Systematic comparison of a color reporter gene and drug resistance genes for the determination of retroviral titers

Functional analysis of gammaretroviral vector transduction by quantitative PCR

BACKGROUND

In a clinical setting of gene therapy, quantitative methods are required to determine recombinant viral titres and transgene mRNA expression, avoiding the use of reporter genes.

METHODS

We describe procedures based on quantitative polymerase chain reaction (qPCR) designed to assess functional titres of murine leukaemia virus (MLV) vectors, determine proviral copy numbers in transduced cells, and estimate retroviral transgene expression in both target cell lines and mice with transduced chimeric haematopoiesis.

RESULTS

Compared to EGFP titration, proviral DNA detection by qPCR was more accurate in assessing the number of infective particles in supernatants, such that average viral titres in terms of proviral copies per cell were two-fold higher. Transgene mRNA expression was directly determined from the vectors used without the need for reporter assays. A new parameter, defined here as the 'transcription index' (TI), served to establish the association between transcribed transgenic mRNA and each proviral insertion. The TI represents the potential expression of every vector or insertion in each cell type, and is thus useful as a control parameter for monitoring preclinical or clinical protocols.

CONCLUSIONS

The practical use of qPCR is demonstrated as a valuable alternative to reporter genes for the assessment and surveillance of insertion numbers and transgene expression. In combination with protein expression, this approach should be capable of establishing safer therapeutic gene doses, avoiding the potential side effects of high transduction and expression levels.

Comparison of HIV-1 and EIAV-based lentiviral vectors in corneal transduction

In this study we compare the ability of self-inactivating Human Immunodeficiency Virus 1 (HIV-1) and Equine Infectious Anaemia Virus (EIAV)-based vectors to mediate gene transfer to rabbit and human corneas and to a murine corneal endothelial cell line. Both vectors were pseudotyped with vesicular stomatitis virus-G (VSV-G) envelope and contained marker transgenes under the control of an internal CMV promoter. For specificity of action, the heterologous promoter in the EIAV-vector was exchanged for an inducible E-Selectin promoter, previously shown to regulate gene-expression in a plasmid system. We show that EIAV is more efficient than HIV in transducing human and rabbit corneal endothelial cells. Rabbit corneal endothelial cells are transduced in higher quantity than human corneal endothelial cells. In the inducible system, however, we detected impairment between the vector and its internal E-Selectin promoter. Instead of controlled transgene expression or silencing of promoter activity, the U3-modified long-terminal-repeats (LTR) impaired the conditional activity of the E-Selectin promoter. Significant transgene expression was seen without stimulation of the inducible promoter. We show efficient transduction by lentiviruses of a corneal endothelial cell line and of full thickness corneas from different species, confirming that those vectors would be appropriate tools for gene therapy of selected corneal diseases. However, the modification within the U3-LTR did not adequately allow regulated transgene expression. These findings have important implications for vector design for diagnostic or therapeutic opportunities.

Host RNA polymerase II makes minimal contributions to retroviral frame-shift mutations

The rate of mutation during retrovirus replication is high. Mutations can occur during transcription of the viral genomic RNA from the integrated provirus or during reverse transcription from viral RNA to form viral DNA or during replication of the proviral DNA as the host cell is dividing. Therefore, three polymerases may all contribute to retroviral evolution: host RNA polymerase II, viral reverse transcriptases and host DNA polymerases, respectively. Since the rate of mutation for host DNA polymerase is very low, mutations are more likely to be caused by the host RNA polymerase II and/or the viral reverse transcriptase. A system was established to detect the frequency of frame-shift mutations caused by cellular RNA polymerase II, as well as the rate of retroviral mutation during a single cycle of replication in vivo. In this study, it was determined that RNA polymerase II contributes less than 3 % to frame-shift mutations that occur during retrovirus replication. Therefore, the majority of frame-shift mutations detected within the viral genome are the result of errors during reverse transcription.

Stable expression of three genes from a tricistronic retroviral vector containing a picornavirus and 9-nt cellular internal ribosome entry site elements

Retroviral vectors are used widely to deliver heterologous genes into cells. In order to express three genes from a single RNA molecule, a retroviral vector that contains two divergent internal ribosome entry site (IRES) sequences has been constructed successfully. To eliminate the high frequency of recombination within a mulicistronic retrovirus vector, a 9-nt segment of a cellular mRNA IRES and a picornaviral IRES were used, since these two IRES sequences have minimal sequence homology. After a single round of replication, most cells infected with this vector stably expressed the three genes while approximately 40% of cells infected with another tricistronic retroviral vector that contains two copies of an identical IRES sequence lost expression of the gene located between these two sequences.

Intramolecular recombinations of Moloney murine leukemia virus occur during minus-strand DNA synthesis

Retroviral recombination can occur between two viral RNA molecules (intermolecular) or between two sequences within the same RNA molecule (intramolecular). The rate of retroviral intramolecular recombination is high. Previous studies showed that, after a single round of replication, 50 to 60% of retroviral recombinations occur between two identical sequences within a Moloney murine leukemia virus-based vector. Recombination can occur at any polymerization step within the retroviral replication cycle. Although reverse transcriptase is assumed to contribute to the template switches, previous studies could not distinguish between changes introduced by host RNA polymerase II (Pol II) or by reverse transcriptase. A cell culture system has been established to detect the individual contribution of host RNA Pol II, host DNA polymerase or viral reverse transcriptase, as well as the recombination events taking place during minus-strand DNA synthesis and plus-strand DNA synthesis in a single round of viral intramolecular replication. Studies in this report demonstrate that intramolecular recombination between two identical sequences during transcription by host RNA Pol II is minimal and that most recombinations occur during minus-strand DNA synthesis catalyzed by viral reverse transcriptase.

Rapid screening for high-titer retroviral packaging cell lines using an in situ fluorescence assay

The production of high-titer recombinant retrovirus is a major determinant of the efficiency of target cell transduction. Titer assessment for producer clones that contain vectors encoding proteins that can be detected using fluorescence is typically performed by flow cytometry. However, this method is both costly and labor intensive, severely limiting the number of clones that can be screened for each construct. In this report we describe a rapid, high-throughput screening method for viral quantitation of producer clone supernatant on target cells using a 96-well format. Plates were assayed using a multichannel fluorescent reader to determine the percentage of target cells expressing green (EGFP), cyan (ECFP), yellow (EYFP) or red (DsRed) fluorescent reporter genes, or their combinations. The relative fluorescence counts of target cells incubated with viral supernatant from each packaging cell clone correlated with the level of transduction, and hence, viral titer. Correlation of cell fluorescence between the fluorescent plate reader assay and flow cytometric assessment was high (r(2) = 0.96). Independent detection of different fluorescent reporters enabled multiplex assays to be performed. Simultaneous cell density analysis using alamarBlue fluorescence was proportional to cell number per well (r(2) = 1.0). In situ titer assessment of 66 FLYRD packaging cells encoding the EGFP reporter gene identified clones (>10(7) colony forming units per milliliter [CFU/ml]) that provided titers up to sevenfold over the parent population. The application of this rapid, high-throughput screening method overcomes many limitations imposed by the current flow cytometric screening method. This robust assay maximizes the chance of identifying rare high-titer packaging clones and offers a further opportunity to optimize gene transfer protocols.

Is it all DNA repair? Methodological considerations for detecting neurogenesis in the adult brain

Since the early 1960s, in vivo observations have shown the generation of new neurons from dividing precursor cells. Nevertheless, these experiments suffered from skepticism, suggesting that the prevailing labeling method, which incorporates tagged thymidine analogs, such as [3H]-thymidine or bromodeoxyuridine (BrdU), may not be detecting a proliferative event, but could rather mark DNA repair in postmitotic neurons. Even today many scientists outside the field are still skeptical, because the question of specificity for thymidine labeling has not been sufficiently answered. This current paper aims at evaluating the arguments that are used by proponents and skeptics of this method by (i) presenting histological evidence of specificity of BrdU labeling for neural stem cell/progenitor activity in the adult brain; (ii) validating and comparing BrdU labeling with other histological methods; and (iii) combining BrdU and labeling methods for apoptosis to argue against DNA repair being a major contribution of BrdU-positive cells.

Evidence for retroviral intramolecular recombinations

As a consequence of being diploid, retroviruses have a high recombination rate. Naturally occurring retroviruses contain two repeat sequences (R regions) flanking either end of their RNA genomes, and recombination between these two R regions occurs at a high rate. We deduced that recombination may occur between two sequences within the same RNA molecule (intramolecular) as well as between sequences present within two separate RNA molecules (intermolecular). Intramolecular recombination would usually result in a deletion within the progeny provirus. In this report, we demonstrate that intramolecular recombination between two identical sequences occurred within a chimeric RNA vector. In addition, high rates of recombination between two identical sequences within the same RNA molecule resulted mostly from intramolecular recombination.

A novel retroviral vector that allows the magnetic selection of infected cells

Retroviral vectors are used widely in research and are also being designed for use in gene therapy trials. In practice, these vectors usually contain a marker gene, which is often a drug selection gene. In this report, a novel retroviral vector has been constructed which contains a gene that allows selection for infected cells by a magnet. This gene is a single-chain antibody (sFv) to a specific hapten molecule 4-ethoxymethylene-2-phenyl-2-oxazolin-5-one (phOx). sFv specific for phOx is displayed on the surface of infected cells. This feature allows binding to phOx-BSA coated magnetic beads which are used to isolate the infected cells.

Determination of the frequency of retroviral recombination between two identical sequences within a provirus

Retroviruses use RNA as their genetic material within viral particles and DNA (provirus) as their genetic material within cells. The rate of recombination during reverse transcription between two identical sequences within the same RNA molecule is very high. In this study, we have developed a sensitive system to study recombination occurring within the proviral sequence. This system includes a murine Moloney leukemia virus vector which contains a neomycin resistance gene (neo) and two mutated green fluorescent protein genes (gfp) in tandem positions. The 3' end of the first gfp and the 5' end of the second gfp gene are both mutated, so that neither of these two gfp genes is functional. However, if recombination occurs between the two gfp genes it will create a functional gfp protein. Cells containing such a functional recombinant gfp appear green under fluorescence microscopy. The rate of recombination between the two gfp sequences during a single round of replication is as high as 51%. Green cells appear during proliferation of a clonal clear-cell population and allow a small portion of these recombinations between sequences of proviral DNA to be detected. The frequency of recombination at the proviral DNA level is about 10(-5) events/cell division, which is very low compared with the frequency of recombination (51%) caused by reverse transcriptase and/or RNA polymerase II.

The cellular mismatch repair system is able to repair mismatches within MLV retroviral double-stranded DNA at a low frequency

Eukaryotic cells possess several distinct mismatch repair pathways. A mismatch can be introduced in retroviral double-stranded DNA by a pre-existing mutation within the primer binding site (PBS) of the viral RNA genome. In order to evaluate mismatch repair of retroviral double-stranded DNA, Moloney leukemia virus (MLV)-based vectors with a mutation in their PBS were used to infect mismatch repair-competent as well as mismatch repair-deficient cell lines. If the target cells were capable of repairing the mismatch before an infected cell divided, the mismatch within the PBS could be repaired to the wild-type or mutant PBS. If the target cells were unable to repair the mismatch, half the cells in the colony should contain the mutant PBS while the other half should contain the wild-type PBS. To evaluate these predictions, individual colonies were isolated and analyzed by PCR. Almost all mismatch-deficient cell colonies analyzed (cell lines HCT 116 and PMS2-/-) contained both the wild-type and mutated PBS, therefore, mismatches within retroviral double-strand DNA could not be repaired by the mismatch-deficient cells. In contrast, mismatches in approximately 25% of the mismatch repair-competent cell clones analyzed (cell lines HeLa and PMS2+/+) were repaired, while 75% were not. Therefore, the cellular mismatch repair system is able to repair mismatches within viral double-stranded DNA, but at a low frequency.

Most retroviral recombinations occur during minus-strand DNA synthesis

Retroviral RNA molecules are plus, or sense in polarity, equivalent to mRNA. During reverse transcription, the first strand of the DNA molecule synthesized is minus-strand DNA. After the minus strand is polymerized, the plus-strand DNA is synthesized using the minus-strand DNA as the template. In this study, a helper cell line that contains two proviruses with two different mutated gfp genes was constructed. Recombination between the two frameshift mutant genes resulted in a functional gfp. If recombination occurs during minus-strand DNA synthesis, the plus-strand DNA will also contain the functional sequence. After the cell divides, all of its offspring will be green. However, if recombination occurs during plus-strand DNA synthesis, then only the plus-strand DNA will contain the wild-type gfp sequence and the minus-strand DNA will still carry the frameshift mutation. The double-stranded DNA containing this mismatch was subsequently integrated into the host chromosomal DNA of D17 cells, which were unable to repair the majority of mismatches within the retroviral double-strand DNA. After the cell divided, one daughter cell contained the wild-type gfp sequence and the other daughter cell contained the frameshift mutation in the gfp sequence. Under fluorescence microscopy, half the cells in the offspring were green and the other half of the cells were colorless or clear. Thus, we demonstrated that more than 98%, if not all, retroviral recombinations occurred during minus-strand DNA synthesis.