, it is advisable to use medical technologies that increase the level of HIF-1 expression in everyday (thermocomfortable) conditions in key tissues the brain, liver, and myocardium.

Application of Novel Transcription Factor Machine Learning Model and Targeted Drug Combination Therapy Strategy in Triple Negative Breast Cancer.

Transcription factors (TFs) have been shown to play a key role in the occurrence and development of tumors, including triple-negative breast cancer (TNBC), with a worse prognosis. Machine learning is widely used for establishing prediction models and screening key tumor drivers. Current studies lack TF integration in TNBC, so targeted research on TF prognostic models and targeted drugs is beneficial to improve clinical translational application. The purpose of this study was to use the Least Absolute Shrinkage and Selection Operator to build a prognostic TFs model after cohort normalization based on housekeeping gene expression levels. Potential targeted drugs were then screened on the basis of molecular docking, and a multi-drug combination strategy was used for both in vivo and in vitro experimental studies. The machine learning model of TFs built by E2F8, FOXM1, and MYBL2 has broad applicability, with an AUC value of up to 0.877 at one year. As a high-risk clinical factor, its abnormal disorder may lead to upregulation of the activity of pathways related to cell proliferation. This model can also be used to predict the adverse effects of immunotherapy in patients with TNBC. Molecular docking was used to screen three drugs that target TFs: Trichostatin A (TSA), Doxorubicin (DOX), and Calcitriol. In vitro and in vivo experiments showed that TSA + DOX was able to effectively reduce DOX dosage, and TSA + DOX + Calcitriol may be able to effectively reduce the toxic side effects of DOX on the heart. In conclusion, the machine learning model based on three TFs provides new biomarkers for clinical and prognostic diagnosis of TNBC, and the combination targeted drug strategy offers a novel research perspective for TNBC treatment.

MGUS'ta azalmış GADD45A gen ifadesi seviyesi

Purpose: Monoclonal gammopathy of undetermined significance (MGUS) is a plasma cell dyscrasia. It is known that MGUS has an increased risk of progression to multiple myeloma (MM), and also prepares the ground for diseases such as Waldenstrom macroglobulinemia (WM), non-Hodgkin lymphoma, and chronic lymphocytic leukemia (CLL). Our study aimed to evaluate whether some important p53 pathway genes differ in terms of expression in MGUS and healthy individuals.
 Materials and methods: For the study, bone marrow was collected from 8 healthy individuals and 8 individuals diagnosed with MGUS, and RNA samples were isolated. Expression levels of various genes involved in the p53 pathway were compared using the RT2-profiler PCR array. β-actin housekeeping gene expression level was used for normalization. The Pearson Correlation analysis and Receiver Operating Characteristic (ROC) analysis were conducted.
 Results: Among the genes whose expression levels were examined in this study, it was determined that the expression level of only the GADD45A gene decreased significantly in MGUS compared to the control group (p=0.027). Pearson correlation data showed that GADD45A gene expression was highly correlated with 12 of the other genes (APAF1, CDK4, PCNA, BAX, CDKN2A, CASP9, CHECK2, MDM2, RB1, P53, BCL2, CHEK1) examined in the p53 pathway (r>0.7). In addition, according to the ROC analysis, GADD45A is detected to have a strong discrimination power between MGUS and healthy individuals (AUC=0.797 and p=0.015).
 Conclusion: The decreased expression of the GADD45A gene in the MGUS group compared to the control group may be useful as a new biomarker to detect the risk of progression from MGUS to MM.

Third-generation sequencing reveals the adaptive role of the epigenome in three deep-sea polychaetes.

The roles of DNA methylation in invertebrates are poorly characterised, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppress the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.

Identification and validation of the optimal reference genes for standardizing the gene expression profiling diagnostic panel of Ph-like B-lineage acute lymphoblastic leukemia.

Gene expression profiling is the criterion standard for recognizing Ph-like ALL signatures among B-ALLs. The prerequisite of GEP is the accurate normalization of target genes with stable expression of housekeeping genes in a quantitative PCR. HKGs exhibit differential expression in the different experimental conditions and affect the target genes' expression, leading to imprecise qPCR results. The selection of stable HKGs is crucial in GEP experiments, especially in identifying high-risk Ph-like ALL cases. We have evaluated the expression stability of nine HKGs (GAPDH, ACTB, GUSB, RNA18S, EEF2, PGK1, B2M, TBP and ABL1) in identified Ph-like ALLs and Ph-negative (n = 23 each) using six algorithms, 4 traditional softwares; geNorm, BestKeeper, NormFinder, Delta Cq value method, and two algorithms, RefFinderTM and ComprFinder. Further, we have validated the expression of 8 overexpressed normalized genes in Ph-like ALL cases (JCHAIN, CA6, MUC4, SPATS2L, BMPR1B, CRLF2, ADGRF1 and NRXN3). GeNorm, BestKeeper, NormFinder, Delta Cq value method, RefFinderTM and ComprFinder algorithm analysis revealed that EEF2, GAPDH, and PGK1 form the best representative HKGs in Ph-like ALL cases, while RNA18s, ß-actin, and ABL1 in Ph-negative ALLs. Lastly, we performed a correlation analysis and found that the combination of EEF2, GAPDH, and PGK1 represents the best combination with a very high correlation in Ph-like ALL cases. This is the first report that shows EEF2, GAPDH, and PGK1 are the best HKG genes and can be used in the diagnostic panel of Ph-like ALL cases using qPCR at baseline diagnosis.

Expression of housekeeping genes varies depending on mevalonate pathway inhibition in cancer cells

Statins have anticancer effects and may be used as anticancer agents via drug repositioning. In reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays, the internal reference gene must not be affected by any experimental conditions. As statins exert a wide range of effects on cells by inhibiting the mevalonate pathway, it is possible that statin treatment might alter the expression of housekeeping genes used as internal reference genes, thereby misleading the assessment of obtained gene expression data. Here, we evaluated the expression stability of internal reference genes in atorvastatin-treated cancer cell lines. We treated both statin-sensitive and statin-resistant cancer cell lines with atorvastatin at seven different concentrations and performed RT-qPCR on 15 housekeeping genes whose expression stability was then assessed using five different algorithms. In both statin-sensitive and statin-resistant cancer cell lines, atorvastatin affected the expression of certain internal reference genes in a dose-dependent and cancer cell line-dependent manner; therefore, caution should be exercised when comparing target gene expression between cells. Our findings emphasize the importance of the validation of internal reference genes in gene expression analyses in drug treatment-based cancer research.

Hyperactive behaviour of growth differentiation factor- 15 (GDF-15) in conjunction with iron trafficking transporters and suppression of Nrf-2 gene in diabetes and metabolic syndrome.

Multiple parallel factors are frequently interrogated with various toxic radicals which are abundantly generated in the liver, heart, and pancreas in stress conditions. They are actively involved in the development of diabetes and metabolic aberrations. However, whether over-activation of GDF-15mRNA and influxes of iron-by-iron trafficking genes are directly suppressing the Nrf-2 gene in patients with diabetes and metabolic aberrations in context with undiagnosed individuals with diabetes and metabolic aberrations? Therefore, we have investigated inter and intra- related Zip8/14 mRNA, GDF-15mRNA, and Nrf-2 mRNA expressions in diabetes and metabolic syndrome as it is expected to be up to 134 million by 2045 in India. We recruited 120 subjects from the Department of Medicine, Endocrinology and Metabolic Clinic, All India Institute of Medical Sciences, New Delhi, India. Various investigations related to anthropometry, nutritional, hematological, biochemical, cytokine, and oxidative stress were measured in diabetes, metabolic syndrome, diabetes with metabolic aberration, and healthy controls. Relative expression of GDF-15, ZIP8, ZIP14, Nrf-2, and housekeeping genes was done in all subjects. Stress-responsive cytokines are highly expressed in patients with metabolic aberration with respect to body weight, IR, waist circumference, and fat mass. IL-1β, TNF-α, and IL-6 levels were significantly higher in metabolic syndrome, whereas Adiponectin levels were profoundly lower side. MDA levels were significantly raised in diabetes with metabolic syndrome while SOD activities were lowered (p = 0.001). GDF-15 mRNA expression was 1.79-fold upregulated in group III as compared with Group I while 2-threefold down-regulation of Nrf-2 expression was observed in diabetes with metabolic aberration groups. Zip 8 mRNA expressions were downregulated (p = 0.014), and Zip 14 mRNA expressions were upregulated (p = 0.06) in diabetes and metabolic aberrations. The association of GDF-15 and Nrf-2 mRNA expression was found contradictory and highly interlinked with ROS. Zip 8/14mRNA expressions were also dysregulated in diabetes and metabolic-associated complications.

Expression of the hypoxia-inducible factor as a predictor of the resistance of the organism of laboratory animals to hypoxia

BACKGROUND:One of the key transcriptional regulators that determine the bodys resistance to hypoxia is the hypoxia-inducible factorHIF-1, the study of the role of which in the bodys resistance to extreme influences can justify new directions in medical technologies for its increase.
 AIM:To evaluate the quantitative contribution of the level of expression of the hypoxia-inducible factorHIF-1in various tissues of laboratory animals to the increase in the resistance of animals to the effects of hypoxic hypoxia.
 MATERIALS AND METHODS:The study was carried out on outbred white laboratory rats obtained from the Rappolovo nursery weighing 180220 g. To conduct the study, animals were previously tested for an individual level of resistance to hypoxia, which made it possible to form experimental groups from highly resistant and low resistant animals. Biological material was taken from all animals (whole blood, plasma, tissues of the heart, liver, kidneys, brain), in which the expression of theHIF-1andTSPOgenes (housekeeping gene) was determined by the Real-Time-PCR method. Total RNA was isolated from the test material by affinity sorption,synthesis of the first strand of cDNA, amplification, followed by determination of the expression level of theHIF-1gene in rats was carried out according to the instructions and the manufacturers protocol by PCR with detection of the accumulation of reaction products in real time (Real-Time PCR) using a CFX-96 detecting amplifier (Bio-Rad, USA) and specific primers and probes for theHIF-1gene in rats (DNK-Sintez, Russia). Statistical processing of the obtained data was carried out using the ANOVA analysis of variance.
 RESULTS:It has been established that the level of resistance of animals to hypoxia is largely determined by their genetic characteristics. Even under normoxic conditions, the expression of theTSPOhousekeeping gene in animals with a high level of resistance to hypoxia differed with a high degree of reliability from low-resistance animals (in the kidneys, liver, and brain, on average, by 4060%; in the heart, by 25%). The values of the expression of this gene, determined in whole blood or plasma, make it possible to differentiate groups of animals according to the level of resistance to hypoxia. A similar ratio between animals with high and low resistance is also observed in tissues obtained immediately after hypoxic exposure. An analysis of the reaction of the genomic regulation system to extreme exposure showed that it increased the expression of the TSPO gene by 1.62 times equally in all tissues, regardless of the level of animal resistance. For theHIF-1gene, similar patterns were found, but the severity of their manifestations is more and significant.
 CONCLUSIONS:The main organ that provides a high level of resistance to hypoxia associated with the basic (under normoxic conditions) expression ofHIF-1is the brain. The expression of the hypoxia-inducible factor in it is more than 300 times higher than the expression of the housekeeping genes. The second most important organ is the liver, in whichHIF-1expression activity is more than 15 times higher than the expression of housekeeping genes. Under conditions of moderate hypoxia, a compensatory-adaptive reaction is noted, associated with the activation of hypoxic defense mechanisms in blood and liver cells, and in low-resistant animals, also in the brain tissue. In the myocardium, such a compensatory-adaptive reaction is activated only in the group of highly resistant animals. A high level of basal expression of theHIF-1transcription factor under daily (normoxic) conditions may be a predictor of a high level of resistance to hypoxia in a given animal.

Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies

BackgroundAs the housekeeping genes (HKG) generally involved in maintaining essential cell functions are typically assumed to exhibit constant expression levels across cell types, they are commonly employed as internal controls in gene expression studies. Nevertheless, HKG may vary gene expression profile according to different variables introducing systematic errors into experimental results. Sex bias can indeed affect expression display, however, up to date, sex has not been typically considered as a biological variable.MethodsIn this study, we evaluate the expression profiles of six classical housekeeping genes (four metabolic: GAPDH, HPRT, PPIA, and UBC, and two ribosomal: 18S and RPL19) to determine expression stability in adipose tissues (AT) of Homo sapiens and Mus musculus and check sex bias and their overall suitability as internal controls. We also assess the expression stability of all genes included in distinct whole-transcriptome microarrays available from the Gene Expression Omnibus database to identify sex-unbiased housekeeping genes (suHKG) suitable for use as internal controls. We perform a novel computational strategy based on meta-analysis techniques to identify any sexual dimorphisms in mRNA expression stability in AT and to properly validate potential candidates.ResultsJust above half of the considered studies informed properly about the sex of the human samples, however, not enough female mouse samples were found to be included in this analysis. We found differences in the HKG expression stability in humans between female and male samples, with females presenting greater instability. We propose a suHKG signature including experimentally validated classical HKG like PPIA and RPL19 and novel potential markers for human AT and discarding others like the extensively used 18S gene due to a sex-based variability display in adipose tissue. Orthologs have also been assayed and proposed for mouse WAT suHKG signature. All results generated during this study are readily available by accessing an open web resource (https://bioinfo.cipf.es/metafun-HKG) for consultation and reuse in further studies.ConclusionsThis sex-based research proves that certain classical housekeeping genes fail to function adequately as controls when analyzing human adipose tissue considering sex as a variable. We confirm RPL19 and PPIA suitability as sex-unbiased human and mouse housekeeping genes derived from sex-specific expression profiles, and propose new ones such as RPS8 and UBB.

Transcriptome analyses of murine right and left maxilla-mandibular complex.

The objective of the study was to investigate differential gene expression between murine right and left maxilla-mandibular (MxMn) complexes. Wild-type (WT) C57BL/6 embryonic (E) day 14.5 (n = 3) and 18.5 (n = 3) murine embryos. The E14.5 and 18.5 embryos were harvested and hemi-sectioned the MxMn complexes into right and left halves in the mid-sagittal plane. We isolated total RNA using Trizol reagent and further purified using the RNA-easy kit (QIAGEN). We confirmed equal expression of house-keeping genes in right and left halves using RT-PCR and then performed paired-end whole mRNA sequencing in LC Sciences (Houston, TX) followed by differential transcript analyses (>1 or <-1 log fold change; p < .05; q < .05; and FPKM >0.5 in 2/3 samples). The Mouse Genome Informatics and Online Mendelian Inheritance in Man databases as well as gnomAD constraint scores were used to prioritize differentially expressed transcripts. There were 19 upregulated and 19 downregulated transcripts at E14.5 and 8 upregulated and 17 downregulated transcripts at E18.5 time-points. These differentially expressed transcripts were statistically significant and shown to be associated with craniofacial phenotypes in mouse models. These transcripts also have significant gnomAD constraint scores and are enriched in biological processes critical for embryogenesis. We identified significant differential expression of transcripts between E14.5 and 18.5 murine right and left MxMn complexes. These findings when extrapolated to humans, they may provide a biological basis for facial asymmetry. Further experiments are required to validate these findings in murine models with craniofacial asymmetry.