WO2022191801A2 - Integrase defective hiv-based lentivirus mediated new generation covid-19 vaccine encoding sars-cov-2 spike protein - Google Patents
Integrase defective hiv-based lentivirus mediated new generation covid-19 vaccine encoding sars-cov-2 spike protein Download PDFInfo
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Classifications
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/12—Viral antigens
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/12—Antivirals
- A61P31/14—Antivirals for RNA viruses
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
- C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
- C12N15/86—Viral vectors
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- A—HUMAN NECESSITIES
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- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
- A61K2039/53—DNA (RNA) vaccination
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2740/00—Reverse transcribing RNA viruses
- C12N2740/00011—Details
- C12N2740/10011—Retroviridae
- C12N2740/16011—Human Immunodeficiency Virus, HIV
- C12N2740/16041—Use of virus, viral particle or viral elements as a vector
- C12N2740/16043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2740/00—Reverse transcribing RNA viruses
- C12N2740/00011—Details
- C12N2740/10011—Retroviridae
- C12N2740/16011—Human Immunodeficiency Virus, HIV
- C12N2740/16041—Use of virus, viral particle or viral elements as a vector
- C12N2740/16045—Special targeting system for viral vectors
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
- C12N2770/00011—Details
- C12N2770/20011—Coronaviridae
- C12N2770/20022—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
- C12N2770/00011—Details
- C12N2770/20011—Coronaviridae
- C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
Definitions
- the present invention relates to the generation of an integrase defective HIV-based lentivirus vaccine encoding spike (S) protein with different promoter options pseudotyped either with Lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) that provides more specific and effective transduction to dendritic cells or vesicular stomatitis virus glycoprotein (VSV-G) with extensive tissue tropism against COVID-19 disease, which is defined as the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2.
- S Lymphocytic choriomeningitis virus glycoprotein
- COVID-19 epidemic caused by the virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a pandemic disease on March 11 , 2020 by the World Health Organization (WHO). Said virus is thought to stem from a bat-derived zoonotic virus due to its genetic resemblance to bat coronaviruses. According to epidemiological studies, it was determined that the reproduction number of the disease was 5.7 in the original Wuhan strain in the absence of vaccination and immunity. COVID-19 disease, which is accompanied by the complaints of fever, dry cough, respiratory difficulties, headache, and pneumonia in patients, causes severe acute respiratory syndrome that results in death.
- SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
- WHO World Health Organization
- An ideal vaccine would be expected to demonstrate a good safety profile in different populations (e.g., persons with weakened immunity, children, elders, pregnant women, etc.). On the other hand, it should rapidly stimulate protective immunity within 2 weeks and display at least 70% effectiveness with minimal side effects. In addition, it should also trigger a potentially humoral and cellular immune response that can provide long term protection lasting at least 1 year. Moreover, it should be suitable for large-scale production and be storable at room temperature in order to avoid cold chain transportation problems. Furthermore, the vaccine development process may be interrupted by differences in disease severity, transmission rate, and geographic distribution of different viral strains.
- the L and S subtypes of the virus have been identified, and 149 mutations have been detected in 103 different SARS-CoV-2 strains, the number of which is increasing day by day.
- the D614G mutation was detected in the spike protein of the SARS-CoV-2 virus, and in a short time, the D614G mutation became the common form of the virus worldwide, replacing the original SARS-CoV-2 strain.
- the D614G mutation which increases the infectivity of the disease, did not cause a serious infection and an effect that could change the therapeutic efficacy of vaccines.
- SARS-CoV-2 VOC 202012/01 Another variant of SARS-CoV-2 (SARS- CoV-2 VOC 202012/01) emerged in the UK on 14 December 2020; and this variant, characterized by a change in 23 nucleotides, increased its infectivity without affecting the severity of the disease. At the end of 2020, it was reported that variant VOC- 202012/01 has appeared in 31 countries.
- SARS-CoV-2 a member of the betacoronavirus family, shows 79.5% homology with SARS-CoV, and 50% homology with the Middle East Respiratory Syndrome (MERS) coronavirus.
- SARS-CoV-2 has a positive-stranded RNA genome of approximately 29,700 nucleotides in length.
- the 5' end of the genome encodes a long ORFlab polyprotein consisting of 15-16 non-structural proteins, while the 3' end encodes 4 major structural proteins (spike (S), nucleocapsid (N), membrane (M), and envelope (E)).
- the spike protein of the SARS-CoV-2 virus weighs 140 kDa in monomeric form and contains 1273 amino acids (aa).
- the spike protein which naturally forms a trimer, has 2 subunits called S1 and S2.
- Spike protein plays an important role in viral transduction and pathogenesis.
- the S1 subunit recognizes and binds to the host ACE2 receptors, then the S2 subunit undergoes conformational changes leading to the fusion of the viral envelope and the host cell membrane.
- the receptor binding domain (RBD) of the spike protein is located at the C-terminal end of the S1 subunit, while the fusion peptide (FP) that mediates membrane fusion is located at the S2 subunit.
- Subunit vaccines differently from the inactivated virus vaccines, contain only antigenic portions of the virus in order to induce protective immune response. However, it requires the use of adjuvant and repeated doses to be effective.
- DNA vaccines are vaccines that have a low immune response and can cause toxic effects when used in repeated doses. They are more stable and have higher transfection efficiency than mRNA-based vaccines. However, they carry the risk of insertional mutagenesis due to vector integration. mRNAs have emerged in recent years as promising alternatives to traditional vaccine approaches. Major technological innovations and researches in the technology of mRNA synthesis, modification, and transfer have allowed mRNA to become a potential therapeutic approach in vaccine development. Rapid, inexpensive, and scalable production of mRNAs is another advantage of imRNA-based vaccines. However, although imRNA vaccines are easy to design, their unstable physiological conditions limit their use.
- Peptide-based vaccines are small fragments of chemically synthesized antigens. Their large-scale production is very easy, however, their low molecular weight and complex structure cause low immunogenicity. Therefore, it requires structural changes, special transfer systems, and adjuvants in its formulations.
- Dendritic cells are professional antigen-presenting cells and are cells that trigger T and B cell mediated immune responses.
- antigens are directly transferred in vivo to dendritic cells by viral vectors paving the way for dendritic cells to present antigen for a longer time and to create a more effective immune response with genetic immunization.
- Viral vectors are the preferred vectors in vaccine development studies as gene transfer vectors since their structure is well known and they are naturally immunogenic. Potential applications of viral vector vaccines in humans range from infectious diseases to cancer.
- adenovirus (Ad) adeno-associated virus (AAV), poxviruses, and lentiviruses are most preferred.
- antiviral vaccines depend on their capacity to generate a strong and durable antiviral immune response.
- Dendritic cells which are the most effective professional antigen-presenting cells in the body, are effective immune modulators that can stimulate antigen-specific T cells in vivo against infectious agents.
- gene transfer to dendritic cells and macrophages by non-viral methods is very difficult with currently available gene transfer systems.
- viral vectors especially adenovirus-based systems, are the most effective gene transfer tools to induce T cell response [2]
- efficient gene synthesis is essential for immunogenicity, the clinical use of adenoviral vectors for immunization has been very limited due to the immune response to the vector.
- Dominant immune response to virus antigens is one of the greatest obstacles for generating transgenic antigen-specific immune response. This poses a problem both in terms of immunity to the pre-existing virus in the target population, and immune-dominant T-cell immunity that may develop against the virus after vector injection.
- lentiviral vectors are more effective in creating antigen- specific T-cell immune response compared to adenoviral vectors. Lentiviral vectors are capable of transducing human and mouse dendritic cells 2-10 times more than adenoviruses [3, 4] According to these studies, it has been stated that 10-100 times more adenoviral vector is required for dendritic cell transduction with the same efficiency.
- transduction of dendritic cells with lentiviral vectors does not affect dendritic cell functions such as antigen presentation and potential to stimulate antigen-specific T cells [5].
- dendritic cell functions such as antigen presentation and potential to stimulate antigen-specific T cells [5].
- the structure of each vaccine developed for different diseases is different from each other.
- the design and efficiency optimization of lentiviral vectors for genetic immunization is a difficult process, each lentiviral vector differs within itself, and the use and efficiency of each lentiviral vector is genuine to the designed vector.
- the present invention relates to the generation of an integrase defective HIV-based lentivirus vaccine encoding spike (S) protein with different promoter options pseudotyped either with Lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) that provides more specific and effective transduction to dendritic cells or vesicular stomatitis virus glycoprotein (VSV-G) with extensive tissue tropism against COVID-19 disease, which is defined as the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2.
- S Lymphocytic choriomeningitis virus glycoprotein
- the first object of the present invention is to develop a vaccine that is more effective in creating antigen-specific T-cell immune response and that does not have the risk of integration into the genome, in addition to generating neutralizing antibodies against SARS-CoV-2.
- a more effective transfer of antigen-encoding gene is accomplished to dendritic cells, thereby providing an efficient antigen presentation and transgene- specific cytotoxic T lymphocyte (CTL) activation in humans and rodents by means of the use of HIV-based lentiviral vector in the vaccine of the present invention.
- CTL cytotoxic T lymphocyte
- More immunogenic epitopes are presented compared to the shortened versions by means of the full-length spike protein contained in the vaccine.
- the 3rd generation lentiviral vectors used in spike gene transfer have superior properties due to the viral genetic elements carried thereon.
- the transgene mRNA takes charge in the posttranscriptional regulation of the transgene mRNA and increases the expression of the transgene by 2 to 5 times by means of the sequence encoding the WPRE (Woodchuck Posttranscriptional Regulatory Element) gene.
- Lentiviruses are prevented from producing a repackable viral genome after transducing the target cell by means of the dU3 deletion in the 3' LTR region.
- the RRE sequence is the binding domain of the Rev protein inside the env gene, which ensures that the transcript emerges from the nucleus in an nontruncated state when this protein is bound.
- the psi (Y) signal sequence is responsible for recognizing the viral genome and enclosing it in the capsid.
- the sequence encoding the cPPT (central polypurine tract) gene in the vector increases the transgene expression and transduction efficiency of the lentiviral vector.
- Different promoter options such as the CMV (high level short term expression) or the EF1-a promoter (low level long term expression), ensure that the transferred gene is expressed at different levels in various cell types.
- Another object of the present invention is to overcome the dominant immune response against vectors in the prior art by means of antigen encoding gene transfers with lentiviral vectors.
- Another object of the present invention is to provide a permanent but non- toxic/immunogenic gene transfer in dendritic cells, which, by means of the structure of the lentiviral vector, transduces dendritic cells most effectively.
- the vaccine of the present invention is of lentiviral vector origin, it transduces many different cells, both in vivo and in vitro, without being affected by the proliferation state of the cells.
- the vector is capable of transducing both mature and immature human dendritic cells.
- This lentiviral vector provides an efficient antigen presentation by transducing differentiated dendritic cells without causing an immune response to the vector and thereby creating a strong immune response.
- the transduction efficiency of the lentiviral vector and the transgene synthesis are provided to increase by means of the sequence encoding the cPPT (central polypurine tract) gene in the vector.
- the CMV or EF1-a promoter contained in the vector By means of the CMV or EF1-a promoter contained in the vector, the desired level (high short-term or low- long-term) expression of the transferred gene is ensured in various cell types.
- Another object of the present invention is to create a long-lasting strong antibody response even when used at low doses, and protect the organism from infection against the same virus by said response. Since the effectiveness of the T cell-mediated immune response depends on the antigen presentation time, a long-term antibody response is created with the present invention, by means of the long-lasting antigen presentation thereof.
- antigen-specific immune response is generated even with a single dose application without causing an immune response against the vector.
- Recombinant lentivirus-mediated direct immunization which is the subject of the invention, also creates a long-term memory T cell response.
- An efficient cellular (CD4+ and CD8+ T cell mediated) and humoral immune response is generated by means of the present invention.
- Developing a highly effective vaccine against COVID-19 disease is provided, which is safe to use, does not require the use of adjuvant, creates an effective immune response, has high immunogenicity, is not integrated into the genome and is not replicated, that is resistant to changing physiological conditions, can express and present antigens for a long time, does not create a dominant immune response against virus antigens.
- FIG. 1 Lentiviral gene transfer plasmid (12,369 base pairs long) carrying the codon optimized spike protein sequence containing the EF1 -a promoter region.
- Rous Sarcoma Virus promoter region (RSV)
- CMV CMV enhancer-promoter region
- SEQUENCE ID NO: 1 spike DNA sequence having sequence OF SEQ ID NO:2 or SEQ ID NO:3
- the present invention relates to the generation of an integrase defective HIV-based lentivirus vaccine encoding spike (S) protein with different promoter options pseudotyped either with Lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) that provides more specific and effective transduction to dendritic cells or vesicular stomatitis virus glycoprotein (VSV-G) with extensive tissue tropism against COVID-19 disease, which is defined as the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2.
- S Lymphocytic choriomeningitis virus glycoprotein
- the spike (S) protein in the vaccine content is found on the surface of the SARS- CoV-2 virus itself, it is easily recognized by the host immune system in case of exposure to the virus and develops an immune response against the virus, and it causes the virus to enter the cell by binding to the ACE2 receptor and show its pathogenic effect.
- the gene encoding the S protein was selected as the gene to be expressed in the vaccine content of the present invention due to the fact that homologous S proteins of SARS-CoV and MERS-CoV viruses have been used before in vaccine development studies and have been shown to be quite effective.
- the sequence (GenBank ID.
- tissue plasminogen activator (tPA) precursor peptide sequence is added before the sequence (S gene with SEQ ID NO:1 , SEQ ID NO:2 or SEQ ID NO:3, or S gene specific for different variants) encoding the spike protein in the vector, which is the subject of the invention, in order to increase antigen presentation, and secretion thereof.
- SARS vaccines encoding the full-length spike protein have been reported to induce immune responses in subjects that lead to liver and lung damage, with an effect called antibody-dependent enhancement (ADE). Although the domain of the SARS-CoV spike protein responsible for the formation of harmful immune responses is not yet known, said side effect is not observed by means of the formation of effective neutralizing antibodies provided by the vaccine of the present invention.
- the immune response created by direct injection of the lentiviral gene therapy vector used in the vaccine of the present invention is less dependent on CD4+ helper T cells in terms of receiving a primary and memory CTL response.
- the CD8+ T cell immune response formed by this lentiviral vector persists longer than with other viral vectors.
- the formation of more CD127+ antigen-specific CD8+ T cells with lentiviral vector immunization compared to peptide- based applications triggers lentiviral vector-mediated memory T cell formation.
- the CD8+ T cell response may be re-formed for a second time without generating an immune response against the vector.
- the prolonged CD8+ cellular immune response and CTL activation observed in the lentiviral vector immunization of the present invention is thought to be due to prolonged antigen presentation.
- the lentiviral vector vaccine of the present invention transduces many different cells both in vivo and in vitro, without being affected by the proliferation of the cells. This lentiviral vector provides an efficient antigen presentation by transducing differentiated dendritic cells without causing an immune response to the vector and thereby creating a strong immune response.
- the lentiviral vector of the present invention is capable of transducing both mature and immature human dendritic cells. This vector allows a permanent but non- toxic/immunogenic gene transfer into dendritic cells.
- the vector in the vaccine which is the subject of the invention, transduces dendritic cells in the most efficient way, and it triggers an antigen-specific immune response even with a single dose without causing an immune response against the vector.
- Third generation lentiviral vectors are used in the present invention.
- this third generation lentiviral vector there are different promoters (such as cytomegalovirus (CMV) enhancer-promoter region or Elongation factor 1 alpha promoter (EF1-a)) before the S gene to enable viral genome transcription in producer cells.
- CMV cytomegalovirus
- EF1-a Elongation factor 1 alpha promoter
- CMV is a virus-derived promoter used for the high production of recombinant proteins in mammalian cells, however, it exhibits decreasing expression over time due to genome inactivation.
- using the inactivation-resistant EF1-a promoter instead of the CMV promoter provides lower but longer-term expression.
- the risk of protooncogene transactivation present in the use of a lentiviral vector is minimized since the third generation self-inactive (SIN) lentiviral vector, in which the promoter domain in the 3' LTR is removed, is used within the scope of the present invention.
- the lentiviral vector used is an integration defective lentiviral vector (IDLV) carrying self-inactivated promoters and having a mutation (D64V mutation) in the integrase gene.
- IDLV integration defective lentiviral vector
- the integration defective lentivirus used in the present invention is a vector that has high gene transfer efficiency both in vitro and in vivo, that is self-inactive (SIN), non-genome-integrated, and non-replicating.
- Integrase-defective lentiviral vectors have mutations in the catalytic domain of the viral integrase gene. Instead of integration into the genome, flanking LTR elements form durable episomal forms through recombination in the host nucleus.
- the integrase defective lentiviral vector of the present invention easily infects stationary dendritic cells and macrophages, which are very effective cells in creating an immune response, and enables the proliferation of antigen-specific T cells.
- the lentiviruses here do not require neutralization of immunogenic epitopes as needed on adenovirus and AAV prior to injection.
- lentiviruses can only infect CD4+ T cells due to their natural cell tropism since endogenous HIV-1 capsid proteins recognize these receptors.
- cell tropism was expanded by using envelope glycoproteins (such as vesicular stomatitis virus glycoprotein (VSV-G) or lymphocytic choriomeningitis virus glycoprotein (LCMV-GP)) of different viruses.
- VSV-G vesicular stomatitis virus glycoprotein
- LCMV-GP lymphocytic choriomeningitis virus glycoprotein
- VSV-G provides effective resistance to the lipid envelope sheath, which is normally very fragile and required during the virus purification process.
- An example of the invention uses VSV-G. VSV-G prevents complement-mediated deactivation when given with polyethylene glycol (PEG), and thereby increasing the transduction of spleen and bone marrow cells by lentiviruses.
- PEG polyethylene glycol
- the other protein used for pseudotyping is LCMV-GP, which gives the vectors the ability to naturally recognize dendritic cells better. The fact that LCMV-GP is less toxic compared to the VSV-G protein provides an advantage in using this protein for pseudotyping.
- the structure cloned into the lentiviral gene transfer vector contains the gene sequence encoding the native spike protein (SEQ ID NO:4) and is indicated by SEQ ID NO:1 in the sequence list.
- the structure cloned into the transfer vector contains the gene sequence encoding the codon optimized spike protein (SEQ ID NO:5) and is indicated by SEQ ID NO:2 in the sequence list.
- the structure cloned into the lentiviral gene transfer vector contains the gene sequence encoding the codon optimized spike protein (SEQ ID NO:6) with the D614G mutation and is indicated by SEQ ID NO:3.
- the structure cloned into the lentiviral gene transfer vector contains the SARS-CoV-2 spike (S) gene sequence specific to different variants.
- spike protein-based vaccines not only block the binding of the virus to the cell receptor, but also prevent the virus from coming out of its envelope within the cell.
- Spike protein is the most suitable candidate gene to be used in the development of COVID-19 vaccine since spike protein creates a protective immune response against SARS-CoV infection by generating neutralizing antibodies and T cell response.
- LTR long terminal repeat domains
- RSV Rous Sarcoma Virus
- sequence (1 ) encoding the RSV (Rous Sarcoma Virus) promoter domain between 1 -229 base pairs in the 5' LTR domain of the plasmids. This promoter region is responsible for the high expression of the lentiviral vector independent of the tat molecule and the efficient production of viral RNA.
- psi packaging signal sequence (3) between 457-582 base pairs. This element serves as the packaging signal of this plasmid developed for gene transfer in order to produce lentivirus.
- RRE Rev response element
- sequence (5) encoding the cPPT (central polypurine tract) gene between 1804-1921 base pairs. This element is effective in increasing the transduction efficiency and transgene expression of lentiviral vectors to be produced by the created lentiviral gene transfer vector.
- the CMV promoter is a domain that allows the transferred gene to be expressed at a high level in various cell types.
- sequence (7) encoding the elongation factor 1 alpha (EF1 -a) promoter region between 1977-3155 base pairs.
- the EF1-a promoter is a domain that ensures long term and stable expression of the transferred gene in various cell types ( Figure 2 and Figure 4).
- sequence (9) encoding the WPRE (Woodchuck Posttranscriptional Regulatory Element) between 6557-7145 base pairs ( Figure 1 ). This element is responsible for the high expression of the transferred gene.
- deletion domain (10) in the 3' LTR region which is between 8075- 8308 base pairs, was formed by the deletion of a part of the normal LTR domain. While this deletion has no negative effects on vector formation and lentiviral packaging, it has the ability to prevent lentiviruses from producing a repackable viral genome after transducing the target cell. By means of this property, lentiviral vectors produced with this gene transfer plasmid gain a self-inactivating feature.
- the gene transfer plasmid with the CMV promoter which was created together with the domains (with intermediate bases from cloning) such as the antibiotic resistance gene and the origin of replication, which contains the basic features used in cloning technologies, consists of a total of 11 ,554 base pairs and is in a circular structure ( Figure 1).
- the gene transfer plasmid with the CMV promoter consists of 11 ,786 base pairs ( Figure 3).
- Gene transfer plasmid with EF1 -a promoter which is another example of the present invention, consists of 12,360 base pairs in total and is in a circular structure ( Figure 2).
- the gene transfer plasmid with the EF1 -a promoter consists of 12,396 base pairs ( Figure 4).
- the promoter and H IV tat gene in the 5' LTR were removed from the genome, while the rev gene was designed to be expressed from a separate plasmid.
- RSV was inserted into the 5' LTR domains, and CMV or EF1 -a promoter was placed before the S gene in order to ensure viral genome transcription in producer cells.
- viruses produced are first purified from cellular debris by low-speed centrifugation and filtration, and then concentrated by high-speed ultracentrifugation with a sucrose bed and preserved in Hank's balanced salt solution (HBSS). Then, it is subjected to purification process by anion exchange chromatography in order to make it suitable for in vivo use.
- HBSS Hank's balanced salt solution
- the gene transfer plasmid encoding the spike gene ( Figure 1 , 2, 3 or 4) can be transferred to bacterial cells by transformation process after being cloned once.
- lentiviral vectors carrying the SARS-CoV-2 spike gene are produced by cotransfecting it to 293T cells by 3 different plasmids carrying gag-pol (integrase defective (D64V mutant), (addgene, psPAX2-D64V #63586)), rev (addgene, pRSV-Rev #12253), and VSV-G (pMD2.G addgene #12259)/LCVM-GP (addgene, pHCMV-LCMV-WE #15793) in cylindrical cell culture bottles, with the aid of lentiviral elements cloned on the plasmid.
- SARS-CoV-2 spike (S) gene carrying the SARS-CoV-2 spike (S) gene with the SEQ ID NO:1 , or codon optimized SARS-CoV-2 spike (S) gene with SEQ ID NO:2, or codon optimized SARS- CoV-2 spike (S) gene with D614G mutation with SEQ ID NO:3, or SARS-CoV-2 spike (S) gene specific to different variants with plasmids encoding gag/pol(D64V), rev, and selected envelope glycoprotein; replication defective HIV-based third generation lentiviral vector pseudotyped with lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) or vesicular stomatitis virus glycoprotein (VSV-G) is produced and used as a vaccine.
- LCMV-GP lymphocytic choriomeningitis virus glycoprotein
- VSV-G vesicular stomatitis virus glycoprotein
- lentiviral vectors (Pseudotyped vectors containing the S gene with the SEQ ID NO:1 , or codon optimized S gene with SEQ ID NO:2, or codon optimized S gene with D614G mutation with SEQ ID NO:3) are obtained that do not have replication ability due to the elements carried by the vector and that can remain episomal without integrating the spike gene it carries into the genome of the transferred target cell.
- many optional products can be obtained instead of a single product by using different promoter and pseudotyping options together with different transgene vector.
- lentiviral vectors encoding spike genes are eligible for in vivo use in preclinical and clinical studies by using the gene transfer vectors described within the scope of the present invention.
- a vaccine lentiviral gene therapy vector
- the vaccine of the present invention produced with said vectors can be administered through the intradermal, intramuscular, or intranasal routes.
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Abstract
The present invention relates to the development of an integrase defective HIV-based lentivirus vaccine encoding spike protein against COVID-19 disease, which is defined as severe acute respiratory syndrome (SARS) caused by SARS-CoV-2. Spike proteins released during SARS-CoV-2 infection are molecules that provide the formation of neutralizing antibodies responsible for protective immunity and that activate the T cell response. Compared to plasmid DNA or peptide-based vaccines, a viral vector that infects cells is more effective in inducing a cellular and humoral response to the vaccine antigen. In addition, viral-based vaccines are vectors that can be used safely and can create an immune response without the requirement of adjuvant use. The vaccine developed against COVID-19 that is the subject of the invention is a lentivirus-based vaccine carrying spike protein encoding gene based on a third generation replication-defective, integrase-impaired, VSV-G/LCMV-GP pseudotyped vector, and it is a new generation SARS-CoV-2 vaccine that prevents the virus from binding and entering the cell, providing both neutralizing antibody formation and triggering the cellular immune response.
Description
INTEGRASE DEFECTIVE HIV-BASED LENTIVIRUS MEDIATED NEW GENERATION COVID-19 VACCINE ENCODING SARS-CoV-2 SPIKE PROTEIN Technical Field of the Invention
The present invention relates to the generation of an integrase defective HIV-based lentivirus vaccine encoding spike (S) protein with different promoter options pseudotyped either with Lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) that provides more specific and effective transduction to dendritic cells or vesicular stomatitis virus glycoprotein (VSV-G) with extensive tissue tropism against COVID-19 disease, which is defined as the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2.
State of the Art The COVID-19 epidemic, caused by the virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a pandemic disease on March 11 , 2020 by the World Health Organization (WHO). Said virus is thought to stem from a bat-derived zoonotic virus due to its genetic resemblance to bat coronaviruses. According to epidemiological studies, it was determined that the reproduction number of the disease was 5.7 in the original Wuhan strain in the absence of vaccination and immunity. COVID-19 disease, which is accompanied by the complaints of fever, dry cough, respiratory difficulties, headache, and pneumonia in patients, causes severe acute respiratory syndrome that results in death.
It is important to develop an effective and safe vaccine for SARS-CoV-2 since vaccination is the most effective way to protect against communicable diseases [1 ]. An ideal vaccine would be expected to demonstrate a good safety profile in different populations (e.g., persons with weakened immunity, children, elders, pregnant women, etc.). On the other hand, it should rapidly stimulate protective immunity within 2 weeks and display at least 70% effectiveness with minimal side effects. In addition, it should also trigger a potentially humoral and cellular immune response that can provide long term protection lasting at least 1 year. Moreover, it should be suitable for large-scale
production and be storable at room temperature in order to avoid cold chain transportation problems. Furthermore, the vaccine development process may be interrupted by differences in disease severity, transmission rate, and geographic distribution of different viral strains. Up to today, the L and S subtypes of the virus have been identified, and 149 mutations have been detected in 103 different SARS-CoV-2 strains, the number of which is increasing day by day. For example, in early 2020, the D614G mutation was detected in the spike protein of the SARS-CoV-2 virus, and in a short time, the D614G mutation became the common form of the virus worldwide, replacing the original SARS-CoV-2 strain. The D614G mutation, which increases the infectivity of the disease, did not cause a serious infection and an effect that could change the therapeutic efficacy of vaccines. Another variant of SARS-CoV-2 (SARS- CoV-2 VOC 202012/01) emerged in the UK on 14 December 2020; and this variant, characterized by a change in 23 nucleotides, increased its infectivity without affecting the severity of the disease. At the end of 2020, it was reported that variant VOC- 202012/01 has appeared in 31 countries.
Correct antigen and vector selection is important in order to ensure sufficient immune response after vaccination. In this case, the molecular structure of the virus must be well clarified in order to develop an effective SARS-CoV-2 vaccine. The genome sequence of SARS-CoV-2, a member of the betacoronavirus family, shows 79.5% homology with SARS-CoV, and 50% homology with the Middle East Respiratory Syndrome (MERS) coronavirus. SARS-CoV-2 has a positive-stranded RNA genome of approximately 29,700 nucleotides in length. The 5' end of the genome encodes a long ORFlab polyprotein consisting of 15-16 non-structural proteins, while the 3' end encodes 4 major structural proteins (spike (S), nucleocapsid (N), membrane (M), and envelope (E)).
The spike protein of the SARS-CoV-2 virus weighs 140 kDa in monomeric form and contains 1273 amino acids (aa). The spike protein, which naturally forms a trimer, has 2 subunits called S1 and S2. Spike protein plays an important role in viral transduction and pathogenesis. The S1 subunit recognizes and binds to the host ACE2 receptors, then the S2 subunit undergoes conformational changes leading to the fusion of the viral envelope and the host cell membrane. The receptor binding domain (RBD) of the spike protein is located at the C-terminal end of the S1 subunit, while the fusion peptide (FP) that mediates membrane fusion is located at the S2 subunit. The discovery of the
prefusion conformation of the trimeric spike protein and the RBD/ACE2 interaction substantially contributed to the development of a vaccine against SARS-CoV-2. In the prior art, different fragments of the spike protein (full-length spike protein, RBD region, S1 subunit, N-terminal end (NTD) and FP) were separately tested as antigens in vaccine development. Full-length spike protein is a better antigen candidate compared to its shortened versions since it presents a more immunogenic epitope. Numerous vaccine development studies based on the full-length spike protein of SARS-CoV have been reported.
There are many different types of vaccines in the prior art. Working with concentrated live SARS-CoV-2 virus for use in a vaccine may expose researchers to a serious risk of infection, and may even cause symptoms of SARS in people who have been vaccinated with the virus that has not been fully inactivated. Due to the ease of production of inactivated or attenuated SARS-CoV-2 virus, it may be the first vaccine to be used in the clinic for SARS-CoV-2. Live-attenuated viruses may reproduce in a vaccinated person and induce an immune response with mild or no side effects. Contrary to infection with wild-type virus, live-attenuated viral vaccines can produce an immune response that provides the necessary amount of antigenic stimulation for the formation of memory cells. Flowever, there are some safety concerns in terms of the use of these vaccines. Live-attenuated pathogens may rarely transform into a pathogenic form and cause disease in vaccinated individuals. Moreover, an effective immune response may not be obtained in people with weakened immune systems.
Subunit vaccines, differently from the inactivated virus vaccines, contain only antigenic portions of the virus in order to induce protective immune response. However, it requires the use of adjuvant and repeated doses to be effective. DNA vaccines, on the other hand, are vaccines that have a low immune response and can cause toxic effects when used in repeated doses. They are more stable and have higher transfection efficiency than mRNA-based vaccines. However, they carry the risk of insertional mutagenesis due to vector integration. mRNAs have emerged in recent years as promising alternatives to traditional vaccine approaches. Major technological innovations and researches in the technology of mRNA synthesis, modification, and transfer have allowed mRNA to become a potential therapeutic approach in vaccine development. Rapid, inexpensive, and scalable production of mRNAs is another
advantage of imRNA-based vaccines. However, although imRNA vaccines are easy to design, their unstable physiological conditions limit their use.
Peptide-based vaccines are small fragments of chemically synthesized antigens. Their large-scale production is very easy, however, their low molecular weight and complex structure cause low immunogenicity. Therefore, it requires structural changes, special transfer systems, and adjuvants in its formulations.
In the control of infectious diseases, it is very important to create an effective immune response. Genetic immunization is one of the most effective tools to achieve this goal. Dendritic cells are professional antigen-presenting cells and are cells that trigger T and B cell mediated immune responses. With the discovery of viral vectors, antigens are directly transferred in vivo to dendritic cells by viral vectors paving the way for dendritic cells to present antigen for a longer time and to create a more effective immune response with genetic immunization. Viral vectors are the preferred vectors in vaccine development studies as gene transfer vectors since their structure is well known and they are naturally immunogenic. Potential applications of viral vector vaccines in humans range from infectious diseases to cancer. Among viral vectors, adenovirus (Ad), adeno-associated virus (AAV), poxviruses, and lentiviruses are most preferred.
The success of antiviral vaccines depends on their capacity to generate a strong and durable antiviral immune response. Dendritic cells, which are the most effective professional antigen-presenting cells in the body, are effective immune modulators that can stimulate antigen-specific T cells in vivo against infectious agents. However, gene transfer to dendritic cells and macrophages by non-viral methods is very difficult with currently available gene transfer systems. On the other hand, viral vectors, especially adenovirus-based systems, are the most effective gene transfer tools to induce T cell response [2] Although efficient gene synthesis is essential for immunogenicity, the clinical use of adenoviral vectors for immunization has been very limited due to the immune response to the vector. Dominant immune response to virus antigens is one of the greatest obstacles for generating transgenic antigen-specific immune response. This poses a problem both in terms of immunity to the pre-existing virus in the target population, and immune-dominant T-cell immunity that may develop against the virus after vector injection.
There are studies showing that lentiviral vectors are more effective in creating antigen- specific T-cell immune response compared to adenoviral vectors. Lentiviral vectors are capable of transducing human and mouse dendritic cells 2-10 times more than adenoviruses [3, 4] According to these studies, it has been stated that 10-100 times more adenoviral vector is required for dendritic cell transduction with the same efficiency. More importantly, compared to transduction with adenoviral vector, transduction of dendritic cells with lentiviral vectors does not affect dendritic cell functions such as antigen presentation and potential to stimulate antigen-specific T cells [5]. However, as is known in the art, the structure of each vaccine developed for different diseases is different from each other. The design and efficiency optimization of lentiviral vectors for genetic immunization is a difficult process, each lentiviral vector differs within itself, and the use and efficiency of each lentiviral vector is genuine to the designed vector.
The solutions in the state of the art are not sufficiently effective and suitable for preventing COVID-19 disease due to the fact that use of live-attenuated pathogens used in SARS-CoV-2 vaccines in the state of the art is not safe enough for each individual, the need for adjuvant use in subunit vaccines, the low immune response in DNA vaccines and the risk of insertional mutagenesis due to vector integration, peptide-based vaccines show low immunogenicity, mRNA vaccines are unstable to changing physiological conditions, and limitation of clinical use of adenovirus-based systems due to the dominant immune response to virus antigens. For these reasons, there is a need to develop new generation vaccines that are safe to use, do not require the use of adjuvant, create an effective immune response, have high immunogenicity, that are not integrated into the genome and are not replicated, that are resistant to changing physiological conditions, can express and present antigens for a long time, do not create a dominant immune response against virus antigens, and that has high efficacy on COVID-19 disease caused by SARS-CoV-2.
Brief Description and Objects of the Invention
The present invention relates to the generation of an integrase defective HIV-based lentivirus vaccine encoding spike (S) protein with different promoter options pseudotyped either with Lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) that provides more specific and effective transduction to dendritic cells or vesicular stomatitis virus glycoprotein (VSV-G) with extensive tissue tropism against COVID-19 disease, which is defined as the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2.
The first object of the present invention is to develop a vaccine that is more effective in creating antigen-specific T-cell immune response and that does not have the risk of integration into the genome, in addition to generating neutralizing antibodies against SARS-CoV-2. A more effective transfer of antigen-encoding gene is accomplished to dendritic cells, thereby providing an efficient antigen presentation and transgene- specific cytotoxic T lymphocyte (CTL) activation in humans and rodents by means of the use of HIV-based lentiviral vector in the vaccine of the present invention. More immunogenic epitopes are presented compared to the shortened versions by means of the full-length spike protein contained in the vaccine. The 3rd generation lentiviral vectors used in spike gene transfer have superior properties due to the viral genetic elements carried thereon. For example, it takes charge in the posttranscriptional regulation of the transgene mRNA and increases the expression of the transgene by 2 to 5 times by means of the sequence encoding the WPRE (Woodchuck Posttranscriptional Regulatory Element) gene. Lentiviruses are prevented from producing a repackable viral genome after transducing the target cell by means of the dU3 deletion in the 3' LTR region. In addition, the RRE sequence is the binding domain of the Rev protein inside the env gene, which ensures that the transcript emerges from the nucleus in an nontruncated state when this protein is bound. The psi (Y) signal sequence is responsible for recognizing the viral genome and enclosing it in the capsid. The sequence encoding the cPPT (central polypurine tract) gene in the vector increases the transgene expression and transduction efficiency of the lentiviral vector. Different promoter options, such as the CMV (high level short term expression) or the EF1-a promoter (low level long term expression), ensure that the transferred gene is expressed at different levels in various cell types.
Another object of the present invention is to overcome the dominant immune response against vectors in the prior art by means of antigen encoding gene transfers with lentiviral vectors.
Another object of the present invention is to provide a permanent but non- toxic/immunogenic gene transfer in dendritic cells, which, by means of the structure of the lentiviral vector, transduces dendritic cells most effectively. Since the vaccine of the present invention is of lentiviral vector origin, it transduces many different cells, both in vivo and in vitro, without being affected by the proliferation state of the cells. The vector is capable of transducing both mature and immature human dendritic cells. This lentiviral vector provides an efficient antigen presentation by transducing differentiated dendritic cells without causing an immune response to the vector and thereby creating a strong immune response. The transduction efficiency of the lentiviral vector and the transgene synthesis are provided to increase by means of the sequence encoding the cPPT (central polypurine tract) gene in the vector. By means of the CMV or EF1-a promoter contained in the vector, the desired level (high short-term or low- long-term) expression of the transferred gene is ensured in various cell types.
Another object of the present invention is to create a long-lasting strong antibody response even when used at low doses, and protect the organism from infection against the same virus by said response. Since the effectiveness of the T cell-mediated immune response depends on the antigen presentation time, a long-term antibody response is created with the present invention, by means of the long-lasting antigen presentation thereof. By means of the use of HIV-based lentivirus vector in the vaccine of the present invention, antigen-specific immune response is generated even with a single dose application without causing an immune response against the vector. Recombinant lentivirus-mediated direct immunization, which is the subject of the invention, also creates a long-term memory T cell response. An efficient cellular (CD4+ and CD8+ T cell mediated) and humoral immune response is generated by means of the present invention.
Developing a highly effective vaccine against COVID-19 disease is provided, which is safe to use, does not require the use of adjuvant, creates an effective immune response, has high immunogenicity, is not integrated into the genome and is not replicated, that is resistant to changing physiological conditions, can express and
present antigens for a long time, does not create a dominant immune response against virus antigens.
Description of the Figures Figure 1. Lentiviral gene transfer plasmid (11 ,554 base pairs long) carrying the natural spike protein sequence containing the CMV enhancer-promoter region.
Figure 2. Lentiviral gene transfer plasmid (12,360 base pairs long) carrying the native spike protein sequence containing the EF1 -a promoter region.
Figure 3. Lentiviral gene transfer plasmid (11 ,759 base pairs long) carrying the codon optimized spike protein sequence containing the CMV enhancer-promoter region.
Figure 4. Lentiviral gene transfer plasmid (12,369 base pairs long) carrying the codon optimized spike protein sequence containing the EF1 -a promoter region.
Definitions of the Elements Forming the Invention The parts and components in the figures are enumerated for a better explanation of the integrase defective HIV-based lentivirus vaccine encoding spike protein of the present invention, and correspondence of every number is given below:
The parts in the figures are enumerated and their correspondence are;
1 ) Rous Sarcoma Virus promoter region (RSV)
2) 5' Long terminal repeats (LTR)
3) Packaging signal (HIV-1 )
4) Rev response element (RRE)
5) Central Polypurine Tract element (cPPT)
6) CMV enhancer-promoter region (CMV)
7) EF1 -a promoter region
8) SEQUENCE ID NO: 1 , spike DNA sequence having sequence OF SEQ ID NO:2 or SEQ ID NO:3
9) Woodchuck Posttranscriptional Regulatory Element (WPRE)
10) 3' LTR deletion domain (U3)
Detailed Description of the Invention
The present invention relates to the generation of an integrase defective HIV-based lentivirus vaccine encoding spike (S) protein with different promoter options pseudotyped either with Lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) that provides more specific and effective transduction to dendritic cells or vesicular stomatitis virus glycoprotein (VSV-G) with extensive tissue tropism against COVID-19 disease, which is defined as the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2.
Since the spike (S) protein in the vaccine content is found on the surface of the SARS- CoV-2 virus itself, it is easily recognized by the host immune system in case of exposure to the virus and develops an immune response against the virus, and it causes the virus to enter the cell by binding to the ACE2 receptor and show its pathogenic effect. The gene encoding the S protein was selected as the gene to be expressed in the vaccine content of the present invention due to the fact that homologous S proteins of SARS-CoV and MERS-CoV viruses have been used before in vaccine development studies and have been shown to be quite effective. The sequence (GenBank ID. E04506) encoding the tissue plasminogen activator (tPA) precursor peptide sequence is added before the sequence (S gene with SEQ ID NO:1 , SEQ ID NO:2 or SEQ ID NO:3, or S gene specific for different variants) encoding the spike protein in the vector, which is the subject of the invention, in order to increase antigen presentation, and secretion thereof. SARS vaccines encoding the full-length spike protein have been reported to induce immune responses in subjects that lead to liver and lung damage, with an effect called antibody-dependent enhancement (ADE). Although the domain of the SARS-CoV spike protein responsible for the formation of harmful immune responses is not yet known, said side effect is not observed by means of the formation of effective neutralizing antibodies provided by the vaccine of the present invention.
It has been determined that the immune response created by direct injection of the lentiviral gene therapy vector used in the vaccine of the present invention is less dependent on CD4+ helper T cells in terms of receiving a primary and memory CTL response. The CD8+ T cell immune response formed by this lentiviral vector persists longer than with other viral vectors. At the same time, the formation of more CD127+
antigen-specific CD8+ T cells with lentiviral vector immunization compared to peptide- based applications triggers lentiviral vector-mediated memory T cell formation. Also, when immunization is repeated by using the same lentiviral vector, the CD8+ T cell response may be re-formed for a second time without generating an immune response against the vector.
The prolonged CD8+ cellular immune response and CTL activation observed in the lentiviral vector immunization of the present invention is thought to be due to prolonged antigen presentation. The lentiviral vector vaccine of the present invention transduces many different cells both in vivo and in vitro, without being affected by the proliferation of the cells. This lentiviral vector provides an efficient antigen presentation by transducing differentiated dendritic cells without causing an immune response to the vector and thereby creating a strong immune response.
The lentiviral vector of the present invention is capable of transducing both mature and immature human dendritic cells. This vector allows a permanent but non- toxic/immunogenic gene transfer into dendritic cells. The vector in the vaccine, which is the subject of the invention, transduces dendritic cells in the most efficient way, and it triggers an antigen-specific immune response even with a single dose without causing an immune response against the vector.
Third generation lentiviral vectors are used in the present invention. In this third generation lentiviral vector, there are different promoters (such as cytomegalovirus (CMV) enhancer-promoter region or Elongation factor 1 alpha promoter (EF1-a)) before the S gene to enable viral genome transcription in producer cells. CMV is a virus-derived promoter used for the high production of recombinant proteins in mammalian cells, however, it exhibits decreasing expression over time due to genome inactivation. In an example of the present invention, using the inactivation-resistant EF1-a promoter instead of the CMV promoter provides lower but longer-term expression.
The risk of protooncogene transactivation present in the use of a lentiviral vector is minimized since the third generation self-inactive (SIN) lentiviral vector, in which the promoter domain in the 3' LTR is removed, is used within the scope of the present invention. The lentiviral vector used is an integration defective lentiviral vector (IDLV) carrying self-inactivated promoters and having a mutation (D64V mutation) in the
integrase gene. The integration defective lentivirus used in the present invention is a vector that has high gene transfer efficiency both in vitro and in vivo, that is self-inactive (SIN), non-genome-integrated, and non-replicating. As long as the transduced cells do not divide, the integrated lentiviral vector provides a high level of transgene synthesis. Integrase-defective lentiviral vectors have mutations in the catalytic domain of the viral integrase gene. Instead of integration into the genome, flanking LTR elements form durable episomal forms through recombination in the host nucleus. The integrase defective lentiviral vector of the present invention easily infects stationary dendritic cells and macrophages, which are very effective cells in creating an immune response, and enables the proliferation of antigen-specific T cells. The lentiviruses here do not require neutralization of immunogenic epitopes as needed on adenovirus and AAV prior to injection. However, lentiviruses can only infect CD4+ T cells due to their natural cell tropism since endogenous HIV-1 capsid proteins recognize these receptors. However, since the vector used within the scope of the present invention can carry (pseudotyping) capsid glycoproteins of other viruses, cell tropism was expanded by using envelope glycoproteins (such as vesicular stomatitis virus glycoprotein (VSV-G) or lymphocytic choriomeningitis virus glycoprotein (LCMV-GP)) of different viruses.
The cell repertoire that lentiviruses may infect has expanded since VSV-G used for this purpose binds to the LDL receptor synthesized on many cell surfaces. In addition thereto, VSV-G provides effective resistance to the lipid envelope sheath, which is normally very fragile and required during the virus purification process. An example of the invention uses VSV-G. VSV-G prevents complement-mediated deactivation when given with polyethylene glycol (PEG), and thereby increasing the transduction of spleen and bone marrow cells by lentiviruses. In another example of the present invention, the other protein used for pseudotyping is LCMV-GP, which gives the vectors the ability to naturally recognize dendritic cells better. The fact that LCMV-GP is less toxic compared to the VSV-G protein provides an advantage in using this protein for pseudotyping.
In an example of the present invention, the structure cloned into the lentiviral gene transfer vector contains the gene sequence encoding the native spike protein (SEQ ID NO:4) and is indicated by SEQ ID NO:1 in the sequence list. In another example of the present invention, the structure cloned into the transfer vector contains the gene
sequence encoding the codon optimized spike protein (SEQ ID NO:5) and is indicated by SEQ ID NO:2 in the sequence list. In another example of the present invention, the structure cloned into the lentiviral gene transfer vector contains the gene sequence encoding the codon optimized spike protein (SEQ ID NO:6) with the D614G mutation and is indicated by SEQ ID NO:3. In an example of the present invention, the structure cloned into the lentiviral gene transfer vector contains the SARS-CoV-2 spike (S) gene sequence specific to different variants.
The RBD domain of the spike protein is in the S1 subunit and interacts with the cell's ACE2 receptor, while the S2 subunit provides the fusion of the virus and the cell. Therefore, spike protein-based vaccines not only block the binding of the virus to the cell receptor, but also prevent the virus from coming out of its envelope within the cell. Spike protein is the most suitable candidate gene to be used in the development of COVID-19 vaccine since spike protein creates a protective immune response against SARS-CoV infection by generating neutralizing antibodies and T cell response.
There are important elements in the lentiviral gene transfer plasmid encoding the generated natural spike gene, the safety of the transfer vehicle, its post-production titer and its expression in cells. There are also long terminal repeat domains called LTR (2,10) at the 5' and 3' ends of these elements.
There is sequence (1 ) encoding the RSV (Rous Sarcoma Virus) promoter domain between 1 -229 base pairs in the 5' LTR domain of the plasmids. This promoter region is responsible for the high expression of the lentiviral vector independent of the tat molecule and the efficient production of viral RNA.
There is psi packaging signal sequence (3) between 457-582 base pairs. This element serves as the packaging signal of this plasmid developed for gene transfer in order to produce lentivirus.
There is sequence (4) encoding the RRE (Rev response element) gene between 1075- 1308 base pairs. This element gives the generated gene transfer plasmid the ability to prevent the expression of gag and pol proteins carried on other packaging plasmids in the absence of Rev during the lentiviral vector production stage.
There is sequence (5) encoding the cPPT (central polypurine tract) gene between 1804-1921 base pairs. This element is effective in increasing the transduction
efficiency and transgene expression of lentiviral vectors to be produced by the created lentiviral gene transfer vector.
There is sequence (6) encoding the CMV (cytomegalovirus) enhancer-promoter region (6) between 1944-2451 base pairs. The CMV promoter is a domain that allows the transferred gene to be expressed at a high level in various cell types.
There is sequence (7) encoding the elongation factor 1 alpha (EF1 -a) promoter region between 1977-3155 base pairs. The EF1-a promoter is a domain that ensures long term and stable expression of the transferred gene in various cell types (Figure 2 and Figure 4). After the gene sequence to be transferred, there is sequence (9) encoding the WPRE (Woodchuck Posttranscriptional Regulatory Element) between 6557-7145 base pairs (Figure 1 ). This element is responsible for the high expression of the transferred gene.
Conclusively, the deletion domain (10) in the 3' LTR region, which is between 8075- 8308 base pairs, was formed by the deletion of a part of the normal LTR domain. While this deletion has no negative effects on vector formation and lentiviral packaging, it has the ability to prevent lentiviruses from producing a repackable viral genome after transducing the target cell. By means of this property, lentiviral vectors produced with this gene transfer plasmid gain a self-inactivating feature.
In addition to all these important elements in the created plasmid, the gene transfer plasmid with the CMV promoter, which was created together with the domains (with intermediate bases from cloning) such as the antibiotic resistance gene and the origin of replication, which contains the basic features used in cloning technologies, consists of a total of 11 ,554 base pairs and is in a circular structure (Figure 1). In another example of the present invention, the gene transfer plasmid with the CMV promoter consists of 11 ,786 base pairs (Figure 3). Gene transfer plasmid with EF1 -a promoter, which is another example of the present invention, consists of 12,360 base pairs in total and is in a circular structure (Figure 2). In another example of the present invention, the gene transfer plasmid with the EF1 -a promoter consists of 12,396 base pairs (Figure 4). In third generation lentiviral vectors, the promoter and H IV tat gene in the 5' LTR were removed from the genome, while the rev gene was designed to be expressed from a
separate plasmid. In addition thereto, RSV was inserted into the 5' LTR domains, and CMV or EF1 -a promoter was placed before the S gene in order to ensure viral genome transcription in producer cells. Conclusively, self-inactive (SIN) third-generation vectors was developed, which cannot transcribe full-length RNA post-integration by deletion of promoter elements in the 3' LTR, thereby further increasing the biosafety of the vectors. Since only three HIV-1 genes (gag, pol, and rev) are required for the production of third generation lentiviral vectors, this system offers the best profile in terms of safety. Third generation lentiviruses were produced by co-transfection of plasmids required for vector production into the producer cell (293T) in cylindrical cell culture bottles or bioreactors by the plasmid (transfer plasmid) encoding the desired gene. While vaccines can be produced for clinical studies using this method, petri dishes can not be used for production purposes. The viruses produced are first purified from cellular debris by low-speed centrifugation and filtration, and then concentrated by high-speed ultracentrifugation with a sucrose bed and preserved in Hank's balanced salt solution (HBSS). Then, it is subjected to purification process by anion exchange chromatography in order to make it suitable for in vivo use.
In order to be used in vaccine production within the scope of the present invention, the gene transfer plasmid encoding the spike gene (Figure 1 , 2, 3 or 4) can be transferred to bacterial cells by transformation process after being cloned once. After said gene transfer plasmid that was produced before the production of the lentiviral vector was isolated from bacteria, lentiviral vectors carrying the SARS-CoV-2 spike gene are produced by cotransfecting it to 293T cells by 3 different plasmids carrying gag-pol (integrase defective (D64V mutant), (addgene, psPAX2-D64V #63586)), rev (addgene, pRSV-Rev #12253), and VSV-G (pMD2.G addgene #12259)/LCVM-GP (addgene, pHCMV-LCMV-WE #15793) in cylindrical cell culture bottles, with the aid of lentiviral elements cloned on the plasmid. As a result of the co-transfection of the gene transfer plasmid carrying the SARS-CoV-2 spike (S) gene with the SEQ ID NO:1 , or codon optimized SARS-CoV-2 spike (S) gene with SEQ ID NO:2, or codon optimized SARS- CoV-2 spike (S) gene with D614G mutation with SEQ ID NO:3, or SARS-CoV-2 spike (S) gene specific to different variants with plasmids encoding gag/pol(D64V), rev, and selected envelope glycoprotein; replication defective HIV-based third generation lentiviral vector pseudotyped with lymphocytic choriomeningitis virus glycoprotein
(LCMV-GP) or vesicular stomatitis virus glycoprotein (VSV-G) is produced and used as a vaccine.
At the end of the production, lentiviral vectors (Pseudotyped vectors containing the S gene with the SEQ ID NO:1 , or codon optimized S gene with SEQ ID NO:2, or codon optimized S gene with D614G mutation with SEQ ID NO:3) are obtained that do not have replication ability due to the elements carried by the vector and that can remain episomal without integrating the spike gene it carries into the genome of the transferred target cell. In addition, many optional products can be obtained instead of a single product by using different promoter and pseudotyping options together with different transgene vector.
Consequently, produced lentiviral vectors encoding spike genes are eligible for in vivo use in preclinical and clinical studies by using the gene transfer vectors described within the scope of the present invention. In this context, a vaccine (lentiviral gene therapy vector) to be used as a preventative measure against COVID-19 disease has been developed in line with the characteristics specific to the vector produced, and it has been made possible that developing lentivirus encoding spike gene in high quantity and high titer with large-scale production of bioreactor. The vaccine of the present invention produced with said vectors can be administered through the intradermal, intramuscular, or intranasal routes.
References
1. Dong, Y., et al., A systematic review of SARS-CoV-2 vaccine candidates. Signal Transduct Target Ther, 2020. 5(1): p. 237.
2. Barouch, D.H. and G.J. Nabel, Adenovirus vector-based vaccines for human immunodeficiency virus type 1. Hum Gene Ther, 2005. 16(2): p. 149-56.
3. Esslinger, C., et al., In vivo administration of a lentiviral vaccine targets DCs and induces efficient CD8(+) T cell responses. J Clin Invest, 2003. 111(11): p. 1673- SI .
4. Esslinger, C., P. Romero, and H.R. MacDonald, Efficient transduction of dendritic cells and induction of a T-cell response by third-generation lentivectors. Hum Gene
Ther, 2002. 13(9): p. 1091-100.
5. Gruber, A., et al., Dendritic cells transduced by multiply deleted HIV-1 vectors exhibit normal phenotypes and functions and elicit an HIV-specific cytotoxic T- lymphocyte response in vitro. Blood, 2000. 96(4): p. 1327-33.
Claims
1. A replication defective HIV-based third-generation lentiviral gene therapy vector for use in vaccine applications against SARS-CoV-2-induced COVID-19 disease, characterized in that, it comprises;
• 5' LTR RSV promoter, psi packaging signal, RRE element, cPPT element, WPRE element, 3' LTR deletion domain,
• Elongation factor 1 alpha (EF1-a) promoter region,
• SARS-CoV-2 spike (S) gene with the SEQ ID NO:1 , codon optimized SARS-CoV-2 spike (S) gene with SEQ ID NO:2, or codon optimized SARS- CoV-2 spike (S) gene with D614G mutation with SEQ ID NO:3, or SARS- CoV-2 spike (S) gene specific to different variants, and, is pseudotyped with lymphocytic choriomeningitis virus glycoprotein (LCMV-GP).
2. A lentiviral gene therapy vector according to Claim 1 , characterized in that, it comprises tissue plasminogen activator (tPA) precursor sequence before the S gene.
3. A replication defective HIV-based third-generation lentiviral gene therapy vector for use in vaccine applications against SARS-CoV-2-induced COVID-19 disease, characterized in that, it comprises;
• 5' LTR RSV promoter, psi packaging signal, RRE element, cPPT element, WPRE element, 3' LTR deletion domain,
• Elongation factor 1 alpha (EF1 -a) promoter region,
• SARS-CoV-2 spike (S) gene with the SEQ ID NO:1 , codon optimized SARS-CoV-2 spike (S) gene with SEQ ID NO:2, or codon optimized SARS-CoV-2 spike (S) gene with D614G mutation with SEQ ID NO:3, or SARS-CoV-2 spike (S) gene specific to different variants, and, is pseudotyped with vesicular stomatitis virus glycoprotein (VSV-G).
4. A lentiviral gene therapy vector according to Claim 3, characterized in that, it comprises tissue plasminogen activator (tPA) precursor sequence before the S gene.
5. A method for producing the lentiviral gene therapy vector according to any one of the preceding claims, characterized in that, it comprises the process steps of;
• Co-transfecting lentiviral gene transfer plasmid with plasmids encoding integrase-defective gag/pol (D64V), rev, and envelope glycoprotein into 293T cells in cylindrical cell culture bottles or bioreactors,
• Harvesting the lentiviral vector produced by cotransfection from 293T cells,
• Purifying the vector by anion exchange chromatography
6. A lentiviral gene therapy vector for use in vaccine applications against SARS- CoV-2 virus according to any one of the preceding claims, characterized in that, it is suitable for intradermal, intramuscular, or intranasal use.
7. A vaccine according to Claim 1 or Claim 2 against the COVID-19 disease caused by SARS-CoV-2, comprising replication defective HIV-based third generation lentiviral vector carrying 5' LTR RSV promoter, psi packaging signal, RRE element, cPPT element, WPRE element, 3' LTR deletion domain, elongation factor 1 alpha (EF1-a) promoter domain pseudotyped with lymphocytic choriomeningitis virus glycoprotein (LCMV-GP), and carrying SARS-CoV-2 spike (S) gene with the SEQ ID NO:1 , or codon optimized SARS- CoV-2 spike (S) gene with SEQ ID NO:2, or codon optimized SARS-CoV-2 spike (S) gene with D614G mutation with SEQ ID NO:3, or SARS-CoV-2 spike (S) gene specific to different variants.
8. A vaccine according to Claim 3 or Claim 4 against the COVID-19 disease caused by SARS-CoV-2, comprising replication defective HIV-based third generation lentiviral vector carrying 5' LTR RSV promoter, psi packaging signal, RRE element, cPPT element, WPRE element, 3' LTR deletion domain, elongation factor 1 alpha (EF1 -a) promoter domain pseudotyped with vesicular stomatitis virus glycoprotein (VSV-G), and carrying SARS-CoV-2 spike (S)
gene with the SEQ ID N0:1 , or codon optimized SARS-CoV-2 spike (S) gene with SEQ ID NO:2, or codon optimized SARS-CoV-2 spike (S) gene with D614G mutation with SEQ ID NO:3, or SARS-CoV-2 spike (S) gene specific to different variants.
9. A vaccine according to Claim 7 or 8, characterized in that, it is suitable for intradermal, intramuscular, or intranasal use.
10.A vaccine according to Claim 9, characterized in that, it is suitable for use with polyethylene glycol (PEG) in intradermal, intramuscular, or intranasal use.
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