Patent Grant
10704061
The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 270077_402USPC_SEQUENCE_LISTING.txt. The text file is 192 KB, was created on Nov. 14, 2016, and is being submitted electronically via EFS-Web.
The present invention relates to lentiviral gene transfer vectors pseudotyped with hemagglutinin-neuraminidase (HN) and fusion (F) proteins from a respiratory paramyxovirus, comprising a promoter and a transgene; and methods of making the same. The present invention also relates to the use of said vectors in gene therapy, particularly for the treatment of respiratory tract diseases such as Cystic Fibrosis (CF).
Lentiviruses belong to a genus of viruses of the Retroviridae family, and are characterised by a long incubation period. Lentiviruses can deliver a significant amount of viral RNA into the DNA of the host cell and have the unique ability among retroviruses of being able to infect non-dividing cells, so they are one of the most efficient methods of a gene delivery vector.
Lentiviral vectors, especially those derived from HIV-1, are widely studied and frequently used vectors. The evolution of the lentiviral vectors backbone and the ability of viruses to deliver recombinant DNA molecules (transgenes) into target cells have led to their use in many applications. Two possible applications of viral vectors include restoration of functional genes in genetic therapy and in vitro recombinant protein production.
Pseudotyping is the process of producing viruses or viral vectors in combination with foreign viral envelope proteins. As such, the foreign viral envelope proteins can be used to alter host tropism or an increased/decreased stability of the virus particles. For example, pseudotyping allows one to specify the character of the envelope proteins. A frequently used protein is the glycoprotein G of the Vesicular stomatitis virus (VSV), short VSV-G.
Efficient and controllable retroviral expression of a transgene is understood to require the presence of intron sequences. However, incorporation of such introns into retroviral vectors involves elaborate and time-consuming methods owing to the multi-step processes employed.
To date, viral gene transfer agents have not been useful for the treatment of diseases, without the transduction of stem cell populations, because of the host adaptive immune response, which prevents successful repeat administration.
Moreover, gene transfer to the airway epithelium has proven more difficult than originally anticipated. For example, the use of lentiviral pseudotypes that require disruption of epithelial integrity to transduce the airways, for example by the use of detergents such as lysophosphatidylcholine or ethylene glycol bis(2-aminoethyl ether)-N,N,N′N′-tetraacetic acid, has been linked to an increased risk of sepsis.
One example of a clinical setting which would benefit from gene transfer to the airway epithelium is treatment of Cystic Fibrosis (CF). CF is a fatal genetic disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, which acts as a chloride channel in airway epithelial cells. CF is characterised by recurrent chest infections, increased airway secretions, and eventually respiratory failure. In the UK, the current median age at death is ˜25 years. For most genotypes, there are no treatments targeting the basic defect; current treatments for symptomatic relief require hours of self-administered therapy daily. Gene therapy, unlike small molecule drugs, is independent of CFTR mutational class and is thus applicable to all affected CF individuals. However, to date no viral vector has met the requirements for clinical use, and the same applies to other diseases, particularly many other respiratory tract diseases.
In this regard, at least three major problems have been encountered. Gene transfer efficiency is generally poor, at least in part because the respective receptors for many viral vectors appear to be predominantly localised to the basolateral surface of the airway epithelium. Second, penetration of the respiratory tract mucus layer is generally poor. Finally, the ability to administer viral vectors repeatedly, mandatory for the life-long treatment of a self-renewing epithelium, is limited.
Administration of the vectors for clinical application is another pertinent factor. Therefore, viral stability through use of clinically relevant devices (e.g. bronchoscope and nebuliser) must be maintained for treatment efficacy.
Another example of a potential target for gene therapy is α1-antitrypsin (A1AT) deficiency. A1AT deficiency is an inherited disorder that may cause lung disease and liver disease. Symptoms include shortness of breath/wheezing, reduced ability to exercise, weight loss, recurring respiratory infections, fatigue and rapid heartbeat upon standing. Affected individuals often develop emphysema. About 10-15% percent of patients with A1AT deficiency develop liver disease. Individuals with A1AT deficiency are also at risk of developing a hepatocellular carcinoma.
A1AT is a secreted protein, produced mainly in the liver and then trafficked to the lung, with smaller amounts also being produced in the lung itself. The main function of A1AT is to bind and neutralise neutrophil elastase. A1AT gene therapy is likely to be of therapeutic value in patients with A1AT deficiency, CF and chronic obstructive pulmonary disease (COPD), where increasing or introducing A1AT may improve lung function.
A1AT therapy is also potentially valuable for the treatment of non-respiratory/non-pulmonary diseases, such as type 1 and type 2 diabetes, acute myocardial infarction, rheumatoid arthritis, inflammatory bowel disease, transplant rejection, graft versus host (GvH) disease, multiple sclerosis and infections, particularly viral infections, due to the effect of A1AT deficiency on other tissues/organs, such as the liver and pancreas (see, for example, Lewis Mol. Med. 2012; 18:957-970, which is herein incorporated by reference).
A1AT deficiency is an attractive target disease for gene therapy because the therapeutic threshold levels are well defined. A comparison of A1AT levels in subjects with the risk of developing emphysema/COPD determined a protective threshold level of 11 μM in serum, with levels below 11 μM are used as threshold for initiating protein augmentation therapy where available. A1AT levels in airway lining fluid are only ˜10% of serum level, because the lung epithelium constitutes a barrier and the therapeutic threshold in airway surface lining fluid is therefore considered to be 1.1 μM (see Ferraroti et al. Thorax. 2012 August; 67(8):669-74 and Abusriwil & Stockley 2006 Current Opinion in Pulmonary Medicine 12:125-131, each of which is herein incorporated by reference).
Six FDA-approved commercial formulations of A1AT protein isolated from pooled human blood are in clinical use in the US for the treatment of patients with severe A1AT deficiency (via weekly intravenous injections). Enzyme replacement therapy (ERT) is expensive ($100,000/year) and although biochemical efficacy for ERT protein augmentation therapy has been proven clinical efficacy has been more difficult to prove.
A1AT ERT is currently not accessible in all countries and currently not available in the UK. In addition, it is difficult to achieve sufficiently sustained tissue levels using current therapies, which may in part be responsible for the modest clinical efficacy observed so far.
Other attractive targets for gene therapy include cardiovascular diseases and blood disorders, particularly blood clotting deficiencies such as Haemophilia (A and B), von Willebrand disease and Factor VII deficiency.
Haemophilia, particularly Haemophilia A, is an attractive target for gene therapy. Haemophilia A is an inherited bleeding disorder caused by a deficiency or mutation of Factor VIII (FVIII). Its inheritance is sex-linked, with almost all patients being male. Bleeding is typically into the joints. Bleeding into the muscle, mucosal tissue and central nervous system (CNS) is uncommon but can occur. Disease severity is inversely proportional to the level of FVIII: less than 1% (<0.01 IU/ml) results in severe disease, with bleeding after minimal injury; between 1-5% (0.01 IU/ml-0.05 IU/ml) causes moderate disease, with bleeding after mild injury; and greater than 5% (>0.05 IU/ml) causes mild disease, with bleeding only after significant trauma or surgery.
There is accordingly a need for a gene therapy vector that is able to circumvent one or more of the problems described above.
The present inventors have developed a lentiviral vector, which has been pseudotyped with hemagglutinin-neuraminidase (HN) and fusion (F) proteins from a respiratory paramyxovirus, comprising a promoter and a transgene. Typically the backbone of the vector is from a simian immunodeficiency virus (SIV), such as SIV1 or African green monkey SIV (SIV-AGM). Preferably the backbone of a viral vector of the invention is from SIV-AGM. The HN and F proteins function, respectively, to attach to sialic acids and mediate cell fusion for vector entry to target cells. The present inventors have discovered that this specifically F/HN-pseudotyped lentiviral vector can efficiently transduce airway epithelium, resulting in transgene expression sustained for periods beyond the proposed lifespan of airway epithelial cells. Importantly, the present inventors have also found that re-administration does not result in a loss of efficacy. These features make the vectors of the present invention attractive candidates for treating diseases via their use in expressing therapeutic proteins: (i) within the cells of the respiratory tract; (ii) secreted into the lumen of the respiratory tract; and (iii) secreted into the circulatory system.
The present invention addresses one or more of the above needs by providing lentiviral vectors pseudotyped with hemagglutinin-neuraminidase (HN) and fusion (F) proteins from a respiratory paramyxovirus, comprising a promoter and a transgene. In one embodiment, the promoter is preferably a hybrid human CMV enhancer/EF1a (hCEF) promoter. The present invention also provides methods of manufacturing said vectors, compositions comprising said vectors, and uses thereof in therapy.
The vectors of the present invention enable higher and sustained gene expression through efficient gene transfer. The above-identified problems are addressed by the present invention which provides F/HN-pseudotyped lentiviral vectors which are capable of: (i) airway transduction without disruption of epithelial integrity; (ii) persistent gene expression; (iii) lack of chronic toxicity; and (iv) efficient repeat administration. Long term/persistent stable gene expression, preferably at a therapeutically-effective level, may be achieved using repeat doses of a vector of the present invention. Alternatively, a single dose may be used to achieve the desired long-term expression.
By contrast with known lentiviral vectors, the lentiviral vectors of the invention exhibit efficient airway cell uptake, enhanced transgene expression, and suffer no loss of efficacy upon repeated administration.
Thus, advantageously, the lentiviral vectors of the present invention can be used in gene therapy. By way of example, the efficient airway cell uptake properties of the vectors of the invention make them highly suitable for treating respiratory tract diseases. The lentiviral vectors of the invention can also be used in methods of gene therapy to promote secretion of therapeutic proteins. By way of further example, the invention provides secretion of therapeutic proteins into the lumen of the respiratory tract or the circulatory system. Thus, administration of a vector of the invention and its uptake by airway cells may enable the use of the lungs (or nose or airways) as a “factory” to produce a therapeutic protein that is then secreted and enters the general circulation at therapeutic levels, where it can travel to cells/tissues of interest to elicit a therapeutic effect. In contrast to intracellular or membrane proteins, the production of such secreted proteins does not rely on specific disease target cells being transduced, which is a significant advantage and achieves high levels of protein expression. Thus, other diseases which are not respiratory tract diseases, such as cardiovascular diseases and blood disorders, particularly blood clotting deficiencies, can also be treated by the vectors of the present invention.
As an example, Alpha-1 Antitrypsin (A1AT) is a secreted anti-protease that is produced mainly in the liver and then trafficked to the lung, with smaller amounts also being produced in the lung itself. The main function of A1AT is to bind and neutralise/inhibit neutrophil elastase. Gene therapy with A1AT according to the present invention is relevant to A1AT deficient patient, as well as in other lung diseases such as cystic fibrosis or chronic obstructive pulmonary disease (COPD), and offers the opportunity to overcome some of the problems encountered by enzyme replacement therapy.
The present inventors have previously demonstrated that there is a significant correlation between neutrophil elastase (NE) and A1AT in sputum samples from cystic fibrosis patients, showing that the body produces A1AT in response to NE challenge. The present inventors have also shown that there is a statistically significant correlation between NE and lung clearance index, a marker of small airways disease, implying that increased NE has a negative impact on lung function. As presented herein, the inventors have now surprisingly demonstrated that the lentiviral vectors of the invention can achieve high concentrations of A1AT and long term (at least 90 days) A1AT expression in vivo. Thus, gene therapy with A1AT may neutralise NE, improving the lung function of patients with cystic fibrosis and/or COPD (and having a therapeutic effect in other indications as described herein). Accordingly, the present invention relates to the use of a lentiviral vector as described herein for the administration of an A1AT transgene and gene therapy of conditions including, but not limited to, A1AT deficiency, cystic fibrosis and/or COPD. Administration of lentiviral A1AT directly to the nasal epithelium and/or lung may overcome some of the limitations currently faced by enzyme replacement therapy (A1AT isolated from human blood and administered intravenously every week), providing stable, long-lasting expression in the target tissue (lung/nasal epithelium), ease of administration and unlimited availability.
In some embodiments, transduction with a lentiviral vector of the invention leads to secretion of the recombinant protein into the lumen of the lung as well as into the circulation. One benefit of this is that the therapeutic protein reaches the interstitium. In the case of A1AT deficiency, this is advantageous because NE inhibition is also required at this site. A1AT gene therapy may therefore also be beneficial in other disease indications, non-limiting examples of which include type 1 and type 2 diabetes, acute myocardial infarction, ischemic heart disease, rheumatoid arthritis, inflammatory bowel disease, transplant rejection, graft versus host (GvH) disease, multiple sclerosis, liver disease, cirrhosis, vasculitides and infections, such as bacterial and/or viral infections.
A1AT has numerous other anti-inflammatory and tissue-protective effects, for example in pre-clinical models of diabetes, graft versus host disease and inflammatory bowel disease. The production of A1AT in the lung and/or nose following transduction according to the present invention may, therefore, be more widely applicable, including to these indications.
Other examples of diseases that may be treated with gene therapy of a secreted protein according to the present invention include cardiovascular diseases and blood disorders, particularly blood clotting deficiencies such as haemophilia (A and B), von Willebrand disease and Factor VII deficiency.
In some embodiments, Haemophilia A may be treated according to the present invention. Disease severity is inversely proportional to the level of FVIII, and an increase in FVIII of 2-5% (0.02-0.05 IU/ml) is enough to be therapeutically effective.
In some embodiments the nose is a preferred production site for a therapeutic protein using a gene therapy vector of the invention for at least one of the following reasons: (i) extracellular barriers such as inflammatory cells and sputum are less pronounced in the nose; (ii) ease of vector administration; (iii) smaller quantities of vector required; and (iv) ethical considerations. Thus, transduction of nasal epithelial cells with a lentiviral vector of the invention may result in efficient (high-level) and long-lasting expression of the therapeutic transgene of interest.
The vectors of the present invention enable long term gene expression, resulting in long term expression of a therapeutic protein. As described herein, the phrases “long term expression”, “sustained expression” and “persistent expression” are used interchangeably. Long term expression according to the present invention means expression of a therapeutic gene and/or protein, preferably at therapeutic levels, for at least 45 days, at least 60 days, at least 90 days, at least 120 days, at least 180 days, at least 250 days, at least 360 days, at least 450 days, at least 730 days or more. Preferably long term expression means expression for at least 90 days, at least 120 days, at least 180 days, at least 250 days, at least 360 days, at least 450 days, at least 720 days or more, more preferably at least 360 days, at least 450 days, at least 720 days or more. This long term expression may be achieved by repeated doses or by a single dose.
Repeated doses may be administered twice-daily, daily, twice-weekly, weekly, monthly, every two months, every three months, every four months, every six months, yearly, every two years, or more. Dosing may be continued for as long as required, for example, for at least six months, at least one year, two years, three years, four years, five years, ten years, fifteen years, twenty years, or more, up to for the lifetime of the patient to be treated.
Lentiviral vectors, such as those of the invention, can integrate into the genome of transduced cells and lead to long-lasting expression, making them suitable for transduction of stem/progenitor cells. In the lung, several cell types with regenerative capacity have been identified as responsible for maintaining specific cell lineages in the conducting airways and alveoli. These include basal cells and submucosal gland duct cells in the upper airways, Clara cells and neuroendocrine cells in the bronchiolar airways, bronchioalveolar stem cells in the terminal bronchioles and type II pneumocytes in the alveoli. Therefore, and without being bound by theory, it is believed that the vectors of the present invention bring about long term gene expression of the transgene of interest by introducing the transgene into one or more long-lived airway epithelial cells or cell types, such as basal cells and submucosal gland duct cells in the upper airways, Clara cells and neuroendocrine cells in the bronchiolar airways, bronchioalveolar stem cells in the terminal bronchioles and type II pneumocytes in the alveoli.
Accordingly, the lentiviral vectors of the invention may transduce one or more cells or cell lines with regenerative potential within the lung (including the airways and respiratory tract) to achieve long term gene expression. In a preferred embodiment the lentiviral vector of the invention transduces basal cells, such as those in the upper airways/respiratory tract. Basal cells have a central role in processes of epithelial maintenance and repair following injury. In addition, basal cells are widely distributed along the human respiratory epithelium, with a relative distribution ranging from 30% (larger airways) to 6% (smaller airways).
The lentiviral vectors of the invention may be used to transduce isolated and expanded stem/progenitor cells ex vivo prior administration to a patient. Preferably, the lentiviral vectors of the invention are used to transduce cells within the lung (or airways/respiratory tract) in vivo.
The vectors of the present invention enable high levels of gene expression, resulting in high levels (preferably therapeutic levels) of expression of a therapeutic protein. Expression may be measured by any appropriate method (qualitative or quantitative, preferably quantitative), and concentrations given in any appropriate unit of measurement, for example ng/ml. A high level of expression according to the present invention may mean expression of a therapeutic gene and/or protein at a concentration of at least 10 ng/ml, at least 20 ng/ml, at least 30 ng/ml, at least 40 ng/ml, at least 50 ng/ml, at least 60 ng/ml, at least 70 ng/ml, at least 80 ng/ml, at least 90 ng/ml, at least 100 ng/ml, at least 200 ng/ml, at least 300 ng/ml, at least 400 ng/ml, at least 500 ng/ml, at least 600 ng/ml, at least 700 ng/ml, at least 800 ng/ml, at least 900 ng/ml, at least 1,000 ng/ml, at least 2,000 ng/ml, at least 3,000 ng/ml, at least 4,000 ng/ml, at least 5,000 ng/ml, at least 10,000, at least 15,000 ng/ml, at least 20,000 ng/ml or more. Therapeutic expression may be defined using these same values.
The lentiviral vectors of the present invention typically provide high expression levels of a transgene when administered to a patient. The terms high expression and therapeutic expression are used interchangeably herein.
A high level of expression according to the present invention may mean expression of a therapeutic gene and/or protein at a concentration of at least about 100 nM, at least about 200 nM, at least about 300 nM, at least about 400 nM, at least about 500 nM, at least about 600 nM, at least about 700 nM, at least about 800 nM, at least about 900 nM, at least about 1 μM, at least about 1.1 μM, at least about 1.2 μM, at least about 1.3 μM, at least about 1.4 μM, at least about 1.5 μM, at least about 2 μM, at least about 3 μM, at least about 4 μM, at least about 5 μM, at least about 6 μM, at least about 7 μM, at least about 8 μM, at least about 9 μM, at least about 10 μM, at least about 11 μM, at least about 12 μM, at least about 13 μM, at least about 14 μM, at least about 15 μM, at least about 20 μM, at least about 25 μM, at least about 30 μM, at least about 40 μM, at least about 50 μM, at least about 75 μM, or at least about 100 μM or more. Therapeutic expression may be defined using these same values.
A high level of expression according to the present invention may mean expression of a therapeutic gene (typically measured by mRNA expression) at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 15%, at least about 20% or more compared with the expression level of the corresponding endogenous (defective) mRNA. Therapeutic expression may be defined using these same values. For example, a typical expression level of endogenous CFTR mRNA may be quantified in terms of the number of copies of the mRNA per lung cell, for example one copy of the endogenous CFTR mRNA per lung cell, two copies of the endogenous CFTR mRNA per lung cell, three copies of the endogenous CFTR mRNA per lung cell, four copies of the endogenous CFTR mRNA per lung cell, five copies of the endogenous CFTR mRNA per lung cell, or more, preferably two copies of the endogenous CFTR mRNA per lung cell. The expression of the therapeutic gene of the invention, such as a functional CFTR gene, may be quantified relative to the endogenous gene, such as the endogenous (dysfunctional) CFTR genes in terms of mRNA copies per cell or any other appropriate unit.
A high level of expression according to the present invention may mean expression of a therapeutic gene and/or protein at a concentration of at least about 0.5%, at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more compared with the wild type level of the therapeutic gene and/or protein, wherein the wild type level is the level in a normal individual without the disease. In some embodiments, wild type expression is given as 100%, with any improvement in gene expression measured relative to that. As a non-limiting example, if in a normal individual without the disease the expression of the functional gene is given as 100%, and in an individual with the disease, the expression of the functional gene is 0%, a therapeutic level of expression of the gene or protein may be at least about 0.5%, at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, or more compared with the wild type level of the therapeutic gene and/or protein. As another non-limiting example, if in a normal individual without the disease the expression of the functional gene is given as 100%, and in an individual with the disease, the expression of the functional gene is 50%, a therapeutic level of expression of the gene or protein may be at least about 55%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more compared with the wild type level of the therapeutic gene and/or protein.
For secreted proteins such as A1AT, typically the concentration in the lung or epithelial lining fluid (as measured using BAL) is approximately ten times that in serum. As a non-limiting example, if the concentration of secreted protein in the lung or epithelial lining fluid is in the region of 750 ng/ml, the serum concentration of the protein is in the region of 75 ng/ml.
Expression levels of a therapeutic gene and/or protein of the invention may be measured in the lung tissue, epithelial lining fluid and/or serum/plasma as appropriate. A high and/or therapeutic expression level may therefore refer to the concentration in the lung, epithelial lining fluid and/or serum/plasma.
As a non-limiting example, a therapeutic expression level of CFTR is typically 1-5% of the therapeutic CFTR mRNA compared with the expression level of the endogenous (defective) CFTR mRNA.
As another non-limiting example, a therapeutic expression level of A1AT is typically at least about 1 μM in the epithelial lining fluid, and/or at least about 0.1 μM in the serum. In a preferred embodiment, a therapeutic expression level of A1AT in the epithelial lining fluid is at least about 1.1 μM, and/or a therapeutic serum expression level of A1AT according to the present invention is at least about 11 μM. As another non-limiting example, a therapeutic expression level of A1AT in the epithelial lining fluid (ELF, i.e. the fluid lining the airways and airspaces in the lungs) is 70 μg/ml (compared with a “normal” target level of ATT (A1AT) in the ELF of 200 μg/ml).
As another non-limiting example, a therapeutic expression level of FVIII protein is typically at least about 1-3% or at least about 1-6% of the expression level in a normal individual who does not suffer from haemophilia.
The therapeutic gene included in the vector of the invention may be modified to facilitate expression. For example, the gene sequence may be in CpG-depleted and/or codon-optimised form to facilitate gene expression. Standard techniques for modifying the gene sequence in this way are known in the art.
The promoter included in the vector of the invention may be specifically selected and/or modified to further refine regulation of expression of the therapeutic gene. Again, suitable promoters and standard techniques for their modification are known in the art. As a non-limiting example, a number of suitable (CpG-free) promoters suitable for use in the present invention are described in Pringle et al. (J. Mol. Med. Berl. 2012, 90(12): 1487-96), which is herein incorporated by reference in its entirety.
The vector of the invention may be modified to allow shut down of gene expression. Standard techniques for modifying the vector in this way are known in the art. As a non-limiting example, Tet-responsive promoters are widely used.
The vectors of the present invention also demonstrate remarkable resistance to shear forces with only modest reduction in transduction ability when passaged through clinically-relevant delivery devices such as bronchoscopes, spray bottles and nebulisers.
In one embodiment, the invention provides F/HN lentiviral vectors comprising a promoter and a transgene, having no intron positioned between the promoter and the transgene. In one embodiment, the vector of the present invention is delivered to cells of the respiratory tract. In embodiment, the lentivirus is SIV. In one embodiment, the promoter is a hybrid human CMV enhancer/EF1a (hCEF) promoter. Typically said promoter of the invention lacks the intron corresponding to nucleotides 570-709 and the exon corresponding to nucleotides 728-733 of the hCEF promoter. A preferred example of an hCEF promoter sequence of the invention is provided by SEQ ID NO: 6. The promoter may be a CMV promoter. An example of a CMV promoter sequence is provided by SEQ ID NO: 17. Other promoters for transgene expression are known in the art and their suitability for the lentiviral vectors of the invention determined using routine techniques known in the art. Non-limiting examples of other promoters include UbC and UCOE. As described herein, the promoter may be modified to further regulate expression of the transgene of the invention.
In one embodiment, the transgene encodes a CFTR. An example of a CFTR cDNA is provided by SEQ ID NO: 7.
In one embodiment, the transgene encodes an A1AT. An example of an A1AT transgene is provided by SEQ ID NO: 15, or by the complementary sequence of SEQ ID NO: 26. SEQ ID NO: 15 is a codon-optimized CpG depleted A1AT transgene designed by the present inventors to enhance translation in human cells. Such optimisation has been shown to enhance gene expression by up to 15-fold. Thus, in one embodiment, the invention provides a polynucleotide comprising or consisting of the nucleotide sequence of SEQ ID NO: 15. Variants of same sequence (as defined herein) which possess the same technical effect of enhancing translation compared with the unmodified (wild-type) A1AT gene sequence are also encompassed by the present invention. The invention further provides a polypeptide encoded by said A1AT transgene, as exemplified by the polypeptide of SEQ ID NO: 27, plasmids (particularly vector genome plasmids as defined herein) and lentiviral vectors comprising said A1AT transgene. In a preferred embodiment, aspects of the invention relating to A1AT gene therapy according to the present invention use the A1AT transgene sequence of SEQ ID NO: 15.
In one embodiment, the transgene encodes a FVIII. Examples of a FVIII transgene are provided by SEQ ID NOs: 16 and 30, or by the respective complementary sequences of SEQ ID NO: 28 and 31.
Lentiviral vectors suitable for use in the present invention include Human immunodeficiency virus (HIV), Simian immunodeficiency virus (SIV), Feline immunodeficiency virus (FIV), Equine infectious anaemia virus (EIAV), and Visna/maedi virus. In one embodiment of the invention, an SIV vector is used, preferably SIV-AGM. In another embodiment, an HIV vector is used.
The lentiviral vectors of the present invention are pseudotyped with hemagglutinin-neuraminidase (HN) and fusion (F) proteins from a respiratory paramyxovirus. In one embodiment, the respiratory paramyxovirus is a Sendai virus (murine parainfluenza virus type 1).
In one embodiment of the invention, the lentiviral vector is integrase-competent (IC). In an alternative embodiment, the lentiviral vector is integrase-deficient (ID).
In another embodiment of the invention, the transgene of the invention is any one or more of DNAH5, DNAH11, DNAI1, and DNAI2, or other known related gene.
In one embodiment of the invention, the respiratory tract epithelium is targeted for delivery of the vector. In this embodiment, the transgene encodes Alpha-1 Antitrypsin (A1AT), Surfactant Protein B (SFTPB), or Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF). In another embodiment, the transgene encodes a monoclonal antibody (mAb) against an infectious agent. In one embodiment, transgene encodes anti-TNF alpha. In a further embodiment, the transgene encodes a therapeutic protein implicated in an inflammatory, immune or metabolic condition.
In one embodiment of the invention, the vector is delivered to the cells of the respiratory tract to allow production of proteins to be secreted into circulatory system. In this embodiment, the transgene encodes for Factor VII, Factor VIII, Factor IX, Factor X, Factor XI and/or von Willebrand's factor. Such a vector may be used in the treatment of diseases, particularly cardiovascular diseases and blood disorders, preferably blood clotting deficiencies such as Haemophilia. In another embodiment, the transgene encodes a monoclonal antibody (mAb) against an infectious agent. In one embodiment, the transgene encodes a protein implicated in an inflammatory, immune or metabolic condition, such as, lysosomal storage disease.
In accordance with the invention, there is provided an F/HN-SIV lentiviral vector comprising an hCEF promoter and a CFTR transgene, having no intron positioned between the promoter and the transgene. Similarly, there is no intron between the promoter and the transgene in the vector genome (pDNA1) plasmid (for example, pGM326 as described herein, illustrated in
The invention also provides an F/HN-SIV lentiviral vector comprising an hCEF promoter and an A1AT transgene, having no intron positioned between the promoter and the transgene. Such a lentiviral vector may be produced by the method described herein, using a plasmid carrying the A1AT transgene and a promoter. Similarly, there is no intron between the promoter and the A1AT transgene in the vector genome (pDNA1) plasmid. An exemplary sequence of such a plasmid is given in SEQ ID NO: 9 (F/HN-SIV-hCEF-soA1AT, illustrated in
The invention also provides an F/HN-SIV lentiviral vector comprising (i) an hCEF promoter or a CMV promoter; and (ii) an FVIII transgene; wherein no intron is positioned between the promoter and the transgene. Such a lentiviral vector may be produced by the method described herein, using a plasmid carrying the FVIII transgene and a promoter. Similarly, there is no intron between the promoter and the FVIII transgene in the vector genome (pDNA1) plasmid. Exemplary sequences of such plasmids are given in SEQ ID NO: 11 to 14 (illustrated in
The lentiviral vector as described above comprises a transgene. The transgene comprises a nucleic acid sequence encoding a gene product, e.g., a protein.
For example, in one embodiment, the nucleic acid sequence encoding a CFTR, A1AT or FVIII comprises (or consists of) a nucleic acid sequence having at least 90% (such as at least 90, 92, 94, 95, 96, 97, 98, 99 or 100%) sequence identity to the CFTR, A1AT or FVIII nucleic acid sequence respectively. In a further embodiment, the nucleic acid sequence encoding CFTR, A1AT or FVIII comprises (or consists of) a nucleic acid sequence having at least 95% (such as at least 95, 96, 97, 98, 99 or 100%) sequence identity to the CFTR, A1AT or FVIII nucleic acid sequence respectively. In one embodiment, the nucleic acid sequence encoding CFTR is provided by SEQ ID NO: 7, the nucleic acid sequence encoding A1AT is provided by SEQ ID NO: 15, or by the complementary sequence of SEQ ID NO: 26 and/or the nucleic acid sequence encoding FVIII is provided by SEQ ID NO: 16 and 30, or by the respective complementary sequences of SEQ ID NO: 28 and 31, or variants thereof.
The term “polypeptide” as used herein also encompasses variant sequences. Thus, the polypeptide encoded by the transgene of the invention may have at least 90% (such as at least 90, 92, 94, 95, 96, 97, 98, 99 or 100%) sequence identity to a functional CFTR, A1AT or FVIII polypeptide sequence respectively. In a further embodiment, the amino acid sequence of the CFTR, A1AT or FVIII transgene comprises (or consists of) an amino acid sequence having at least 95% (such as at least 95, 96, 97, 98, 99 or 100%) sequence identity to the functional CFTR, A1AT or FVIII polypeptide sequence respectively. In one embodiment, the amino acid sequence of the A1AT protein encoded by the transgene of the invention comprises (or consists of) the amino acid sequence of SEQ ID NO: 27, or variants thereof. Preferably said variant A1AT proteins of the invention have at least 90% (such as at least 90, 92, 94, 95, 96, 97, 98, 99 or 100%), more preferably at least 95% or more sequence identity with SEQ ID NO: 27.
In one embodiment, the nucleic acid sequence encoding CFTR, A1AT or FVIII comprises (or consists of) the CFTR, A1AT or FVII complementary DNA sequence respectively. In one embodiment, the CFTR, A1AT or FVIII transgene is a sequence-optimised CFTR, A1AT or FVIII (soCFTR2, soA1AT or FVIII). An example is provided by SEQ ID NOS: 7, 15 and 16 respectively. An exemplary complementary sequence-optimised A1AT sequence is given by SEQ ID NO: 26. Exemplary complementary sequence optimised FVIII sequences are given by SEQ ID NOs: 28 and 31.
In one embodiment of the invention, the F/HN vector transgene expression is driven by cytomegalovirus (CMV) promoter. In another embodiment, the vector transgene expression is driven by elongation factor 1a (EF1a) promoter. In a preferred embodiment, the vector transgene expression is driven by hybrid human CMV enhancer/EF1a (hCEF) promoter. In one embodiment, the hCEF promoter has all CG dinucleotides replaced with any one of AG, TG or GT. Thus, in one embodiment, the hCEF promoter is CpG-free.
In one embodiment, the lentiviral vector may be produced using the F/HN-SIV-hCEF-soCFTR2-IC plasmid. In this embodiment, CFTR is expressed under control of the hCEF promoter. This lentiviral vector may be described as comprising F/HN-SIV-hCEF-soCFTR2-IC, as it comprises the SIV F/HN elements, as well as an integrase competent expression cassette comprising CFTR under the control of the hCEF promoter. This lentiviral vector of the invention is capable of producing long-lasting, repeatable, high-level expression in airway cells without inducing an undue immune response. Consequently, the invention provides an efficient means of in vivo gene therapy, for example, CFTR gene transfer into the CF lung for the treatment of CF lung disease.
In a preferred embodiment, the lentiviral vector may be produced using the F/HN-SIV-hCEF-soA1AT plasmid. In this embodiment, A1AT is expressed under control of the hCEF promoter. This lentiviral vector may be described as comprising F/HN-SIV-hCEF-soA1AT, as it comprises the SIV F/HN elements, as well as an expression cassette comprising A1AT under the control of the hCEF promoter. This lentiviral vector of the invention is capable of producing long-lasting, repeatable, high-level expression in airway cells without inducing an undue immune response. Consequently, the invention provides an efficient means of in vivo gene therapy, for example, A1AT gene transfer into a patient's lung or nose for the production of A1AT which is then secreted into the circulatory system (as described herein). Thus, this vector and other vectors of the invention comprising the A1AT transgene may be used in the treatment of A1AT deficiency, or other indications as described herein.
In another preferred embodiment, the lentiviral vectors may be produced using the F/HN-SIV-CMV-HFVIII-V3, F/HN-SIV-hCEF-HFVIII-V3, F/HN-Sly-CMV-HFVIII-N6-co and/or F/HN-SIV-hCEF-HFVIII-N6-co plasmids. HFVIII refers to human FVIII. In this embodiment, FVIII is expressed under control of the hCEF or CMV promoter. These lentiviral vectors may be described as comprising F/HN-SIV-CMV-HFVIII-V3, F/HN-SIV-hCEF-HFVIII-V3, F/HN-SIV-CMV-HFVIII-N6-co and F/HN-Sly-hCEF-HFVIII-N6-co respectively, as they comprise the SIV F/HN elements, as well as an expression cassette comprising FVIII under the control of the hCEF/CMV promoter. Viral vector products produced using the F/HN-SIV-CMV-HFVIII-V3, F/HN-SIV-hCEF-HFVIII-V3, F/HN-SIV-CMV-HFVIII-N6-co and/or F/HN-SIV-hCEF-HFVIII-N6-co plasmids are also known as vGM126, vGM127, vGM142 and vGM129 (see
The lentiviral vectors of the invention do not contain an intron between the promoter and the transgene. Similarly, the vector genome plasmids of the invention (used to generate said lentiviral vectors as described herein) also do not contain an intron between the promoter and the transgene. The invention therefore provides, in one embodiment, no intron between the hCEF promoter and the coding sequences to be expressed. In one preferred embodiment, the coding sequence to be expressed is a CFTR, A1AT and/or FVIII nucleic acid sequence.
In one embodiment, the vectors of the invention comprise central polypurine tract (cPPT) and the Woodchuck hepatitis virus posttranscriptional regulatory elements (WPRE). In one embodiment, the WPRE sequence is provided by SEQ ID NO: 8.
In one embodiment the vector of the invention is used for gene therapy. In one embodiment the disease to be treated is CF. In another embodiment of the invention, the disease to be treated is Primary Ciliary Dyskinesia (PCD). In one embodiment, the vector is used to treat acute lung injury. In one embodiment of the invention, the disease to be treated is Surfactant Protein B (SP-B) deficiency, Alpha 1-antitrypsin Deficiency (A1AD), Pulmonary Alveolar Proteinosis (PAP), Chronic obstructive pulmonary disease (COPD). In another embodiment, the disease is an inflammatory, immune or metabolic condition.
The disease to be treated may be a cardiovascular disease or blood disorder, particularly a blood clotting deficiency. Thus, in some embodiments, the disease to be treated is Haemophilia A, Haemophilia B, or Haemophilia C, Factor VII deficiency and/or von Willebrand disease. In yet another embodiment, the disease to be treated is an inflammatory disease, infectious disease or metabolic condition, such as, lysosomal storage disease.
Non-limiting examples of diseases which may be treated using A1AT gene therapy according to the present invention include type 1 and type 2 diabetes, acute myocardial infarction, ischemic heart disease, rheumatoid arthritis, inflammatory bowel disease, transplant rejection, graft versus host (GvH) disease, multiple sclerosis, liver disease, cirrhosis, vasculitides and infections, such as bacterial and/or viral infections.
In one aspect of the invention, the vector can effectively treat a disease by providing a transgene for the correction of the disease. For example, inserting a functional copy of the CFTR gene to ameliorate or prevent lung disease in CF patients, independent of the underlying mutation.
In another embodiment of the invention, a lentiviral production method is provided. In this embodiment, the method of the invention is a scalable GMP-compatible method. Thus, the method of the invention allows the generation of high titre purified F/HN vectors.
The method of the invention comprises the following steps:
In one embodiment of the method of the invention, the one or more plasmids provide the vector genome, the Gag-Pol, Rev, F and HN. Thus, there can be five plasmids for each of the vector genome, the Gag-Pol, Rev, F and HN, respectively. In the preferred 5 plasmid method of the invention, the vector genome plasmid encodes all the genetic material that is packaged into final lentiviral vector, including the transgene. Typically only a portion of the genetic material found in the vector genome plasmid ends up in the virus. The vector genome plasmid may be designated herein as “pDNA1”. The other four plasmids are manufacturing plasmids encoding the Gag-Pol, Rev, F and HN proteins. These plasmids may be designated “pDNA2a”, “pDNA2b”, “pDNA3a” and “pDNA3b” respectively.
In one embodiment of the invention, the lentivirus is SIV, such as SIV1, preferably SIV-AGM. In one embodiment, the F and HN proteins are derived from a Paramyxovirus, such as Sendai virus. In one embodiment, the vector genome plasmid (pDNA1) comprises the transgene and the transgene promoter.
In a specific embodiment relating to CFTR, the five plasmids are characterised by
In an embodiment relating to A1AT, the five plasmids may be characterised by
In an embodiment relating to FVIII, the five plasmids may be characterised by
In these embodiments of the invention, the plasmid as defined in
In the 5 plasmid method of the invention all five plasmids contribute to the formation of the final lentiviral vector. During manufacture of the lentiviral vector, the vector genome plasmid (pDNA1) provides the enhancer/promoter, Psi, RRE, cPPT, mWPRE, SIN LTR, SV40 polyA (see
For other lentiviral vectors of the invention, corresponding elements from the other vector genome plasmids (pDNA1) are required for manufacture (but not found in the final vector), or are present in the final viral vector.
The F and HN proteins from pDNA3a and pDNA3b (preferably Sendai F and HN proteins) are important for infection of target cells with the final lentiviral vector, i.e. for entry of a patients epithelial cells (typically lung or nasal cells as described herein). The products of the pDNA2a and pDNA2b plasmids are important for virus transduction, i.e. for inserting the lentiviral DNA into the host's genome. The promoter, regulatory elements (such as WPRE) and transgene are important for transgene expression within the target cell(s).
In one embodiment, steps (a)-(f) are carried out sequentially. In one embodiment, the cells are HEK293 cells or 293T/17 cells. In one embodiment, the cells are grown in animal-component free (serum-free) media. In one embodiment, the transfection is carried out by the use of PEIPro™. In one embodiment, the nuclease is an endonuclease, for example, Benzonase®. In one embodiment, the trypsin activity is provided by an animal origin free, recombinant enzyme such as TrypLE Select™.
In one embodiment of the invention, the addition of the nuclease is at the pre-harvest stage. In an alternative embodiment, the addition of the nuclease is at the post-harvest stage. In another embodiment, the addition of trypsin is at the pre-harvest stage. In another embodiment, the addition of the trypsin is at the post-harvest stage.
In one embodiment, the purification step comprises a chromatography step. In this embodiment, mixed-mode size exclusion chromatography (SEC) is used. In one embodiment, anion exchange chromatography is used. In this embodiment, no salt gradient is used for the elution step.
In one embodiment, this method is used to produce the lentiviral vectors of the invention. In this embodiment, the vector of the invention comprises the CFTR, A1AT and/or FVIII gene. In an alternative embodiment, the vector of the invention comprises any of the above-mentioned genes, or the genes encoding the above-mentioned proteins.
In one embodiment of the method of the invention, any combination of one or more of the specific plasmid constructs provided by
The invention further provides a method of treating a disease, the method comprising administering a lentiviral vector of the invention to a subject. In this embodiment, the invention provides a lentiviral vector of the invention for use in treatment of a lung disease. In one embodiment, disease is a chronic disease. In a specific embodiment, a method of treating CF is provided. In other embodiments, a method of treating Primary Ciliary Dyskinesia (PCD), Surfactant Protein B (SP-B) deficiency, Alpha 1-antitrypsin Deficiency (A1AD), Pulmonary Alveolar Proteinosis (PAP), Chronic obstructive pulmonary disease (COPD) is provided. In another embodiment, the disease is an inflammatory, immune or metabolic condition.
In another embodiment, the disease may be a cardiovascular disease or blood disorder, particularly a blood clotting deficiency, such as Haemophilia A, Haemophilia B, Haemophilia C, Factor VII deficiency and/or von Willebrand disease, an inflammatory disease, infectious disease or metabolic condition, such as, lysosomal storage disease.
The disease may be type 1 and type 2 diabetes, acute myocardial infarction, ischemic heart disease, rheumatoid arthritis, inflammatory bowel disease, transplant rejection, graft versus host (GvH) disease, multiple sclerosis, liver disease, cirrhosis, vasculitides and infections, such as bacterial and/or viral infections.
The lentiviral vectors of the invention may be administered in any dosage appropriate for achieving the desired therapeutic effect. Appropriate dosages may be determined by a clinician or other medical practitioner using standard techniques and within the normal course of their work. Non-limiting examples of suitable dosages include 1×108 transduction units (TU), 1×109 TU, 1×1010 TU, 1×1011 TU or more.
The invention also provides compositions comprising the lentiviral vectors described above, and a pharmaceutically-acceptable carrier. Non-limiting examples of pharmaceutically acceptable carriers include water, saline, and phosphate-buffered saline. In some embodiments, however, the composition is in lyophilized form, in which case it may include a stabilizer, such as bovine serum albumin (BSA). In some embodiments, it may be desirable to formulate the composition with a preservative, such as thiomersal or sodium azide, to facilitate long-term storage.
The vectors of the invention may be administered by any appropriate route. It may be desired to direct the compositions of the present invention (as described above) to the respiratory system of a subject. Efficient transmission of a therapeutic/prophylactic composition or medicament to the site of infection in the respiratory tract may be achieved by oral or intra-nasal administration, for example, as aerosols (e.g. nasal sprays), or by catheters. Typically the lentiviral vectors of the invention are stable in clinically relevant nebulisers, catheters and aerosols, etc.
Formulations for intra-nasal administration may be in the form of nasal droplets or a nasal spray. An intra-nasal formulation may comprise droplets having approximate diameters in the range of 100-5000 μm, such as 500-4000 μm, 1000-3000 μm or 100-1000 μm. Alternatively, in terms of volume, the droplets may be in the range of about 0.001-100 μl, such as 0.1-50 μl or 1.0-25 μl, or such as 0.001-1 μl.
The aerosol formulation may take the form of a powder, suspension or solution. The size of aerosol particles is relevant to the delivery capability of an aerosol. Smaller particles may travel further down the respiratory airway towards the alveoli than would larger particles. In one embodiment, the aerosol particles have a diameter distribution to facilitate delivery along the entire length of the bronchi, bronchioles, and alveoli. Alternatively, the particle size distribution may be selected to target a particular section of the respiratory airway, for example the alveoli. In the case of aerosol delivery of the medicament, the particles may have diameters in the approximate range of 0.1-50 μm, preferably 1-25 μm, more preferably 1-5 μm.
Aerosol particles may be for delivery using a nebulizer (e.g. via the mouth) or nasal spray. An aerosol formulation may optionally contain a propellant and/or surfactant.
As used herein, the terms “nucleic acid sequence” and “polynucleotide” are used interchangeably and do not imply any length restriction. As used herein, the terms “nucleic acid” and “nucleotide” are used interchangeably. The terms “nucleic acid sequence” and “polynucleotide” embrace DNA (including cDNA) and RNA sequences. The terms “transgene” and “gene” are also used interchangeably and both terms encompass fragments or variants thereof encoding the target protein.
The transgenes of the present invention include nucleic acid sequences that have been removed from their naturally occurring environment, recombinant or cloned DNA isolates, and chemically synthesized analogues or analogues biologically synthesized by heterologous systems.
The polynucleotides of the present invention may be prepared by any means known in the art. For example, large amounts of the polynucleotides may be produced by replication in a suitable host cell. The natural or synthetic DNA fragments coding for a desired fragment will be incorporated into recombinant nucleic acid constructs, typically DNA constructs, capable of introduction into and replication in a prokaryotic or eukaryotic cell. Usually the DNA constructs will be suitable for autonomous replication in a unicellular host, such as yeast or bacteria, but may also be intended for introduction to and integration within the genome of a cultured insect, mammalian, plant or other eukaryotic cell lines.
The polynucleotides of the present invention may also be produced by chemical synthesis, e.g. by the phosphoramidite method or the tri-ester method, and may be performed on commercial automated oligonucleotide synthesizers. A double-stranded fragment may be obtained from the single stranded product of chemical synthesis either by synthesizing the complementary strand and annealing the strand together under appropriate conditions or by adding the complementary strand using DNA polymerase with an appropriate primer sequence.
When applied to a nucleic acid sequence, the term “isolated” in the context of the present invention denotes that the polynucleotide sequence has been removed from its natural genetic milieu and is thus free of other extraneous or unwanted coding sequences (but may include naturally occurring 5′ and 3′ untranslated regions such as promoters and terminators), and is in a form suitable for use within genetically engineered protein production systems. Such isolated molecules are those that are separated from their natural environment.
In view of the degeneracy of the genetic code, considerable sequence variation is possible among the polynucleotides of the present invention. Degenerate codons encompassing all possible codons for a given amino acid are set forth below:
One of ordinary skill in the art will appreciate that flexibility exists when determining a degenerate codon, representative of all possible codons encoding each amino acid. For example, some polynucleotides encompassed by the degenerate sequence may encode variant amino acid sequences, but one of ordinary skill in the art can easily identify such variant sequences by reference to the amino acid sequences of the present invention.
A “variant” nucleic acid sequence has substantial homology or substantial similarity to a reference nucleic acid sequence (or a fragment thereof). A nucleic acid sequence or fragment thereof is “substantially homologous” (or “substantially identical”) to a reference sequence if, when optimally aligned (with appropriate nucleotide insertions or deletions) with the other nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 70%, 75%, 80%, 82, 84, 86, 88, 90, 92, 94, 96, 98 or 99% of the nucleotide bases. Methods for homology determination of nucleic acid sequences are known in the art.
Alternatively, a “variant” nucleic acid sequence is substantially homologous with (or substantially identical to) a reference sequence (or a fragment thereof) if the “variant” and the reference sequence they are capable of hybridizing under stringent (e.g. highly stringent) hybridization conditions. Nucleic acid sequence hybridization will be affected by such conditions as salt concentration (e.g. NaCl), temperature, or organic solvents, in addition to the base composition, length of the complementary strands, and the number of nucleotide base mismatches between the hybridizing nucleic acids, as will be readily appreciated by those skilled in the art. Stringent temperature conditions are preferably employed, and generally include temperatures in excess of 30° C., typically in excess of 37° C. and preferably in excess of 45° C. Stringent salt conditions will ordinarily be less than 1000 mM, typically less than 500 mM, and preferably less than 200 mM. The pH is typically between 7.0 and 8.3. The combination of parameters is much more important than any single parameter.
Methods of determining nucleic acid percentage sequence identity are known in the art. By way of example, when assessing nucleic acid sequence identity, a sequence having a defined number of contiguous nucleotides may be aligned with a nucleic acid sequence (having the same number of contiguous nucleotides) from the corresponding portion of a nucleic acid sequence of the present invention. Tools known in the art for determining nucleic acid percentage sequence identity include Nucleotide BLAST.
One of ordinary skill in the art appreciates that different species exhibit “preferential codon usage”. As used herein, the term “preferential codon usage” refers to codons that are most frequently used in cells of a certain species, thus favouring one or a few representatives of the possible codons encoding each amino acid. For example, the amino acid threonine (Thr) may be encoded by ACA, ACC, ACG, or ACT, but in mammalian host cells ACC is the most commonly used codon; in other species, different codons may be preferential. Preferential codons for a particular host cell species can be introduced into the polynucleotides of the present invention by a variety of methods known in the art. Introduction of preferential codon sequences into recombinant DNA can, for example, enhance production of the protein by making protein translation more efficient within a particular cell type or species.
Thus, in one embodiment of the invention, the nucleic acid sequence is codon optimized for expression in a host cell.
A “fragment” of a polynucleotide of interest comprises a series of consecutive nucleotides from the sequence of said full-length polynucleotide. By way of example, a “fragment” of a polynucleotide of interest may comprise (or consist of) at least 30 consecutive nucleotides from the sequence of said polynucleotide (e.g. at least 35, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800 850, 900, 950 or 1000 consecutive nucleic acid residues of said polynucleotide). A fragment may include at least one antigenic determinant and/or may encode at least one antigenic epitope of the corresponding polypeptide of interest. Typically a fragment as defined herein retains the same function as the full-length polynucleotide or polypeptide.
The present invention will now be described by way of example only with reference to the accompanying drawings, in which:
The invention is now described with reference to the Examples below. These are not limiting on the scope of the invention, and a person skilled in the art would be appreciate that suitable equivalents could be used within the scope of the present invention. Thus, the Examples may be considered component parts of the invention, and the individual aspects described therein may be considered as disclosed independently, or in any combination.
HEK293T, Freestyle 293F (Life Technologies, Paisley, UK) and 293T/17 cells (CRL-11268; ATCC, Manassas, Va.) were maintained in Dulbecco's minimal Eagle's medium (Invitrogen, Carlsbad, Calif.) containing 10% fetal bovine serum and supplemented with penicillin (100 U/ml) and streptomycin (100 μg/ml) or Freestyle™ 293 Expression Medium (Life Technologies).
pCAGGS-Fct4 and pCAGGS-SIVct+HN were constructed as follows:
(i) Plasmid SIVct/HN contains the gene encoding the cytoplasmic tail of SIVagm TMP (reversed) fused to the ectodomain and transmembrane regions of SeV HN protein. Three oligonucleotide pairs were synthesized: pair 1, 5′-TCGAGATGTGGTCTGAGTTAAAAATCAGGAGCAACGACGGAGGTGAAGGACCAGACGCCAACGACCC-3′ (SEQ ID NO: 18) and 5′-CCGGGGGTCGTTGGCGTCTGGTCCTTCACCTCCGTCGTTGCTCCTGATTTTTAACTCAGACCACATC-3′ (SEQ ID NO: 19); pair 2, 5′-CCGGGGAAAGGGGGTGCAACACATCCATATCCAGCCATCTCTACCTGTTTATGGACAGA-3′ (SEQ ID NO: 20) and 5′-ACCCTCTGTCCATAAACAGGTAGAGATGGCTGGATATGGATGTGTTGCACCCCTTTCC-3′ (SEQ ID NO: 21); and pair 3, 5′-GGGTTAGGTGGTTGCTGATTCTCTCATTCACCCAGTGGG-3′ (SEQ ID NO: 22) and 5′-GATCCCCACTGGGTGAATGAGAGAATCAGCAACCACCTA-3′ (SEQ ID NO: 23).
These oligonucleotide pairs were annealed and cloned into the XhoI and BamHI sites of pBluescript KS+ (Stratagene) to yield pKS+SIVct. pCAGGS-SIVct/HN was constructed by cloning the 160-bp XhoI-DraIII fragment from pKS+SIVct and a 1.5-kbp DraIII-Bsu36I fragment from pCAGGS-HN, which carries the wild-type HN gene (HNwt), in the XhoI site of pCAGGS vector, into the XhoI and Bsu36I sites of pCAGGS. This plasmid was constructed so that the cytoplasmic tail of the HN protein was replaced with the cytoplasmic tail of SIVagm TMP.
For construction of pCAGGS-SIVct+HN, the genes encoding the cytoplasmic tail of SIVagm TMP and the N terminus of HN protein were first amplified by PCR from pCAGGS-SIVct/HN with the primer pair 5′-GAGACTCGAGATGTGGTCTGAGTTAAAAATCAGG-3′ (SEQ ID NO: 24) and 5′-AGAGGTAGACCAGTACGAGTCACGTTTGCCCCTATCACCATCCCTAACCCTCTGTCATAAAC-3′ (SEQ ID NO: 25). The resulting PCR fragment was cloned into the XhoI and AccI sites of pKS+SIVct to generate pKS+SIVct-H. Then a XhoI-DraIII fragment from pKS+SIVct-H and a DraIII-Bsu36I fragment from pCAGGS-HN were cloned into the XhoI and Bsu36I sites of pCAGGS to yield pCAGGS-SIVct+HN.
The cPPT and WPRE sequences were inserted in the SIV-derived gene transfer plasmid. An example of the WPRE sequence used is provided in SEQ ID NO: 8.
The plasmid pGM101 contains the colE1 origin of replication, kanamycin resistance gene and promoter and was created by synthetic gene synthesis (GeneArt, Regensburg, Germany; now LifeTechnologies Ltd).
The hybrid CMV/SIV R U5 LTR, partial Gag, RRE, cPPT, SIN U3 and R sequences from pBS/CG2-Rc/s-CMV-D U (Nakajima et al. 2000 Human Gene Therapy 11:1863) were amplified by PCR and inserted along with the hCEF enhancer/Promoter sequence amplified by PCR from pGM169 (Hyde et al. Nature Biotechnology 26:549) and the soCFTR2 cDNA isolated from pGM169 on a NheI-ApaI restriction enzyme fragment into pGM101 to create pGM326.
The CMV enhancer/chicken beta actin promoter along with associated exon/intron sequences, SIV GagPol and RRE sequences and the SV40 polyA/origin of replication were amplified by PCR from pCAGGS/Sagm-gtr (Nakajima et al. 2000 Human Gene Therapy 11:1863) to create pGM297. The CMV enhancer/promoter along with associated exon/intron sequences and SV40 polyA sequence from pCI (Promega, Madison, Wis., USA) were isolated on a BgIII-BamHI restriction enzyme fragment and the SIV Rev sequence derived from pCAGGS/Sagm-gtr amplified by PCR were inserted into pGM101 to create pGM299.
The CMV enhancer/chicken beta actin promoter along with associated exon/intron sequences, the Fct4 cDNA and SV40 polyA/origin from pCAGGS-Fct4 were isolated on a SalI-HindIII restriction enzyme fragment by a combination of gene synthesis, PCR and restriction enzyme fragment recombination and inserted into pGM101 to create pGM301.
The CMV enhancer/chicken beta actin promoter along with associated exon/intron sequences, the SIVct+HN cDNA and SV40 polyA/origin from pCAGGS-SIVct+HN were isolated on a SalI-HindIII restriction enzyme fragment by a combination of gene synthesis, PCR and restriction enzyme fragment recombination and inserted into pGM101 to create pGM303.
Other pGM plasmids of the invention were made using standard techniques and in accordance with the above disclosure.
Throughout these plasmid DNA assembly approaches, restriction enzymes and PCR polymerases were supplied by New England Biolabs (Ipswich, Mass., USA) and DNA purification reagents were supplied by Qiagen (Limburg, Netherlands).
Four Plasmid System:
Replication-defective self-inactivating SIV vector was constructed with minor modifications. Briefly, the SeV-F/HN-pseudotyped SIV vector was produced by transfecting 293T/17 cells (15 cm diameter culture dishes) with four plasmids complexed to Lipofectamine/Plus reagents (Invitrogen) according to the manufacturer's recommendations [Plasmid-1: 10 μg SIV-derived transfer plasmid carrying a GFP, a luciferase (lux) reporter gene, or a GFP-CFTR fusion construct, Plasmid-2: 3 μg packaging plasmid, Plasmid-3: 2 μg pCAGGS-Fct4, Plasmid 4: 2 μg pCAGGS-SIVct+HN;
Five Plasmid System (Preferred):
SeV-F/HN-pseudotyped SIV vector was produced by transfecting HEK293T or 293T/17 cells cultured in FreeStyle™ 293 Expression Medium with a mixture of five plasmids with the following characteristics: pDNA1 (for example pGM326;
Cell culture media was supplemented at 12-24 post-transfection with sodium butyrate. Sodium butyrate stimulates vector production via inhibiting histone deacetylase resulting in increasing expression of the SIV and Sendai virus fusion protein components encoded by the five plasmids. Cell culture media was supplemented at 44-52 hours and/or 68-76 hours post-transfection with 5 units/mL Benzonase Nuclease (Merck Millipore, Nottingham, UK). The culture supernatant containing the SIV vector was harvested 68-76.5 hours after transfection, and clarified by filtration through a 0.45 μm membrane. The SIV vector is treated by digestion with a protease containing trypsin activity—for example an animal origin free, recombinant enzyme such as TrypLE Select™. Subsequently, SIV vector is typically further purified and concentrated by anion-exchange chromatography and/or tangential flow filtration ultra-filtration/dia-filtration.
This same method was used to generate lentiviral vectors comprising the A1AT and FVIII transgenes, with the plasmids of
Method 1:
The particle titre was determined using real-time reverse transcriptase-PCR. Virus RNA was purified using a QIAamp viral RNA mini-kit (QIAGEN, Strasse, Germany), and reverse transcribed using Superscript II (Invitrogen). The QuantiTect probe PCR system (QIAGEN) and primers for amplifying 131 nucleotides (bp) spanning the WPRE sequence (forward primer: 5′-ggatacgctgctttaatgcc-3′ (SEQ ID NO: 34), reverse primer: 5′-acgccacgttgcctgacaac-3′ (SEQ ID NO: 35)) were used according to the manufacturer's protocol in an ABI PRISM 7700 Sequence Detector System (PE Applied Biosystems, Foster City, Calif.). SIV gene transfer plasmid DNA (3×104 to 2×106 molecules) was used as standard.
Transduction units (TU/ml) were determined by transducing 293T cells with serial dilutions of vector stock and quantification of transduced cells by GFP fluorescence (for F/HN-SIV-GFP and VSV-G-SIV-GFP) or staining with anti-luciferase antibody (for F/HN-SIV-lux).
Method 2 (Preferred):
The particle titre (VP/mL) was typically determined using real-time reverse transcriptase-PCR. Virus RNA was purified using a QIAamp viral RNA mini-kit (QIAGEN, Strasse, Germany), and reverse transcribed using reverse transcriptase (Life Technologies). TaqMan quantitative PCR system (Life Technologies) using primers amplifying a portion of the WPRE sequence in an ABI PRISM 7700 Sequence Detector System (Life Technologies). In vitro transcribed WPRE RNA molecules were used as quantitative standards.
Transduction units (TU/mL) were determined by transducing 293T/17 or Freestyle 293F cells with serial dilutions of SIV vector and quantification of WPRE containing provirus DNA by TaqMan quantitative PCR system (Life Technologies) using primers amplifying a portion of the WPRE sequence in an ABI PRISM 7700 Sequence Detector System (Life Technologies). Plasmid DNA molecules containing WPRE sequences were used as quantitative standards.
Murine tracheal epithelial cells (tEC) were isolated as follows. C57BL/6N Mice were culled and the tracheas were excised from the larynx to the main bronchial branches using sterile surgical instruments. The tissues were placed in a tube containing cold Ham's F-12 medium with 100 U/ml penicillin (P), 100 μg/ml streptomycin (S) and 2.5 mg/ml amphotericin B (A) (Ham's F12/PSA medium) and kept on ice. In a sterile tissue culture hood, the tracheas were cleaned from adherent muscles and connective tissue, cut longitudinally to expose the internal respiratory epithelium, and placed in 0.15% pronase solution in F-12 medium (˜5 ml in 15 ml tube). Tissue digestion was performed overnight (15-18 hr) at 4° C. To block the enzymatic reaction, 10% fetal bovine serum (FBS) was added to the tissue digest. After gently inverting the tube to detach more cells, the tracheas were placed into a new tube containing 10% FBS/Ham's F-12/PS solution, and inverted as before. This step was repeated two more times. The content of the four tubes was pooled together and centrifuged at 500 g for 10 min at 4° C. The pellet was re-suspended in DNase solution (0.5 mg/ml crude pancreatic DNase plus 10 mg/ml BSA in FBS/Ham's F-12/PS solution, about 200 μl/trachea), incubated on ice for 5 minutes, and centrifuged as before.
After removing the supernatant, tEC were resuspended in Progenitor Cell Targeted (PCT) medium (CnT-17, CELLnTEC, Bern, Switzerland), an antibiotics and antimycotics-free formulation specifically designed for human and mouse airways progenitor cells isolation and proliferation. tEC were then plated in a Primaria tissue culture dish (Becton Dickinson Labwere, Franklin Lakes, N.J., USA) and incubated for 3-4 hr in 5% CO2 at 37° C. Non-adherent cells were collected and centrifuged at 500 g for 5 min at 4° C. and counted in a haemocytometer. To generate basal cells-enriched cultures, tEC were suspended in PCT medium and seeded on a Nunclon™ Δ plate (Nunc A/S, Roskilde, Denmark), coated with 50 μg/ml type 1 rat tail collagen at a recommended seeding density of 4×103 cells/cm2. tEC were also cultured in a control basic medium, containing DMEM/Ham's F12 supplemented with L-glutamine (4 mM), HEPES (15 mM) and NaHCO3 (3.4 mM). Plates were incubated at 37° C. with 5% CO2. To determine the proportion of basal cells in the tEC population before and after expansion in PCT medium, cytospin preparations were stained with the anti-KRT5 antibody and the appropriate secondary antibody.
The pool of tEC produced comprised both fully differentiated cells (Clara and ciliated cells) and basal cells. Once seeded onto permeable membranes tEC were able to generate an air liquid interface (ALI) culture system as a result of basal cell proliferation and redifferentiation into secretory and ciliated cells. To establish an alternative and rapid protocol for basal cell expansion, two-dimensional (2D) tEC cultures using a commercially available proprietary Progenitor Cell Targeted (PCT) medium, specifically formulated to support the proliferation of airway progenitor cells while maintaining them in an undifferentiated status were assessed. As a negative control, tEC were exposed to a basic media formulation without addition of specific growth factors. tEC seeded on collagen-coated plastic surfaces (4×103 cells/cm2) and exposed to PCT medium were able to grow rapidly and became confluent within 5-8 days whereas tEC exposed to the growth factor-deficient control medium were unable to adhere and propagate. To establish whether the use of PCT medium resulted in a substantial enrichment of the basal cell population, tEC were harvested at approximately 80% confluence (n=6 wells), fixed and treated with an anti-keratin 5 (Krt5) antibody, a specific marker of basal cells. Freshly isolated tEC were used as controls (n=3 unique preparations). The proportion of Krt5 positive basal cells after expansion in PCT medium was higher (78±1.4%) than in freshly isolated pools of tEC (33±0.6%), demonstrating that murine airway basal cells can be selectively and rapidly expanded from a mixed pool of tEC using a commercial medium.
To determine whether the F/HN-SIV vector can effectively transduce basal cells ex vivo, tEC prepared in Example 5 were grown to approximately 70% confluence over 7 days in PCT medium and transduced with F/HN-SIV carrying a green fluorescent protein reporter gene (F/HN-SIV-GFP) at an MOI 100 and incubated at 37° C. with 5% CO2 for 3 days. tEC derived from wild-type and GFP transgenic animals were cultured under the same conditions and used as negative (no viral transduction) and positive control groups, respectively (n=3-6 wells/group).
To quantify the proportion of GFP-positive cells, basal cells-enriched tEC cultures were detached with the enzyme accutase (CELLnTEC), re-suspended in PBS/1% BSA and subjected to FACS analysis, counting an average of 20.277±2.478 cells/group. The F/HN-SIV vector transduced 26%±0.9% of basal cells-enriched tEC (p<0.0001 when compared to untransduced controls).
To assess whether transduced GFP-expressing cells were basal cells, three days post-infection cells were double stained with antibodies against Krt5 and GFP. Immunofluorescence staining of cultured cells showed that approximately 40% of Krt5-expressing cells also expressed the GFP reporter gene, showing that the F/HN-SIV vector can transduce progenitor basal cells ex vivo.
C57BL/6N mice (female, 6-8 weeks) were used. Mice were anesthetized, placed horizontally on their backs onto a heated board, and a thin catheter (<0.5 mm outer diameter) was inserted ˜2.5 mm from the tip of nose into the left nostril. Using a syringe pump (Cole-Parmer, Vernon Hills, Ill.), vector (100 μl) was then slowly perfused onto the nasal epithelium (1.3 μl/min) for 75 minutes. Despite perfusion of virus into the left nostril, we routinely observe transfection in both left and right nostrils, which is due to dispersion of the solutions throughout the entire nasal cavity. PBS and VSV-G-SIV transduced mice preconditioned with 1% lysophosphatidylcholine as described by Limberis et al., 2002, were used as controls. At indicated time points (3-360 days after transduction), mice were culled to visualize GFP expression. As shown in
Similarly, as shown in
In the repeat administration experiments groups of mice were transduced with either one dose of F/HN-SIV-lux (single-dose group), or two doses of F/HN-SIV-GFP (day 0, day 28), followed by F/HN-SIV-lux on day 56 (repeat-dose group). Importantly, mice receiving F/HN-SIV-lux (single-dose group) and F/HN-SIV-lux on day 56 (repeat-dose group) were of similar age and were transduced at the same time. Gene expression was analysed 30 days after F/HN-SIV-lux administration. For comparison, mice were transfected with the cationic lipid GL67A complexed to a luciferase reporter gene as previously described (Griesenbach, U. et al., Methods Mol Biol. 2008; 433:229-42) and luciferase expression was measured 2 days after transfection.
As shown in
Insertion site profiling was conducted on transduced mice, and survival time investigated as set out in the description of
Nasal epithelial cells were stripped by polidocanol treatment according to the method described (Borthwick et al., Am J Respir Cell Mol Biol. 2001 June; 24(6):662-70), with some modification. In brief, mice were anesthetized and 10 μl polidocanol (2%) was administered to the nose as a bolus by “nasal sniffing”. To confirm the stripping and regeneration of nasal epithelial cells, nasal tissue was perfused with 10 μl of 2% (vol/vol in PBS) polidocanol (nonaethylene glycol mono-dodecyl ether; SIGMA, St Louis, Mo.) and histological analysis undertaken 24 hours and 7 days after treatment (n=3/group).
To analyse transduction of possible progenitor or stem cells, we first administered F/HN-SIV-GFP (4×108 TU/mouse) vector to mouse nasal epithelium. Seven days after transduction, nasal tissue was perfused with 10 μl of 2% (vol/vol in PBS) polidocanol, and this treatment was repeated again 3 weeks later. Histological sections were analysed 58 days after vector administration (30 days after the last polidocanol treatment).
Mice were injected intraperitoneally with 150 mg/kg of D-luciferin (Xenogen, Alameda, Calif.) 10 minutes before imaging and were anesthetized with isoflurane. Bioluminescence (photons/s/cm2/sr) from living mice was measured using an IVIS50 system (Xenogen) at a binning of 4 for 10 minutes, using the software programme Living Image (Xenogen). For anatomical localization a pseudocolor image representing light intensity (blue: least intense, red: most intense) was generated using Living Image software and superimposed over the grayscale reference image. To quantify bioluminescence in the nose, photon emission in a defined area (red box) was measured by marking a standardized area for quantification. The size of the red box was kept constant and was placed over the heads of the animals as indicated in the figure. Importantly, the areas were marked using the grayscale reference image to avoid bias.
Mice were culled and the skin was removed. The head was cut at eye level and skin, jaw, tongue, and the soft tip of the nose were carefully removed. For in situ imaging of GFP expression in the nasal cavity, GFP fluorescence was detected using fluorescence stereoscopic microscopy (Leica, Ernst Leitz Optische Werke, Germany). Subsequently, the tissue was fixed in 4% paraformaldehyde (pH 7.4) overnight at room temperature and was then submerged in 20% EDTA (pH 7.5 for 5 days) for decalcification. The EDTA solution was changed at least every second day. After decalcification, the tissue was incubated in 15% sucrose overnight at room temperature and was then embedded in Tissue Mount (Chiba Medical, Soka, Japan). Ten micrometer sections were cut at six different positions in each mouse head (˜0-6 mm from the tip of nasal bone). GFP expression was observed using a fluorescent microscope (Leica). Quantification and identification of cell types were carried out on six levels per mouse using a ×40 or ×63 objective. Prolonged image exposure was necessary to capture the structure of the nasal epithelium using fluorescent microscopy. This led to pixel saturation of GFP-positive cells and caused GFP-positive cells to appear almost white rather than the common green appearance that we, and others, observe under higher magnification.
Cellular distribution of F/NH-SIV transgene expression was investigated in histological sections. Specifically, EGFP expression was determined in histological sections of the mouse nasal cavity (2 mm from the tip of the nose) at 30 days post treatment.
To detect basal cells following polidocanol treatment horseradish peroxidase (HRP)-based immunostaining was performed using the Envision kit (Dako, Glostrup, Denmark). Briefly, slides were treated with 0.6% hydrogen peroxide in methanol for 15 min, washed in tap water and incubated with 1.5% normal goat serum (Abcam) for 30 min. Slides were then incubated with a rabbit polyclonal anti-Cytokeratin 5 antibody (1:500) (Abcam) for 1 hr following a Goat anti-rabbit IgG conjugated to HRP (provided with the kit) for 30 min. Sections were then washed in PBS and incubated with the peroxidase substrate 3-amino-9-ethylcarbazole (AEC) (provided with the kit) for 5 min. Finally, slides were washed in distilled H2O, counterstained with aqueous Harris' hematoxylin (BDH) for 15 seconds, washed in tap water, and then in distilled H2O.
Immunofluorescence detection of GFP-positive transduced nasal epithelial cells and Krt5 positive basal cells was performed using the following primary and secondary antibodies: goat polyclonal anti-GFP antibody (1:250) (Abcam), rabbit monoclonal anti-KRT5 antibody (1:500) (Abcam), Alexa Fluor 488 donkey anti-Goat IgG (1:200) (Invitrogen, Paisley, UK) and Alexa Fluor 594 goat anti-rabbit IgG (1:200) (Invitrogen). To improve antibody performance, sections were subjected to heat-mediated antigen retrieval in citrate buffer (10 mM citric acid, 0.05% Tween20, pH 6.0) for 20 min on a water bath at 100° C. Stained sections were mounted in ProLong® Gold Antifade Reagent with DAPI (Invitrogen) and analysed with a confocal microscope as before (all Zeiss). GFP-positive basal cells (identification based on morphology and location within the epithelial layer) were quantified on a total of 13 sections/mouse. Sections that displayed putative GFP positive basal cells were selected for double staining with the anti-KRT5 and anti-GFP antibodies to confirm the basal cell phenotype.
Fully differentiated airway epithelial cells grown as ALI cultures were purchased from Epithelix (Geneva, Switzerland). ALIs were transfected with F/HN-SIV-lux at a multiplicity of infection ranging from ˜25 to ˜300 TU/cell. After 6 hours, the virus was removed and ALIs were incubated for 10-26 days. The basolateral medium was changed every 48 hours during this incubation period. At specified time points, the ALIs were lysed in 100 μl reporter lysis buffer and luciferase expression was quantified using the Luciferase Assay System (Promega, Southampton, UK) according to the manufacturer's instructions. The total protein content of the cultures was quantified using the BioRad protein assay kit (BioRad, Hemel Hempstead, UK). Each sample was assayed in duplicate. Luciferase expression was then presented as relative light units/mg total protein. For bioluminescence imaging 100 μg luciferin in PBS were added to the apical membrane.
As shown in
HEK293T cells were transfected with F/HN-SIV-GFP-CFTR or an F/HN-SIV-GFP control virus at a multiplicity of infection of 500 TU/cell and cultured for 2 days. CFTR chloride channel activity was assayed by measuring the rate of 125iodide efflux as previously described (Derand, R., et al., 2003). The 125iodide efflux rates were normalized to the time of forskolin/IBMX addition (time 0). Curves were constructed by plotting rates of 125iodide efflux against time. To reflect the cumulative levels of 125iodide efflux following agonist-stimulation, all comparisons are based on areas under the time-125iodide efflux curves. The area under the curve was calculated by the trapezium rule. Experiments were carried out in duplicate (n=6 wells/group/experiment).
As shown in
F/HN-SIV efficiently transduces sheep & human primary lung cells and mouse lung.
F/HN-SIV-CMV-Lux was used to transduce human nasal brushings (MOI 250) and human and sheep lung slices cultured ex vivo (1×107 TU/slice). As shown in
Primary human CF lung cells cultured at the air-liquid interface (CF hALIs, ˜1×105) were transduced with (3×107 TU) F/HN-SIV-soCFTR2 vectors containing CMV- and hCEF transgene promoters. Vector copy number (copies of pro-viral DNA per copy of endogenous CFTR DNA) was measured at 6-8 days post-transduction. Both the CMW and hCEF promoters were able to achieve a vector copy number of at least 1×101 (
CFTR mRNA expression level (% VE: copies of CFTR mRNA per copy of endogenous CFTR mRNA×100) at 6-8 days post-transduction was also measured. The horizontal dotted line in
Following in vivo delivery of F/HN-SIV-EGFPLux vectors containing CMV, EF1a and hCEF promoters in integrase defective (ID) or integrase competent form (IC or no label) airway cells transgene expression was determined in the nasal (
Two of the five vectors tested (vGM014 EF1a and vGM020 hCEF) achieved expression in the lung above the target level for the whole time course of the experiment. One vector, vGM012 CMW, achieved expression in the lung above the accepted expression level for the whole time course of the experiment.
Bioluminescence was detected following in vivo murine transduction at day 14 post transduction. Representative images are shown in
Bioluminescence was also detected following in vitro transduction of non-CF hALI at day 5-6 post transduction. Representative images are shown
The time-course of luciferase transgene expression in non-CF ALIs was monitored by repeated bioluminescence imaging and was normalised to the delivered dose. As shown in
F/HN-SIV also efficiently transduces sheep lung in vivo. Acriflavine was instilled (3×100 μL aliquots over ˜5 minutes) to a proximal airway under direct bronchoscopic visualisation. The distribution of the acriflavine can be appreciated by the orange colouration of the dissected airway at postmortem (
The acriflavine was largely restricted to the conducting airways and absent from the alveolar regions. The arrow in
The sample blocks were divided into 2-3 approximately equivalent samples and analysed for transgene expression, the results of which are shown in
Human CF intestinal organoids were generated as described by Dekkers J F et al, (Nature Medicine 2013, 19(7): 939-945). Briefly, intestinal biopsies were washed in EDTA containing solutions to dissociate crypt cells. Crypt cells were then transduced with vGM058 (approximately 1×107 transduction units) or a control virus (n=3 wells/condition) and embedded in Matrigel and allowed to form organoids for 3-4 days. CFTR function was assessed by exposing the organoids to forskolin (approximately 5 μM forskolin) which increases intracellular cAMP levels and thereby activates CFTR. In response the CFTR activation the organoids increase chloride transport which leads to water uptake and swelling. Organoids (minimum 10/well) were directly analysed by confocal live-cell microscopy (LSM710, Zeiss, ×5 objective). Forskolin-stimulated organoid swelling was automatically quantified using Volocity imaging software (Improvision). The total organoid area (xy plane) increase relative to that at t=0 of forskolin treatment was calculated and averaged. Forskolin induced swelling was significantly (p<0.001) increased in vGM058 transduced organoids compared to controls (see
Lentiviral vectors were prepared using the SIV backbone and 5 plasmid method described above in Examples 2 and 3 (for the CFTR lentivirus) and using the hCEF promoter as described herein. Two separate lentiviral constructs were generated: one with a human alpha-1-antitrypsin (hAAT) transgene; one with a Gaussia luciferase (Glux) transgene (see
Fully differentiated wild-type human ALI cultures (MucilAir) were purchased from Epithelix SARL (Geneva, CH). ALIs were cultured at 37° C. and 5% CO2 and the basolateral culture medium changed every 2-3 days. The culture medium was stored at −20° C. until further analysis.
ALIs were transduced (on day 0) by pipetting 100 μl of virus (1×107 Tagman transfection units (TTU) onto the apical surface. The virus was removed after 4 hours incubation at 37° C., and the basolateral medium replaced.
At indicated timepoints post-transduction, the apical surface of the ALIs was washed by incubating with sterile PBS for one hour. The washings were removed and stored at −20° C. until further analysis.
A Gaussia luciferase assay (New England Biolabs, Ipswich, USA) was performed according to manufacturer's recommendations. 15 μl of sample was analysed in duplicate, and luminescence determined in an Appliskan plate reader. Glux expression was expressed as RLU/μl fluid (RUL=relative light units).
Lentiviral-mediated gene transfer in human air-liquid interfaces resulted in the long-term expression of secreted reporter protein Gaussia luciferase.
Precision-cut human lung slices were prepared as described in Moreno L et al, Respir Res 2006 Aug. 21; 7:111. Lung slices were placed in 12-well tissue culture plates (1 slice per well) in 1 ml of media and incubated at 37° C. and 5% CO2. The media was changed daily and stored at −20° C. until further analysis.
On day 0 lung slices (n=6 per group) were transduced with SIV hCEF-sogLux (1×106 TTU) or SIV1 hCEF-sohAAT (2×106 TTU) virus diluted in medium to a final volume of 1000 μl and incubated for 4 hours. After the incubation, medium was replaced and stored at −20° C. until further analysis.
Gaussia luciferase expression was determined as described above (Example 16). As shown in
Mouse Lung Transduction:
Female C57BL/6 mice (Charles River, UK) were anaesthetised with isoflurane and given 100 ul of virus by nasal instillation as described in Xenariou S et al, Gene Ther 2007 May; 14(9): 768-75. Animals were given between 1 and 5 doses and observed daily for signs of toxicity.
For Gaussia luciferase, female C57BL/6 mice were anaesthetised on day 0 using isoflurane and given a single 100 ul dose of the SIV1 hCEF-soGLux virus (1×106 TTU) by nasal instillation. Control animals were treated with DMEM (tissue culture medium), the main constituent of the viral preparation used in the study.
For A1AT, female C57bl/6 mice (n=5 per group) were treated with 3 doses of SIV1 hCEF-sohAAT at 10-day intervals (100 μl per dose, 6.8×107 TTU; total dose 2.4×108 TTU). Control animals were instilled with 100 ul of sterilised PBS (the main constituent of the lentivirus production batch used in the study) at each dosing point.
10 days after the third dose, animals were sacrificed and lung tissue homogenate, broncho-alveolar lavage fluid and serum analysed for AAT expression.
In addition, long term expression of A1AT was investigated. On days 1 to 5 of the experiment, C57bl/6 mice were treated with 100 μl of SIV1 hCEF-sohAAT by nasal instillation (5 doses of 4×105 TTU, i.e. 2×10e6 TTU per animal in total). Control animals were instilled with 100 ul of DMEM (tissue culture medium), the main constituent of the lentivirus production batch used in the study. Animals were sacrificed at various timepoints post-transduction and lung tissue homogenate, broncho-alveolar lavage fluid and serum were analysed for AAT expression.
Mouse Tissue Collection:
Mice were sacrificed at the indicated time-points post transduction. Blood was collected by puncturing the left ventricle, and centrifuged at 760 gav for 10 minutes to prepare serum. Serum was subsequently frozen at −80° C.
A bronco-alveolar lavage (BAL) was performed by dissecting the neck, inserting a cannula into the trachea and securing it in place with suture thread. 500 μl of PBS was instilled into the lung, and aspirated three times to obtain thorough washing of the epithelial lining. The sample was immediately snap frozen in liquid nitrogen, and stored at −80° C. for further analysis.
Lungs were then dissected and snap-frozen in liquid nitrogen, and subsequently homogenised in lysing matrix D tubes (MP Biomedicals), centrifuged in a FastPrep machine (ThermoFisher Scientific, Waltham, Mass., USA) at 4 m/s for 45 seconds, and stored at −80° C. for further analysis.
AAT (A1AT) and Gaussia luciferase (Glux) expression was determined as described in Examples 16 and 17 above. In vivo transduction of mouse airway cells with a single dose of the lux reporter gene lentiviral vector of Example 15 resulted in long-term expression (at least 12 months) of the secreted reporter protein Gaussia luciferase, in lung homogenate (
High levels of expression of A1AT were observed in lung homogenate, BAL and serum following lentiviral-mediated transfer of the AAT (A1AT) gene in vivo (
In addition, long-term expression (at least 90 days) of alpha-1-antitrypsin was observed in lung homogenate (
C57bl/6 mice (n=5 per group) were treated with 3 doses of SIV1 hCEF-sohAAT at 10-day intervals (100 μl per dose, 6.8×107 TTU; total dose 2.4×108 TTU). Control animals were instilled with 100 ul of sterilised PBS (the main constituent of the lentivirus production batch used in the study) at each dosing point.
10 days after the third dose, animals were sacrificed and lung tissue homogenate, broncho-alveloar lavage fluid and serum analysed for A1AT expression.
A urea assay (Abcam, Cambridge, UK) was performed according to the manufacturer's instructions.
Firstly, serial dilutions of murine serum and BAL fluid samples were prepared and analysed to determine the appropriate dilution to use in further experiments.
Secondly, corresponding serum and BAL fluid samples from single mice (n=14) were analysed to calculate the fold-difference between urea concentration in serum and BAL fluid, equivalent to the dilutional effect of BAL on epithelial lining fluid (as per Rennard SI et al, J Appl Physiol (1985). 1986 February; 60(2):532-8). The mean dilution of BAL was 41-fold (range 24-88).
Taking into account this dilutional effect, the concentration of ATT (A1AT) in the epithelial lining fluid was calculated. Specifically, the concentration of AAT in the broncho-alveolar lavage fluid was multiplied by the dilution factor, to provide an estimate of the ‘true’ AAT concentration in epithelial lining fluid.
A “protective” target level of ATT (A1AT) in the epithelial lining fluid (ELF, i.e. the fluid lining the airways and airspaces in the lungs) is 70 μg/ml (compared with a “normal” target level of ATT (A1AT) in the ELF of 200 μg/ml). As shown in
Four different FVIII lentiviral vectors were prepared using the SIV backbone and 5 plasmid method described above in Examples 2 and 3 (for the CFTR lentivirus) and 15 (for the A1AT lentivirus). The promoter-transgene plasmids have SEQ ID NOs: 11 to 14 respectively.
The SIV sequence was identical to the CFTR constructs (Examples 2 and 3) except for the promoter and cDNA. The human cytomegalovirus promotor (CMV) or tissue specific hCEFI promotor/enhancer was used as indicated (
SIV-F/HN-FVIII-N6-co contained the wild type human FVIII cDNA from which the BDD domain has been deleted and replaced with codon optimised 226 amino acid 6N-glycosylation fragment.
SIV-FVIII-V3 contains the wild type human FVIII cDNA from which the 226 amino acid glycosylation site has been deleted and replaced with 17 amino acid peptide which expresses 6N-glycosylation triples within the B domain (McIntosh et al., Blood 2013 121(17); 3335-3344).
Human FVIII antigen levels in a murine model were quantified by enzyme-linked immunosorbent assay (ELISA) according to the manufacturer's protocol. Briefly, plasma, BAL and lung were analysed for the presence of FVIII antigen using Asserachrom (FVIII:Ag) Elisa (Stago Diagnostics, France).
Samples were diluted 1:2 and incubated on a mouse monoclonal anti-human factor VIII fragment-coated 96-well plate for 2 hours at room temperature. Following washing, anti-mouse secondary antibody coupled with peroxidase was added to the plate and incubation was carried out for 2 hours at RT. hFVIII:Ag levels were determined spectrophotometric at 450 nm using TMB substrate (data not shown).
Another ELISA assay was used to evaluate FVIII activity in an in vitro HEK293T model (FVIII:C, Affinity Biological, Canada). Supernatants were collected 48 and 72 hours after HEK293T transduction with SIV-F/HN-FVIII-N6 or SIV-F/HN-FVIII-N3. FVIII activity was evaluated by following the manufacturer's instructions using 50 μl supernatants assayed in duplicate. As a negative control the supernatant from untreated HEK293T cells was tested. hFVIII activity was calculated from a standard curve generated using a series of dilutions of normal human pooled plasma (13th British Standard for blood coagulation Factor VIII concentrate, Human; NIBSC).
HEK293T cells were transduced with two different batches of vGM142 (Batch 1-5.9×108 TTU/ml and Batch 2-2.8×108 TTU/ml). HEK293T cells were transduced with vGM142 Batch 1 vector (
As is clear from
Mouse Lung Transduction:
All animal procedures were performed in accordance with the conditions and limitation of the UK Home Office Project and Personal licence regulations under the Animal Scientific Procedure Act (1986).
Wild type C57BL/6 female mice aged 6-8 weeks old (Charles River, UK were anaesthetised using isofluorane and given 100 μl of virus in Dulbecco's phosphate-buffered saline (D-PBS), as described previously (Griesenbach et al., 2012) and the presence of FVIII antigen was assessed.
In two experiments (Group 1 and 2) mice received 3 doses (every other day) of SIV-F/HN-FVIII-N6 (vGM142) and were culled 10 days after the first dose. Group 1 (n=4) were treated with a total vector dose of 1.4×106 TTU/mouse. Group 2 (n=3) were treated with a total vector dose of 1.57×108 TTU/mouse
In one experiment (Group 3) mice were treated with 12 doses (every other day) of SIV-F/HN-FVIII-N6 (vGM142) and culled 28 days after the first dose. Group 3 (n=4) were treated with a total vector dose of 3.36×108 TTU/mouse)
Plasma, BAL fluid and Lung were collected (as described in Example 14). Briefly, the mice were sacrificed at the indicated time-points post transduction. Blood was then collected from heart into the 3.2 trisodium citrate anticoagulant collection tubes, before being centrifuged at 2000-2500×g to obtain plasma. BAL fluid was collected by applying 3 consecutive installations of PBS (500 μl) into mouse lung at room temperature. Supernatants were stored at −80° C. Lungs were collected and stored at −80° C. prior to tissue homogenisation.
The presence of FVIII expression was then assessed. FVIII levels were assessed in lung tissue homogenates (
As is clear from
HEK293 cells are grown in suspension, in Freestyle Expression Media (chemically defined, animal & protein-free), and the cell count is monitored. Glucose concentration is determined and titrated to ˜35 mM. A transfection mixture of pDNA/PEIPro™ is prepared and the cells are transfected at 0.33 mg pDNA/1E9 cells.
Cell count is monitored again and further Freestyle Expression Media is added. Glucose concentration is again determined and titrated to ˜35 mM. 5 u/mL of Benzonase® can be added and three-stage inline virus clarification is carried out. Benzonase® is added followed by TrypLE Select™. The virus is cooled to 0° C. and kept on wet ice for all subsequent steps. After filtering any non-virus particulate matter (mPES 0.45 μm filter), the virus is loaded onto Mustang® Q XT (3 mL membrane/L clarified virus) followed by washing with 0.15M NaCl Tris pH7.5 and elution with 1.0M NaCl Tris pH7.5. The virus fraction is collected and diluted to 0.1-0.2 initial volume with Freestyle media. TrypLE Select™ can be added here if not added above and Benzonase® can be also be added at this stage in addition to or instead of above.
Spectrum Tangential flow filtration (TFF) is carried out (UF to ˜0.1-0.05 initial volume=HV; DF retentate×5 HV against formulation buffer; UF to ˜0.001-0.002 initial volume) and retentate is collected. A second TFF step may be carried out and a smaller TFF unit for DF and/or final UF can be used. Additional steps can include mixed-mode/SEC and 0.45 μm or 0.2 μm sterile filtration.
See the results of this exemplary method of the invention are discussed in the description of
| Number | Date | Country | Kind |
|---|---|---|---|
| 1409089.8 | May 2014 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/GB2015/051201 | 4/23/2015 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2015/177501 | 11/26/2015 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 20090162320 | Mitomo et al. | Jun 2009 | A1 |
| Number | Date | Country |
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| 1 291 419 | Mar 2003 | EP |
| 1 950 307 | Jul 2008 | EP |
| 1950303 | Jul 2008 | EP |
| 0039302 | Jul 2000 | WO |
| 03029274 | Apr 2003 | WO |
| 2003029412 | Apr 2003 | WO |
| 2007110628 | Oct 2007 | WO |
| 2008124724 | Oct 2008 | WO |
| Entry |
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| Number | Date | Country | |
|---|---|---|---|
| 20170096684 A1 | Apr 2017 | US |
