The mouse creatine kinase paired E-box element confers muscle-specific expression to a heterologous promoter

Pushing the Right Buttons: Improving Efficacy of Therapeutic DNA Vectors

Gene therapy represents a potent therapeutical application for regenerative medicine. So far, viral and nonviral approaches suffer from major drawbacks hindering efficient gene therapeutic applicability: the immunogenicity of viral systems on the one hand, and the low gene transfer efficiency of nonviral systems on the other hand. Therefore, there is a high demand for improvements of therapeutical systems at several levels. This review summarizes different DNA vector modifications to enhance biological efficacy and efficiency of therapeutical vectors, aiming for low toxicity, high specificity, and biological efficacy-the cornerstones for successful translation of gene therapy into the clinic. We aim to provide a step-by-step instruction to optimize their vectors to achieve the desired outcome of gene therapy. Our review provides the means to either construct a potent gene therapeutic vector de novo or to specifically address a bottleneck in the chain of events mandatory for therapeutic success. Although most of the introduced techniques can be translated into different areas, this review primarily addresses improvements for applications in transient gene therapy in the field of tissue engineering.

Twist1 directly regulates genes that promote cell proliferation and migration in developing heart valves

Twist1, a basic helix-loop-helix transcription factor, is expressed in mesenchymal precursor populations during embryogenesis and in metastatic cancer cells. In the developing heart, Twist1 is highly expressed in endocardial cushion (ECC) valve mesenchymal cells and is down regulated during valve differentiation and remodeling. Previous studies demonstrated that Twist1 promotes cell proliferation, migration, and expression of primitive extracellular matrix (ECM) molecules in ECC mesenchymal cells. Furthermore, Twist1 expression is induced in human pediatric and adult diseased heart valves. However, the Twist1 downstream target genes that mediate increased cell proliferation and migration during early heart valve development remain largely unknown. Candidate gene and global gene profiling approaches were used to identify transcriptional targets of Twist1 during heart valve development. Candidate target genes were analyzed for evolutionarily conserved regions (ECRs) containing E-box consensus sequences that are potential Twist1 binding sites. ECRs containing conserved E-box sequences were identified for Twist1 responsive genes Tbx20, Cdh11, Sema3C, Rab39b, and Gadd45a. Twist1 binding to these sequences in vivo was determined by chromatin immunoprecipitation (ChIP) assays, and binding was detected in ECCs but not late stage remodeling valves. In addition identified Twist1 target genes are highly expressed in ECCs and have reduced expression during heart valve remodeling in vivo, which is consistent with the expression pattern of Twist1. Together these analyses identify multiple new genes involved in cell proliferation and migration that are differentially expressed in the developing heart valves, are responsive to Twist1 transcriptional function, and contain Twist1-responsive regulatory sequences.

Discovering multiple realistic TFBS motifs based on a generalized model

BACKGROUND

Identification of transcription factor binding sites (TFBSs) is a central problem in Bioinformatics on gene regulation. de novo motif discovery serves as a promising way to predict and better understand TFBSs for biological verifications. Real TFBSs of a motif may vary in their widths and their conservation degrees within a certain range. Deciding a single motif width by existing models may be biased and misleading. Additionally, multiple, possibly overlapping, candidate motifs are desired and necessary for biological verification in practice. However, current techniques either prohibit overlapping TFBSs or lack explicit control of different motifs.

RESULTS

We propose a new generalized model to tackle the motif widths by considering and evaluating a width range of interest simultaneously, which should better address the width uncertainty. Moreover, a meta-convergence framework for genetic algorithms (GAs), is proposed to provide multiple overlapping optimal motifs simultaneously in an effective and flexible way. Users can easily specify the difference amongst expected motif kinds via similarity test. Incorporating Genetic Algorithm with Local Filtering (GALF) for searching, the new GALF-G (G for generalized) algorithm is proposed based on the generalized model and meta-convergence framework.

CONCLUSION

GALF-G was tested extensively on over 970 synthetic, real and benchmark datasets, and is usually better than the state-of-the-art methods. The range model shows an increase in sensitivity compared with the single-width ones, while providing competitive precisions on the E. coli benchmark. Effectiveness can be maintained even using a very small population, exhibiting very competitive efficiency. In discovering multiple overlapping motifs in a real liver-specific dataset, GALF-G outperforms MEME by up to 73% in overall F-scores. GALF-G also helps to discover an additional motif which has probably not been annotated in the dataset. http://www.cse.cuhk.edu.hk/%7Etmchan/GALFG/

Evidence that E-box promoter elements and MyoD transcription factors play a role in the induction of cathepsin B gene expression during human myoblast differentiation

HB13 human myoblasts express physiological and biochemical markers associated with myoblast differentiation in non-human cell culture model systems. During differentiation, HB13 myoblasts also demonstrate fusion-related increases in cathepsin B activity and protein levels. These increases are associated with an increase in levels of cathepsin B mRNA suggesting the involvement of transcriptional regulatory mechanisms. To examine these mechanisms human myoblasts were transfected with cathepsin B nested deletion promoter constructs within the 1.8 kb 5' promoter 1 region of the human catB gene. Transfected myoblasts that were maintained under differentiating conditions demonstrated higher promoter activity than those maintained in proliferating conditions. The highest activity was obtained with pSCB2-3 (-1279/+56 bp), a construct containing two putative upstream E-box elements. Co-transfection experiments demonstrated that MyoD and myogenin transactivate cathepsin B promoter activity. Electrophoretic mobility shift assays of nuclear extracts incubated with an oligonucleotide containing two upstream E-box elements found within the cathepsin B promoter demonstrated two band shifts. The band shifts were abolished using an oligonucleotide with mutations in both E-box elements. Moreover, the shifted bands were super-shifted and abolished when incubated with anti-myogenin and anti-MyoD, respectively. Collectively, these data support myogenic transcription factor-mediated activation of cathepsin B expression during myogenesis.

Muscle specific versus ubiquitous expression of Gag based HIV-1 DNA vaccines: a comparative analysis

Most studies on DNA-based immunization have used viral promoters to drive antigen expression. In this study, we analyzed the properties of the commonly used CMV promoter, the tissue specific murine muscle creatine kinase (MCK) promoter as well as a hybrid MCK/CMV promoter regarding promoter activity and tissue specificity in vitro. Furthermore, the efficiency of inducing HIV-1 Gag specific immune responses in vivo following intramuscular immunization of naked DNA containing a codon optimized synthetic gene was compared. Although antibody titers and cellular immune responses using the MCK construct were slightly reduced as compared to conventional CMV based vector modules, the utilization of nonviral promoters may add significantly to the safety of future DNA vaccines.

Construction of human factor IX expression vectors in retroviral vector frames optimized for muscle cells

Development of a highly refined human factor IX (hFIX) expression vector system is critical for establishing a durable hemophilia B gene therapy. Here we report construction of a series of retroviral vectors and identification of an optimal basic structure and components for expressing hFIX in skeletal muscle cells. These vectors, which are derived from Moloney murine leukemia virus (MoMLV) with its enhancer sequence in the 3' long terminal repeat (LTR) deleted, contained internal hFIX expression units inserted in forward configuration without or with a viral vector intron sequence (pdL or pdLIn vector frame, respectively) or in inverted configuration without a viral vector intron sequence (pdLi frame). Internal expression units contained a hFIX cDNA or hFIX minigene (hIXm1 or hIXm2) derived from the hFIX cDNA by insertion of a shortened first intron sequence of the hFIX gene. Regardless of the promoter and vector frame used, both hIXm1 and hIXm2 gave 10- to 14-fold higher hFIX expression compared to those with hFIX cDNA. Internal hFIX transcriptional control units of these vectors were composed of various promoters linked with or without the muscle creatine kinase enhancer (Me) sequence. Promoters tested included those of alpha-actin (alpha A775), beta-actin (beta A280), cytochrome oxidase (CO1250 and CO650), myogenin (Mg1031 and Mg353), and Rous sarcoma virus (RSV). beta A200, which was derived from beta A280 by eliminating potential polyadenylation sites, was also tested. As extensively examined with the myogenin promoter, presence of one or multiple copies of Me in the vectors elevated the expression activity in myotubes by 4.5- to 19-fold over those without Me, but not significantly in myoblasts. Similar enhancements in expression activity with Me were also observed with other promoters, except those of RSV and CO. The latter two showed only modest enhancements in the presence of Me. As assayed with myotubes in culture, the general order of hFIX expression activity of various promoters with four copies of Me in the three different vector frames was beta A280 approximately beta A200 > Mg353 > Mg1031 approximately RSV approximately CO650 approximately alpha A775 > CO1250. One exception was that CO650 showed significantly less activity in pdLi-type vectors than in the pdLIn vectors. Based on the systematic analyses of various structural components, a group of pdLi vectors consisting of beta A200, two to four copies of Me, and hIXm2 was identified to have the optimal basic vector structure to be used in retrovirus for hFIX expression in differentiated skeletal muscle cells. The present studies provide the critical first step for establishing a highly refined hemophilia B gene therapy based on skeletal muscle-targeted hFIX gene transfer.

Coordinate positioning of MEF2 and myogenin binding sites

The MEF2 and MyoD families of transcriptional regulatory factors both play central roles in the terminal differentiation of skeletal muscle. Further, binding sites for the two families often occur nearby, and there have been a number of indications that members of the two families may bind coordinately. The present study provides evidence that known binding sites for the two occur with precise geometric restrictions related to the DNA helical repeat unit, that pairs of putative sites following these restrictions are indicative of skeletal muscle-specific transcriptional regulatory regions, and that the geometric relationship can help provide a consistent interpretation for data that has until now been difficult to explain.

Prolonged alteration in E-box binding after a single systemic kainate injection: potential relation to F1/GAP-43 gene expression

The presence in hippocampus of a basic helix-loop-helix (bHLH) family of transcription factors (TFs) specifically binding in an electrophoretic mobility shift assay (EMSA) to the E-box recognition element was established by selective blockade of binding both by cold competition and by an antibody to MyoD1, an E-box TF. Protein source was from a micro-dissected preparation enriched in hippocampal granule cells. Specific E-box binding of hippocampal transcription factors was significantly reduced in kainate acid (KA) treated animals. This was observed at 24 and 72 h, but not before (3, 6 h) or after (96 h). This is the first report to our knowledge to study functional regulation of E-box binding protein in adult hippocampus. To determine the generality of this E-box regulatory event, we studied four other situations, in addition to kainate treatment, where axonal growth is known or has been suggested to increase: NGF treatment of PC12 cells, unilateral hilar lesions, long-term potentiation after 1 h, and postnatal rat hippocampal development. In all four cases, decreased E-box binding was observed. The recent link of F1/GAP-43 mRNA induction in hippocampal granule cells by KA to growth of their axons, the mossy fibers in the adult rat, suggests a potential role for the F1/GAP-43 5' flanking promoter region in regulating neurite outgrowth. Since in all cases decreased E-box binding preceded increased F1/GAP-43 mRNA expression, it is suggested that E-box binding to the F1/GAP-43 promoter in hippocampal granule cells could negatively regulate F1/GAP-43 gene expression. Indeed, analysis of recognition elements on the F1/GAP-43 gene revealed an arrangement, previously described in other genes, of multiple adjacent E-box elements. E-box binding of bHLH transcription factors is likely to occur on several different genes in addition to F1/GAP-43. It is, therefore, attractive to think that E-box binding is regulated by in vivo activation of the adult brain and that this gene regulatory event participates in the orchestration of molecular and cellular responses underlying axonal growth.

Anti-cooperative biphasic equilibrium binding of transcription factor upstream stimulatory factor to its cognate DNA monitored by protein fluorescence changes

Upstream stimulatory factor USF is a human transcriptional activation factor, which uses a basic/helix-loop-helix/ leucin zipper (b/HLH/Z) motif to homodimerize and recognize specific sequences in the promoter region of both nuclear and viral genes transcribed by RNA polymerase II. Steady state fluorescence spectroscopy demonstrated that the basic/helix-loop-helix/leucin zipper domain of USF binds its DNA targets with high affinity and specificity, whereas removal of the leucine zipper yielding the basic/helix-loop-helix minimal DNA binding region reduces both affinity and specificity. Stopped flow method provided kinetic evidence for a two-step binding process involving rapid formation of a protein-DNA intermediate followed by a slow isomerization step, which is consistent with the basic region undergoing a random coil to alpha-helix folding transition on specific DNA recognition. The leucine zipper is also necessary for USF to function as a bivalent homotetramer, capable of binding two distinct recognition sites simultaneously and mediating DNA looping under physiologic conditions. Titration studies revealed that the first binding event has a equilibrium constant Keq = (2.2 +/- 2.0) x 10(9) M-1 for major late promoter DNA, whereas the second binding event occurs with a remarkable reduced affinity, Keq = (1.2 +/- 0.8) x 10(8) M-1. This anticooperative feature of DNA binding by the homotetramer suggests that USF stimulates transcription by mediating DNA looping between nearby recognition sites located in class II nuclear and viral gene promoters.