pBR322 contains glucocorticoid regulatory element DNA consensus sequences

Glucocorticoid Receptor-Binding and Transcriptome Signature in Cardiomyocytes

Background

An increase in serum cortisol has been identified as a risk factor for cardiac failure, which highlights the impact of glucocorticoid signaling in cardiomyocytes and its influence in the progression of failure. Dexamethasone, a synthetic glucocorticoid, is sufficient for induction of cardiomyocyte hypertrophy, but little is known of the glucocorticoid receptor (GR) genome‐binding and ‐dependent transcriptional changes that mediate this phenotype.

Methods and Results

In this study using high‐resolution sequencing, we identified genomic targets of GR and associated change in the transcriptome after 1 and 24 hours of dexamethasone treatment. We showed that GR associates with 6482 genes in the cardiac genome, with differential regulation of 738 genes. Interestingly, alignment of the chromatin immunoprecipitation and RNA sequencing data show that, after 1 hour, 69% of differentially regulated genes are associated with GR and identify as regulators of RNA pol II–dependent transcription. Conversely, after 24 hours only 45% of regulated genes are associated with GR and involved in dilated and hypertrophic cardiomyopathies as well as other growth‐related pathways. In addition, our data also reveal that a majority of genes (76.42%) associated with GR show incremental changes in transcript abundance and are genes involved in basic cellular processes that might be regulated by the dynamics of promoter‐paused RNA pol II, as seen in hearts undergoing hypertrophy. In vivo administration of dexamethasone resulted in similar changes in the cardiac transcriptome, as seen in isolated cardiomyocytes.

Conclusions

Our data reveal genome‐wide GR binding sites in cardiomyocytes, identify novel targets and GR‐dependent change in the transcriptome that induces and contributes to cardiomyocyte hypertrophy.

Advances in host and vector development for the production of plasmid DNA vaccines

Recent developments in DNA vaccine research provide a new momentum for this rather young and potentially disruptive technology. Gene-based vaccines are capable of eliciting protective immunity in humans to persistent intracellular pathogens, such as HIV, malaria, and tuberculosis, for which the conventional vaccine technologies have failed so far. The recent identification and characterization of genes coding for tumor antigens has stimulated the development of DNA-based antigen-specific cancer vaccines. Although most academic researchers consider the production of reasonable amounts of plasmid DNA (pDNA) for immunological studies relatively easy to solve, problems often arise during this first phase of production. In this chapter we review the current state of the art of pDNA production at small (shake flasks) and mid-scales (lab-scale bioreactor fermentations) and address new trends in vector design and strain engineering. We will guide the reader through the different stages of process design starting from choosing the most appropriate plasmid backbone, choosing the right Escherichia coli (E. coli) strain for production, and cultivation media and scale-up issues. In addition, we will address some points concerning the safety and potency of the produced plasmids, with special focus on producing antibiotic resistance-free plasmids. The main goal of this chapter is to make immunologists aware of the fact that production of the pDNA vaccine has to be performed with as much as attention and care as the rest of their research.

Plasmid DNA vaccine vector design: impact on efficacy, safety and upstream production

Critical molecular and cellular biological factors impacting design of licensable DNA vaccine vectors that combine high yield and integrity during bacterial production with increased expression in mammalian cells are reviewed. Food and Drug Administration (FDA), World Health Organization (WHO) and European Medical Agencies (EMEA) regulatory guidance's are discussed, as they relate to vector design and plasmid fermentation. While all new vectors will require extensive preclinical testing to validate safety and performance prior to clinical use, regulatory testing burden for follow-on products can be reduced by combining carefully designed synthetic genes with existing validated vector backbones. A flowchart for creation of new synthetic genes, combining rationale design with bioinformatics, is presented. The biology of plasmid replication is reviewed, and process engineering strategies that reduce metabolic burden discussed. Utilizing recently developed low metabolic burden seed stock and fermentation strategies, optimized vectors can now be manufactured in high yields exceeding 2 g/L, with specific plasmid yields of 5% total dry cell weight.

Rational vector design for efficient non-viral gene delivery: challenges facing the use of plasmid DNA

Although non-viral gene delivery is a very straightforward technology, there are currently no FDA-approved gene medicinal products available. Therefore, improving potency, safety, and efficiency of current plasmid DNA vectors will be a major task for the near future. This article will provide an overview on factors influencing production yield and quality as well as safety issues that emerge from the vector design itself. Special focus will be on generating bacterial pDNA vectors by circumventing the use of antibiotic resistance genes, to generate safer gene medicinal products as well as smaller, more efficient DNA vectors.

pDNAVACCultra vector family: high throughput intracellular targeting DNA vaccine plasmids

DNA vaccines have the potential to provide a safe route for protective immunity to neoplasms and infectious agents. However, current DNA vaccine plasmids are not optimal with additional non-essential DNA, nor do they facilitate controlled or flexible targeting of antigens to various intracellular destinations. A family of DNA vaccine vectors, optimized and minimized to comply with FDA guidelines regarding content and elimination of extraneous materials, was constructed. The resulting vectors are much smaller than existing vectors, drive higher levels of target gene expression, facilitate high throughput cloning applications, and allow simultaneous cloning into multiple vectors that feature various intracellular targeting destinations for the protein product. The ability to control expression and trafficking is intended to provide a rapid, rational approach to cancer therapy and emerging infectious diseases.

Modern histochemical methods using enzymes as markers

In the 25 years since the idea that histochemically detectable enzymes could serve as a marker of ligands, the world of histochemistry has undergone a dramatic change. Today slides of immunostained tissue sections may be filed together with hematoxylin- and eosin-stained slides and may be examined at one's leisure. Antigens are now localized at the ultrastructural level as well as at the light microscopic level permitting one to wonder about the intricacies and beauties of living creatures. Genes which mandate our body since the day of conception to the day of death can now easily be probed with enzyme markers. Even with all these success stories, some dreams which I had hoped to accomplish with the method are not yet realized. Unlike the chemical and physical properties of inert objects, living organisms are provided with a fixed genetic program. By recognizing the point in the program which is being executed, one can deduce the potential FUTURE activities of the cells and tissues. I hypothesize that this is not an impossible task since (1) histochemistry and immunohistochemistry already provide us information on the PAST activities of cells and tissues, (2) in situ hybridization describes PRESENT gene activities, and (3) newer methods allow for the determination of potential gene function. Thus it is possible to peek at the future.

New elements of glucocorticoid-receptor binding sites of hormone-regulated genes

The structure of the DNA regions recognized by glucocorticoid-receptor complexes (GIRC) was analyzed using frequency matrices and a modified perceptron method. Some complementary conservative elements which may modulate the efficiency of GIRC binding were found at both sides of the previously established conserved nucleotide sequence (core) (Beato, M. et al. (1987) J. Steroid Biochem. 27, 9-14). A criterion based on the concurrent use of several perceptron matrices to search for the potential GIRC binding site sequences has been worked out. By applying this criterion 73 sites were identified in 28 sequences of glucocorticoid regulated genes and 7 sites were identified in 26 sequences independent from glucocorticoid regulation.

Localization in situ of specific mRNA using thymine-thymine dimerized DNA probes. Sensitive and reliable non-radioactive in situ hybridization

In situ hybridization has been recognized as a powerful technique for localizing specific nucleic acids such as mRNA and viral DNA in individual cells. For in situ hybridization, the use of a non-radioactive probe is considered superior to that of a radioactive one from viewpoints of resolution, probe stability and personal safety. Although various non-radioactive labels are currently available, some interfere with the formation of hybrids and some increase steric hindrance and prevent penetration of the labeled nucleic acid probe into cells and tissues. Recently, we have developed a method using thymine-thymine (T-T) dimerized DNA as a non-radioactive probe. This is simple to make, since it dose not require separation of labeled DNA from unreacted labeling compounds, and T-T dimer will not alter the chemical and physical nature of the probe. In this paper, we describe the tissue processing procedures that are suited for the T-T dimerized DNA probes, and the recent new findings on methodological aspects, particularly the use of synthetic oligodeoxynucleotide probes.

Glucocorticoid receptor binding to defined regions of alpha 2u-globulin genes

A DNA-cellulose competition assay was used to study binding of glucocorticoid receptor complexes to two alpha 2u-globulin genes, RAP 01 and RAO 01. Two binding regions were found in RAP 01, one localized between bp -642 and -452, the other between -252 and -118 from the transcriptional initiation site. Only the second region was found in RAO 01. The binding affinity was comparable to that observed using a long terminal repeat fragment of mouse mammary tumor virus. Both regions contain sequences homologous to a 17-bp consensus proposed for the glucocorticoid receptor binding. Therefore, despite evidence that glucocorticoid induction of alpha 2u-globulin may be indirect, a direct action of the receptor in the 5'-upstream region of the genes cannot be excluded.