Anti-beta s-ribozyme reduces beta s mRNA levels in transgenic mice: potential application to the gene therapy of sickle cell anemia

Zinc finger nucleases for targeted mutagenesis and repair of the sickle-cell disease mutation: An in-silico study

Background

Sickle cell disease (or simply, SCD) is an inherited hemoglobinopathy which is mostly prevalent among persons of African descent. SCD results from a monogenic (Hemoglobin, beta) point-mutation (substitution of the base Adenine with Thymine at position six) that leads to replacement of the amino acid glutamic acid (E) with valine (V). Management of SCD within resource-poor settings is largely syndromic, since the option of cure offered by bone-marrow transplantation (BMT) is risky and unaffordable by most affected individuals. Despite previous reports of repair and inhibition of the sickle beta-globin gene and messenger ribonucleic acids (mRNAs), respectively in erythrocyte precursor cells via gene-targeting using an oligomer-restriction enzyme construct and either ribozyme- or RNA-DNA chimeric oligonucleotides (or simply third strand binding), gene-therapy to treat SCD still remains largely preclinical. In the wake of the advances in target- gene- mutagenesis and repair wrought by zinc finger nuclease (ZFN) technology, it was hypothesized that SCD may be cured by the same. The goal of this study thus, was constructing a database of zinc finger arrays (ZFAs) and engineering ZFNs, that respectively bind and cleave within or around specific sequences in the sickle hemoglobin, beta (−β^S) gene.

Methods and results

First, using the complete 1606 genomic DNA base pair (bp) sequences of the normal hemoglobin-beta (β^A) chain gene, and the ZiFiT-CoDA-ZFA software preset at default, 57 three-finger arrays (ZFAs) that specifically bind 9 base-pair sequences within the normal hemoglobin-beta chain, were computationally assembled. Second, by serial linkage of these ZFAs to the Flavobacterium okeanokoites endonuclease Fok I― four ZFNs with unique specificity to >24 bp target-sequences at the genomic contextual positions 82, 1333, 1334, and 1413 of the β^A chain-gene were constructed in-silico. Third, localizing the point-mutation of SCD at genomic contextual position −69-70-71- bp (a position corresponding to the 6^th codon) of the β^A chain-gene, inspired the final design of five more ZFNs specific to >24 bp target-sequences within the 8,954 bp that are genomically adjacent to the 5′ end of the β^A chain-gene.

Conclusions

This set of 57 ZFAs and 9 ZFNs offers us gene-therapeutic precursors for the targeted mutagenesis and repair of the SCD mutation or genotype.

Modification of globin gene expression by RNA targeting strategies

OBJECTIVE

Sickle cell anemia is a genetic blood disease resulting from production of mutant beta-globin (beta(S)) and has severe clinical consequences. It is known that a higher cellular gamma-globin level, e.g., higher ratio of cellular gamma-globin to beta(S)-globin (gamma/beta(S) ratio), inhibits sickle hemoglobin (HbS) polymerization tendency. Hence, therapeutic treatment of sickle cell anemia has been focused on introducing gamma-globin gene into red blood cells to increase the cellular gamma/beta(S) ratio. Here, we have introduced ribozymes and small interfering RNAs (siRNAs) against beta(S)-globin mRNA into blood cells as a means to increase the gamma/beta(S) ratio.

MATERIALS AND METHODS

Single and multiribozymes against beta(S)-globin mRNA have been tested in vitro and in human erythroleukemia K562beta(S) cells that stably express exogenous beta(S)-globin gene. Primary human hematopoietic progenitor cells were also transfected with multiribozyme and the gamma/(gamma + beta) ratio determined and compared with cells transfected with long hairpin beta-globin cDNA and synthetic siRNA genes.

RESULTS

We have found that the multiribozyme zb21A containing two ribozyme units effectively reduces beta(S)-globin mRNA both in vitro and in K562beta(S) cells. The gamma-globin mRNA to beta(S)-globin mRNA ratio in the multiribozyme transfected cells is about a factor of 2 more than that in the control cells. We have also found that the gamma/(gamma + beta) ratio in the transfected hematopoietic progenitor cells is increased by more than twofold in cells treated with multiribozyme zb21A or siRNA ib5.

CONCLUSION

Our results suggest that introducing multiribozymes or siRNAs into red blood cells is comparable in their effectiveness to increase the ratio of cellular gamma-globin mRNA to beta- or beta(S)-globin mRNA, providing possible strategies to increase the effectiveness of gamma-globin gene transfer as gene therapy for treatment of patients with sickle cell anemia.

Application of hammerhead ribozymes in filamentous fungi

Metabolic engineering in filamentous fungi is a emerging field of research as many fungi produce high value primary and secondary metabolites. Ribozyme technology can be used as a tool for metabolic engineering to influence metabolic pathways and to knock down the expression of specific genes of interest. Hammerhead ribozymes can target virtually any mRNA sequence of choice and prevent gene expression on the post-transcriptional level. They are thus a versatile tool for timed and spatial elimination of unwanted gene products. As current research has only investigated the application of ribozymes in bacteria, yeast and mammalian cells, we decided to carry out a study on whether this technology can also function with filamentous fungi. We employed a sensitive, quantitative reporter-based model system as a proof of concept, using the Escherichia coli beta-glucuronidase transcript (uidA) as the target mRNA and Aspergillus giganteus as the host. This system was used to validate the in vivo activities of seven different hammerhead ribozymes, which were selected by in silico analysis of the uidA mRNA. All ribozymes tested were able to reduce the reporter activity up to a maximum of 100%, demonstrating that ribozyme technology is indeed a useful tool in fungal metabolic engineering.

High-efficiency gene knockdown using chimeric ribozymes in fish embryos

We report an effective gene knockdown technique in rainbow trout embryos using additional RNA components combined with ribozymes (R(z)s). Chimeric R(z)s (tR(z)Cs) containing tRNA(Val), R(z) against GFP, and a constitutive transport element were microinjected into transgenic embryos. tR(z)Cs induced greater gene interference than R(z)s alone. Control tR(z)Cs did not affect unpaired bases of target RNA, and the tR(z)C did not interfere with non-relevant gene expression, suggesting that the tR(z)C-mediated gene-interference effects were sequence-specific. Furthermore, the tR(z)C-containing expression vector specifically suppressed target GFP expression in transgenic trout. tR(z)Cs enhance R(z) cleavage and could therefore be powerful tools for studying unknown gene function in vertebrates.

Extended beta-globin locus control region elements promote consistent therapeutic expression of a gamma-globin lentiviral vector in murine beta-thalassemia

Since increased fetal hemoglobin diminishes the severity of beta-thalassemia and sickle cell anemia, a strategy using autologous, stem cell-targeted gene transfer of a gamma-globin gene may be therapeutically useful. We previously found that a gamma-globin lentiviral vector utilizing the beta-globin promoter and elements from the beta-globin locus control region (LCR) totaling 1.7 kb could correct murine beta-thalassemia. However, therapeutic consistency was compromised by chromosomal position effects on vector expression. In contrast, we show here that the majority of animals that received transplants of beta-thalassemic stem cells transduced with a new vector containing 3.2 kb of LCR sequences expressed high levels of fetal hemoglobin (17%-33%), with an average vector copy number of 1.3. This led to a mean 26 g/L (2.6 g/dL) increase in hemoglobin concentration and enhanced amelioration of other hematologic parameters. Analysis of clonal erythroid cells of secondary spleen colonies from mice that underwent transplantation demonstrated an increased resistance of the larger LCR vector to stable and variegating position effects. This trend was also observed for vector insertion sites located inside genes, where vector expression was often compromised, in contrast to intergenic sites, where higher levels of expression were observed. These data emphasize the importance of overcoming detrimental position effects for consistent therapeutic globin vector expression.

HIP/RPL29 down-regulation accompanies terminal chondrocyte differentiation

HIP is a heparin/heparan sulfate (Hp/HS) binding protein identical to ribosomal protein L29 that displays diverse biological functions. There is strong evidence that abnormal expression and quantitative deficiencies of essential molecules such as extracellular matrix (ECM) proteins, transcription factors, and ribosomal proteins can seriously impair embryonic development. As observed for HS-bearing molecules, high levels of HIP/RPL29 are found in proliferating chondrocytic precursors and chondrocytes of developing growth plate. Here, we demonstrate both in vitro and in developing mouse embryos that HIP/RPL29 is down-regulated in terminally differentiated chondrocytes corresponding to the late hypertrophic zone of the growth plate. Because cartilage serves as a template for endochondral bone formation, we hypothesize that the presence of HIP/RPL29 during early chondrogenesis is essential for normal skeletal growth and patterning. In particular, we believe that HIP/RPL29 expression is required to maintain proliferation of chondrocytes and avoid skeletal shortening. Increasing evidence suggests that multifunctional ribosomal proteins of eukaryotic cells are important regulators of cell growth and differentiation, not simply structural parts of translational machinery. To investigate the role of HIP/RPL29 normal expression during cartilage formation, we designed a ribozyme-mediated knock-down approach to partially down-regulate HIP/RPL29 expression in the multipotent mouse embryonic skin fibroblast cell line C3H/10T (1/2). This technology permitted us to avoid the insufficient expression associated with more severe consequences, such as lethality, and provided advantages similar to those obtained with mutations generating hypomorphic phenotypes. Our results show that partial reduction of HIP/RPL29 levels accelerates differentiation of C3H/10T(1/2) into cartilage-like cells. In conclusion, our data indicate that HIP/RPL29 constitutes an important novel regulator of chondrocytic growth and differentiation.

Successful treatment of murine beta-thalassemia using in vivo selection of genetically modified, drug-resistant hematopoietic stem cells

Successful gene therapy of beta-thalassemia will require replacement of the abnormal erythroid compartment with erythropoiesis derived from genetically corrected, autologous hematopoietic stem cells (HSCs). However, currently attainable gene transfer efficiencies into human HSCs are unlikely to yield sufficient numbers of corrected cells for a clinical benefit. Here, using a murine model of beta-thalassemia, we demonstrate for the first time that selective enrichment in vivo of transplanted, drug-resistant HSCs can be used therapeutically and may therefore be a useful approach to overcome limiting gene transfer. We used an oncoretroviral vector to transfer a methylguanine methyltransferase (MGMT) drug-resistance gene into normal bone marrow cells. These cells were transplanted into beta-thalassemic mice given nonmyeloablative pretransplantation conditioning with temozolomide (TMZ) and O6-benzylguanine (BG). A majority of mice receiving 2 additional courses of TMZ/BG demonstrated in vivo selection of the drug-resistant cells and amelioration of anemia, compared with untreated control animals. These results were extended using a novel gamma-globin/MGMT dual gene lentiviral vector. Following drug treatment, normal mice that received transduced cells had an average 67-fold increase in gamma-globin expressing red cells. These studies demonstrate that MGMT-based in vivo selection may be useful to increase genetically corrected cells to therapeutic levels in patients with beta-thalassemia.

Pathophysiological-based approaches to treatment of sickle cell disease

Sickle hemoglobin (HbS), as a result of its polymer-related and oxidant effects, damages the sickle erythrocyte, provokes inflammation, and causes endothelial injury. All these elements cause the phenotype of sickle cell disease. Novel treatments inhibit HbS polymerization by inducing fetal hemoglobin expression, prevent or repair erythrocyte dehydration by slowing cellular potassium and water loss, and replace HbS-producing erythroid progenitors by stem cell transplantation. Future treatment prospects include gene therapy, interruption of the interaction of sickle cells with the endothelium, inhibition of oxidative damage, and protection of an injured endothelium.

Permanent and panerythroid correction of murine beta thalassemia by multiple lentiviral integration in hematopoietic stem cells

Achieving long-term pancellular expression of a transferred gene at therapeutic level in a given hematopoietic lineage remains an important goal of gene therapy. Advances have recently been made in the genetic correction of the hemoglobinopathies by means of lentiviral vectors and large locus control region (LCR) derivatives. However, panerythroid beta globin gene expression has not yet been achieved in beta thalassemic mice because of incomplete transduction of the hematopoietic stem cell compartment and position effect variegation of proviruses integrated at a single copy per genome. Here, we report the permanent, panerythroid correction of severe beta thalassemia in mice, resulting from a homozygous deletion of the beta major globin gene, by transplantation of syngeneic bone marrow transduced with an HIV-1-derived [beta globin gene/LCR] lentiviral vector also containing the Rev responsive element and the central polypurine tract/DNA flap. The viral titers produced were high enough to achieve transduction of virtually all of the hematopoietic stem cells in the graft with an average of three integrated proviral copies per genome in all transplanted mice; the transduction was sustained for >7 months in both primary and secondary transplants, at which time approximately 95% of the red blood cells in all mice contained human beta globin contributing to 32 +/- 4% of all beta-like globin chains. Hematological parameters approached complete phenotypic correction, as assessed by hemoglobin levels and reticulocyte and red blood cell counts. All circulating red blood cells became and remained normocytic and normochromic, and their density was normalized. Free alpha globin chains were completely cleared from red blood cell membranes, splenomegaly abated, and iron deposit was almost eliminated in liver sections. These findings indicate that virtually complete transduction of the hematopoietic stem cell compartment can be achieved by high-titer lentiviral vectors and that position effect variegation can be mitigated by multiple events of proviral integration to yield balanced, panerythroid expression. These results provide a solid foundation for the initiation of human clinical trials in beta thalassemia patients.

Hammerhead ribozymes for target validation

Expensive failures in the pharmaceutical industry might be avoided by target validation at an early stage. Often, the full consequences of inhibiting a chosen drug target do not emerge until late in the development process. One option is to use hammerhead ribozymes as highly specific ribonucleases targeted exclusively at the mRNA encoding the target protein. The first part of this review is concerned with the mechanism and design of hammerhead ribozymes. This includes the chemistry of their action, specificity of cleavage and ability to discriminate between different mRNAs and selection of suitable cleavage sites. In considering their use for target validation, hammerhead ribozymes are divided into two categories. Endogenous ribozymes are transcribed inside the cell where they act whilst exogenous are introduced into the cell from outside. Exogenous ribozymes are synthesised chemically and must be protected against cellular nucleases. Information is provided on transfection methods and vectors that have been used with endogenous ribozymes as well as synthesis and chemical modification of exogenous ribozymes. Of proteins inhibited in cells or whole organisms, those in animal experiments are emphasised. Comparisons are made with other approaches, especially the use of antisense oligonucleotides or RNA.

Correction of sickle cell disease in transgenic mouse models by gene therapy

Sickle cell disease (SCD) is caused by a single point mutation in the human betaA globin gene that results in the formation of an abnormal hemoglobin [HbS (alpha2betaS2)]. We designed a betaA globin gene variant that prevents HbS polymerization and introduced it into a lentiviral vector we optimized for transfer to hematopoietic stem cells and gene expression in the adult red blood cell lineage. Long-term expression (up to 10 months) was achieved, without preselection, in all transplanted mice with erythroid-specific accumulation of the antisickling protein in up to 52% of total hemoglobin and 99% of circulating red blood cells. In two mouse SCD models, Berkeley and SAD, inhibition of red blood cell dehydration and sickling was achieved with correction of hematological parameters, splenomegaly, and prevention of the characteristic urine concentration defect.

Therapeutic potential of ribozymes in haematological disorders

Ribozymes are RNA molecules that possess the ability to cleave and thus destroy other RNA molecules. As a result of this ability, they are ideal specific agents to use against the messenger RNAs of important genes found to be linked with disease (of cellular and viral origin). This review will briefly describe the different types of ribozyme and the potential they have as therapeutic compounds against viruses, oncogenes and drug resistance in haematological settings. The latest news from the various Phase I and II ribozyme clinical trials is discussed, as is the potential for the ribozymes' future as therapeutic agents.

Multi-ribozyme targeting of human alpha-globin gene expression

One approach to gene therapy for the treatment of hemoglobinopathies has been focused on increasing normal globin gene expression. However, because of the high concentration of hemoglobin in the red blood cell (32-34 g/dl), merely introducing the normal globin gene may not be enough to counteract the effect of an abnormal globin. We propose that in addition to strategies to add normal beta- or gamma-globin production to sickle erythrocytes, a decrease in overall hemoglobin concentration would further decrease the polymerization potential and should be considered with other gene therapy approaches. Ribozymes offer the potential to target a selected gene product. A model system has been set up using the human alpha-globin gene for specific gene suppression by ribozymes by cleaving alpha-globin mRNA transcripts. Ribozymes, specifically targeted to five different sites in the 5' portion of human alpha-globin mRNA, have been designed and tested in vitro. Cleavage of 32P-labeled alpha-globin mRNA by these ribozymes has been observed in vitro and the highest level of activity has been found for a multi-ribozyme combining all five ribozymes. The multi-ribozyme gene along with promoters with varying activities in erythroid cells was transfected into human erythroleukemia K562 cells. The multi-ribozyme gene, under the control of human alpha-2-globin promoter alone and combined with the locus control region enhancer, caused a decrease in the level of alpha-globin mRNA of 50-75% compared to the control, determined by RNase protection and by real-time quantitative PCR. The decrease in alpha-globin transcripts has been found to be correlated with expression of the multi-ribozyme in a dose-dependent manner and does not appear to be mediated by an antisense effect. These results suggest that the multi-ribozyme may be useful in gene therapy as an effective suppressor of a specific globin gene.