Patent Application
20240398921
The Sequence Listing associated with this application is provided electronically in .xml format and is hereby incorporated by reference into the specification. The Sequence Listing is provided as a file entitled 25133-100410_sl.xml, created Feb. 21, 2023 which is about 83 kB in size.
The present invention relates to the discovery of compositions and methods for therapeutic platform for immunization for treatment of infectious diseases and cancer. Methods of the invention include a method of generating a high titer hybrid-VLV vector, methods of treating and/or preventing infectious disease and cancer; and methods of inducing a memory T and B cell immune response against an infectious agent or cancer in a subject administered the VLV composition produced thereby. Furthermore, the invention encompasses a pharmaceutical composition for vaccinating a subject to protect the subject against infection with infectious disease or cancer.
Vaccination is one of the greatest public health success stories. Nowadays vaccines that protect against many of the viruses that once caused fatal childhood diseases are routinely used throughout the world. However, traditional methods of vaccine development using inactivation or attenuation of viruses have failed for some of the most deadly human pathogens, necessitating new approaches. Advances in molecular virology have enabled the genetic manipulation of viruses, which has opened new opportunities for vaccine development. Genetic modification of viruses not only allows for their attenuation but also for incorporation of sequences from other viruses, turning one pathogen into a vaccine carrier for another. Viral vectors have been studied as potential tools to deliver vaccines as they present advantages over traditional vaccines in that they stimulate a broad range of immune responses including antibody (B cell), T helper cell (CD4+ T cell), and cytotoxic T lymphocyte (CTL, CD8+ T cell) mediated immunity. These viral vector vaccines could be used against various infectious and malignant diseases. However, there are limitations on the use of viral vector-based vaccines. For example, preexisting anti-vector immunity against the viral vectors that potentially inactivate the vaccine presents an issue as does the limited cloning capacity for the transgene of interest. Numerous vaccine investigations are in progress to improve the efficiency of this technology and to overcome its limitations.
Enveloped RNA viruses have highly organized structures. One or more nucleocapsid proteins encapsidate their RNA, matrix proteins often lie between the capsid and the membrane, and one or more transmembrane glycoproteins interact with the matrix or nucleocapsid proteins to direct efficient particle assembly. Once the particles are released from cells, one or more glycoproteins bind cellular receptors and catalyze membrane fusion to allow the viruses to enter new cells.
Alphaviruses such as Semliki Forest Virus (SFV) are positive-strand, membrane-enveloped RNA viruses that encode four non-structural proteins called nsP 1-4 and three structural proteins: capsid, and the E1 and E2 transmembrane glycoproteins. The nsp 1-4 proteins are translated from the first two-thirds of the genomic RNA. These proteins form a complex which directs replication of the genomic RNA to form antigenomic RNA, which is then copied to form full-length positive strand RNA and a subgenomic mRNA that encodes the structural proteins. The capsid protein encases the genomic RNA in the cytoplasm to generate a nucleocapsid that buds from the cell surface in a membrane containing the SFV glycoproteins. Alphavirus RNA replication occurs inside light-bulb shaped, membrane-bound compartments called spherules that initially form on the cell surface and are then endocytosed to form cytopathic vacuoles containing multiple spherules. The replicase proteins are localized to the cytoplasmic side of the spherules. How the replicated RNA in the spherules is packaged into nucleocapsids prior to SFV budding is not known. Alphavirus RNA replicons lacking any structural protein genes can still replicate efficiently inside a cell, but they are incapable of propagating beyond the cell.
Vesicular stomatitis virus (VSV) is a negative-strand RNA virus that encodes a single membrane glycoprotein (G), a matrix protein, and a nucleocapsid protein as well as two proteins that form the viral polymerase. Remarkably, when cells are transfected with an SFV RNA replicon encoding only the SFV non-structural proteins and the VSV G protein, infectious membrane-enveloped vesicles containing the VSV G protein are generated These infectious, virus-like vesicles (VLVs) grow to low titers, but can be passaged like a virus in tissue culture cells. The particles contain the replicon RNA and VSV G protein, but unlike enveloped RNA viruses, have a very low density because they do not contain a tightly-packed nucleocapsid protein around the RNA. The mechanism by which these VLVs are generated has not been determined. These VLVs expressing other proteins have proven useful as experimental vaccines. But, there are two significant limitations of the VLV system as a vaccine platform: the relatively low titer of the VLVs and rapid loss of expression of the foreign genes upon passage. Clearly, there is a need for methods of producing more efficient virus-vector vaccine systems that support stable foreign gene expression, while generating high vaccine titers that induce a potent immune response. Such vaccine systems are useful in cancer and/or infectious disease indications. The present invention fulfills this need.
While current antiviral therapies for chronic hepatitis B virus (CHB) infection effectively reduce viremia, they rarely eliminate the virus. Thus, there remains a critical need for new treatment options for this serious disease. Because the human immune system can control HBV but often fails to do so, immunotherapies including therapeutic vaccination represent a promising approach to cure chronic CHB. However, although current HBV vaccine platforms generate potent antibody responses that prevent infection, they typically do not produce the broad CD8 T-cell responses needed to eliminate the virus after infection. Therefore, new vaccine delivery systems that can generate effective therapeutic immune responses to HBV are urgently needed. We have developed an immunotherapy based on our virus like-vesicle (VLV) platform for the treatment of patients with CHB infection.
We have established that an RNA replicon-based vector or VLV carrying RNA encoding one or more of the HBV major antigens [middle surface envelope glycoproteins (MHBs), hepatitis B core antigen (HBcAg), or polymerase] in a single open reading frame (CARG-101) in a polycistronic unit drives a broad multi-specific immune response that produces substantial clearance of HBV in the mouse liver. Treatment of mice chronically infected with adeno-associated virus (AAV)-HBV significantly reduces and, in some animals, eliminates serum HBV surface antigen (HBsAg), a surrogate biomarker for viral persistence in the liver. We have significantly enhanced overall gene expression which led to our next-generation clinical candidate, CARG-201, which induces both T-cell responses and antibodies in comparison to CARG-101. CARG-201 expressing MHBs and HBcAg under separate subgenomic promoters clears serum HBsAg completely in 100% of mice and reduces HBV RNA in the liver to undetectable levels in an AAV mouse model of CHB infection with low antigen burden (HBsAglow). However, in a more stringent AAV-HBV model (HBsAghigh), CARG-201 reduces HBsAg levels by only 80%. As high antigen burden is observed in many CHB patients and is associated with T-cell exhaustion or tolerance, successful immunotherapy should improve immunogenicity and overcome T-cell exhaustion and/or tolerance.
Modifications of CARG-201 in any one of, or one or more of three complementary approaches can enhance efficacy and lead to complete clearance of serum HBsAg levels in animals:
First, we have incorporated polymerase (Pol) antigen into CARG-201 to generate CARG-301 (expressing MHBs, HBcAg, plus Pol). A vaccine that generates multi-antigen specific T cells is better positioned to provide the desired therapeutic effect compared to one or two antigens. Moreover, Pol is a highly immunogenic CD4 and CD8 T-cell target, and because of its high sequence conservation, it may prevent the generation of escape mutants in the T-cell epitope.
Second, we have engineered CARG-201 to incorporate human IgK signal sequence for the polymerase (pol) gene and VSV G glycoprotein signal sequence for the HBc gene. It is known that secreted proteins generally lead to the activation of dendritic cells, the enhancement of HBV antigen presentation, and the generation of new cytotoxic T-cell responses by epitope spreading. In this manner, the quality and quantity of the T-cell responses against HBV antigens may be further enhanced as compared to soluble and non-secreted counterparts. Secreted proteins also contribute to the adaptive immune responses by being taken up by antigen-presenting cells and processed via the major histocompatibility complex (MHC) class II pathway.
Third, we have also targeted for disruption the programmed death-ligand 1 (PD-L1) immune checkpoint by short hairpin RNA (shRNA) to achieve sustained long-term viral suppression or complete elimination of the virus in the liver. Checkpoint inhibition can enhance ex vivo effector T-cell responses from patients with other chronic infections. We predict that disruption of the PD-1/PD-L1 pathway will re-invigorate the otherwise exhausted T-cell function.
The combined effects of shRNA-mediated PD-L1 inhibition and the improved secretion of the HBV antigens as result of ER-targeting confer on these modified multivalent constructs a superior therapeutic index necessary to clear the virus and to halt disease progression and mortality in CHB patients.
A high titer VLV vector comprising a DNA sequence comprising a promoter sequence operably linked to a DNA sequence encoding Semliki Forest virus (SFV) non-structural protein nucleotide sequences, operably linked to an SFV subgenomic RNA promoter, operably linked to DNA encoding an infectious diseases or cancer-associated antigen or fragment thereof, operably linked to a 2A DNA encoding a 2A peptide, which is in turn operably linked to a vesicular stomatitis virus (VSV) G DNA encoding a VSV G protein, wherein the SFV non-structural protein nucleotide sequences comprise at least two of the mutations selected from the group consisting of G-4700-A, A-5424-G, G-5434-A, T-5825-C, T-5930-C, A-6047-G, G-6783-A, G-6963-A, G-7834-A, T-8859-A, T-8864-C, G-9211-A, A-10427-G, G-11560-A, A-11871-G and T-11978-C, wherein the vector lacks nucleotide sequences which encode SFV structural proteins, further wherein when the vector is propagated in cell culture, titers of at least 107 plaque forming units (pfu) per ml of virus like vesicles (VLVs) are obtained.
In an embodiment, the present disclosure provides for a high-titer hybrid virus vector for treatment, prophylaxis or prevention of infectious disease or cancer comprising the following operably linked sequence elements:
In an embodiment, the antigen associated with an infectious disease is one or more of HBV antigens selected from the group consisting of a core (HBcAg) antigen, a middle (M) surface HBs antigen, a large (L) surface HBs antigen, a small(S) surface HBs antigen, an HBeAg antigen, and an HBx antigen.
In an embodiment, the antigen associated with cancer is one or more of TSA or TAA.
In an embodiment, titers of at least 1×109 plaque forming units (pfu) per mL of virus like vesicles (VLVs) are obtained.
In an embodiment, the VLVs are obtained by purification and concentration using centrifugation ultrafiltration, tangential flow filtration, high speed centrifugation, chromatography, or other methods.
In an embodiment, each of the at least two sequence domains included in the fourth DNA sequence are sequence domain encoding an antigen associated with an infectious disease.
In an embodiment, each of the at least two sequence domains included in the fourth DNA sequence are sequence domain encoding an antigen associated with cancer.
In an embodiment, the TSA or TAA are one or more of Alphafetoprotein, Melanoma-associated antigen, CD44 glycoprotein, Aspartate Beta-Hydroxylase, Carcinoembryonic antigen, and a TSA or TAA specific to a cancer.
In an embodiment, the fourth DNA sequence comprises one or more polynucleotide sequences each independently having at least about 80% homology with a sequence according to SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 6, or SEQ ID NO: 8.
In an embodiment, the fourth DNA sequence comprises one or more polynucleotide sequences each independently having at least about 85%, or at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% homology with a sequence according to SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 6, or SEQ ID NO: 8.
In an embodiment, the one or more sequence domains encoding a human short hairpin RNA (shRNA) of the fifth DNA sequence each independently include a polynucleotide sequence having at least about 85%, or at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% homology with a sequence according to SEQ ID NO: 13, SEQ ID NO: 22, or SEQ ID NO: 27.
In an embodiment, the present disclosure provides for a high-titer hybrid virus vector for generating virus-like vesicles (VLVs) for treatment, prophylaxis or prevention of infectious disease or cancer, comprising the following operably linked sequence elements:
In an embodiment, the antigen associated with an infectious disease is one or more of HBV antigens selected from the group consisting of a core (HBcAg) antigen, a middle (M) surface HBs antigen, a large (L) surface HBs antigen, a small(S) surface HBs antigen, an HBeAg antigen, and an HBx antigen.
In an embodiment, titers of at least 1×109 plaque forming units (pfu) per mL of virus like vesicles (VLVs) are obtained.
In an embodiment, the VLVs are obtained by purification and concentration using centrifugation ultrafiltration, tangential flow filtration, high speed centrifugation, chromatography, or other methods.
In an embodiment, each of the at least two sequence domains included in the fourth DNA sequence are sequence domain encoding an antigen associated with an infectious disease.
In an embodiment, each of the at least two sequence domains included in the fourth DNA sequence are sequence domain encoding an antigen associated with cancer.
In an embodiment, the TSA or TAA are one or more of Alphafetoprotein, Melanoma-associated antigen, CD44 glycoprotein, Aspartate Beta-Hydroxylase, Carcinoembryonic antigen, and a TSA or TAA specific to a cancer.
In an embodiment, the one or more sequence domains encoding a human short hairpin RNA (shRNA) of the fifth DNA sequence each independently include a polynucleotide sequence having at least about 80% homology with a sequence according to SEQ ID NO: 13, SEQ ID NO: 22, or SEQ ID NO: 27.
In an embodiment, the one or more sequence domains encoding a human short hairpin RNA (shRNA) of the fifth DNA sequence each independently include a polynucleotide sequence having at least about 85%, or at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% homology with a sequence according to SEQ ID NO: 13, SEQ ID NO: 22, or SEQ ID NO: 27.
In an embodiment, the fourth DNA sequence comprises one or more polynucleotide sequences each independently having at least about 80% homology with a sequence according to SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 6, or SEQ ID NO: 8.
In an embodiment, the fourth DNA sequence comprises one or more polynucleotide sequences each independently having at least about 85%, or at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% homology with a sequence according to SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 6, or SEQ ID NO: 8.
In an embodiment, the fourth DNA sequence comprising a polynucleotide sequence encoding one or more of IL-12 or IL-17.
In an embodiment, the fifth DNA sequence comprises a polynucleotide sequence encoding one or more shRNA sequences targeting PD-L1, PD-L2, CTLA-4, LAG-3, TIM-3, TIGIT, CD90, BTLA, CD160, or PD-1.
In an embodiment, the fourth DNA sequence comprises a polynucleotide sequence encoding one or more cytokine agonist or antagonist polypeptides targeting IL-2, IL-7, IL-15, IL-18, IL-19, IL-35, IL-21, GM-CSF, IL-17, or Flt3L.
In an embodiment, the fourth DNA sequence comprises a polynucleotide sequence encoding one or more polypeptide modulators of a target associated with malignancy selected from PD-L1, CXCL1, or CXCL2.
In an embodiment, the fifth DNA sequence comprises a polynucleotide sequence encoding one or more shRNA modulators of a target associated with malignancy selected from PD-L1, CXCL1, or CXCL2.
In an embodiment, the present disclosure provides for virus-like vesicles (VLVs) containing replicon RNA generated by the high-titer hybrid-virus vectors described herein.
In an embodiment, the present disclosure provides for a composition comprising virus-like vesicles (VLVs) produced by the high-titer hybrid virus vectors described herein.
In an embodiment, the present disclosure provides for a method of treating and/or preventing infectious disease or cancer in a mammalian subject, the method comprising administering a therapeutically effective amount of a VLV composition to a mammalian subject in need thereof.
In an embodiment, the present disclosure provides for a method of immunizing a mammalian subject against infectious disease or cancer, the method comprising administering a therapeutically effective amount of a VLV composition to a mammalian subject in need thereof.
In an embodiment, the present disclosure provides for a method of downregulating genes associated with an infectious disease or cancer, the method comprising administering a therapeutically effective amount of a VLV composition to a mammalian subject in need thereof.
In an embodiment, the mammalian subject is a human or animal.
In an embodiment, the infectious disease is a hepatitis B virus infection.
In an embodiment, the present disclosure provides for the use of VLV compositions as described herein in the manufacture of a medicament for the treatment, prophylaxis, or prevention of an infectious disease or cancer in a mammalian subject in need thereof.
In an embodiment, the mammalian subject is a human or animal.
In an embodiment, the infectious disease is a hepatitis B virus infection.
In an embodiment, the present disclosure provides for a method of producing virus-like vesicles (VLVs) for treatment, prophylaxis, or prevention of infectious disease or cancer comprising the steps of:
In an embodiment, the high-titer virus vector further comprises a DNA promoter sequence, and a DNA sequence encoding alphavirus non-structural protein polynucleotide sequences,
In an embodiment, the antigen associated with an infectious disease is one or more of HBV antigens selected from the group consisting of a core (HBcAg) antigen, a middle (M) surface HBs antigen, a large (L) surface HBs antigen, a small(S) surface HBs antigen, an HBeAg antigen, and an HBx antigen.
In an embodiment, the antigen associated with cancer is one or more of TSA or TAA.
In an embodiment, step b) comprises the following sub-steps:
In an embodiment, the transfection reagent is lipofectamine or PEIpro.
In an embodiment, the transfection agent is lipofectamine.
In an embodiment, the transfection reagent is PEIpro.
In an embodiment, the high titer is at least 1×108 PFU/mL.
In an embodiment, the high titer is at least about 1×109 PFU/mL.
In an embodiment, the infectious disease is HIV, severe acute respiratory syndrome associated coronavirus (SARS-COV), SARS-COV-1, SARS-COV-2, Lyme disease, Escherichia coli 0157: H7 (E. coli) infection, hantavirus infection, dengue fever, West Nile virus infection, Zika virus infection, Plasmodium infection (malaria), tuberculosis, cholera, pertussis, influenza, pneumococcal disease, gonorrhea, HSV, HPV, RSV, Hepatitis B virus infection, Hepatitis C virus infection, Tickborne encephalitis viruses infection, Chikungunya virus infection, Yellow fever, Clostridium difficile infection, or Staphylococcus enterotoxin B infection.
These and other aspects of the present invention will become apparent from the disclosure herein.
Aspects and advantages of the present disclosure will become apparent from the following exemplary embodiments taken in conjunction with the accompanying drawings, of which:
The disclosure is directed to a versatile platform based on virus-like vesicles for infectious disease and cancer immunotherapy applications. The VLV platform is generally useful for the treatment, prophylaxis, and/or prevention of infectious disease or cancer. In an embodiment, an exemplary infectious disease is hepatitus B virus infection (HBV). The platform technology and methods of treatment disclosed herein are applicable to several infectious diseases, including but not limited to emerging diseases, re-emerging diseases, and other infectious diseases. In exemplary embodiments, emerging diseases may include HIV, Severe acute respiratory syndrome associated coronavirus (SARS-COV), SARS-COV-1, SARS-COV-2, Lyme disease, Escherichia coli 0157: H7 (E. coli), hantavirus, dengue fever, West Nile virus, and the Zika virus. In exemplary embodiments, re-emerging diseases may include Plasmodium (malaria), tuberculosis, cholera, pertussis, influenza, pneumococcal disease, and gonorrhea. In exemplary embodiments, other infectious diseases may include HSV, HPV, RSV, Hepatitis B virus, Hepatitis C virus, Tickborne encephalitis viruses, Chikungunya virus, Yellow fever, Clostridium difficile, Staphylococcus enterotoxin B.
As described herein, Hepatitis B virus (HBV) is exemplified as an infectious disease, however the full scope of the disclosure is intended to encompass each of the emerging, re-emerging, and other infectious diseases. In further embodiments, the full scope of the disclosure is intended to encompass any infectious disease known to a person of skill in the art.
The disclosure is also directed to cancer immunotherapy applications. For example, the VLVs may encode for or produce one or more cytokine agonists, cytokine antagonists, short hairpin RNA's, and/or other polynucleotides or polypeptides useful for the treatment, prophylaxis, and/or prevention of a malignancy or cancer. For example, a VLV of the present disclosure may encode IL-12, IL-17, shRNA against one or more of PD-L1, PD-L2, CTLA-4, LAG-3, TIM-3, TIGIT, CD90, BTLA, CD160, PD-1, and/or cytokine agonist or antagonist polypeptides selected from one or more of IL-2, IL-7, IL-15, IL-18, IL-19, IL-35, IL-21, GM-CSF, and IL-17, Flt3L. The platform VLV may alternatively or additionally downregulate genes associated with malignancy, such as PD-L1, CXCL1, and/or CXCL2, among others known to a person of skill in the art.
As used herein, the term “target” may be utilized in connection with any biological target useful in the vectors, plasmids, pharmaceutical compositions and methods of the present disclosure. “Targeting” includes upregulating, downregulating, modulating, acting functinoally as an agonist or an antagonist, or interacting with the biological target in any manner which may cause a biological effect. Examples of agents encoded by the vectors described herein which “target” certain biological targets include polypeptides, polynucleotides, shRNA, siRNA, antibodies or antigen-binding fragments thereof, or any other useful agent which may be encoded by a vector and/or produced in a VLV.
Other embodiments disclosed herein will be readily apparent to a person of skill in the art. U.S. Pat. No. 9,987,353 by Robek et al., issued Jun. 5, 2018, U.S. Pat. No. 10,435,712 by Rose et al., issued Oct. 8, 2019, and PCT/US2021/012834 filed Jan. 8, 2021 (published as WO/2021/142366 on Jul. 15, 2021) each generally relate to VLV technologies and are each incorporated by reference in their entireties herein.
HBV as an example: Significance of the Problem. HBV infection is a major global public health problem. Worldwide, approximately 2 billion people are infected with hepatitis B virus (HBV) during their lifetime, and >240 million have current HBV infection, and about 600,000 people die from HBV-related liver disease every year. Patients with chronic HBV (CHB) infection, including inactive carriers of HBV, have an increased risk of developing liver cirrhosis, hepatic failure, and hepatocellular carcinoma (HCC). Although most of these patients will not develop HBV-related complications, 15-40% will develop serious complications during their lifetime. CHB has various clinical stages defined by HBV DNA titer, presence of hepatitis B e antigen (HBeAg, a secreted form of the core protein) and the presence or absence of liver inflammation measured by liver transaminase levels. CHB infection occurs as a result of continuous interaction between the viral replication and immune responses. T cells are exhausted by the persistent antigen exposure, which contribute to the persistence of HBV infection. When T cells encounter HBV antigens presented by the intrahepatic antigen presenting cells (APCs), such as the dendritic cells (DCs) and Kupffer cells, the costimulatory signals received by T cells are very weak. This result in immune tolerance rather than functional activation. In addition, the immunosuppressive microenvironment is formed in the liver of patients with CHB with high proportion of regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs). These provide T cells with inhibitory signals and disturb T cell-mediated anti-HBV functions.
Limitations of the current HBV vaccine. Despite its success in preventing HBV infection, the current HBV vaccine (recombinant HBsAg adsorbed to alum) has a number of characteristics that are suboptimal. First, it does not induce a protective antibody response in all immunized individuals. Second, between two and four doses of the vaccine are recommended to induce long-lasting immunity. This need for repeated immunization makes the vaccine somewhat challenging to administer in many regions of the world, especially those lacking the appropriate medical infrastructure. Third, the protective antibody response wanes after immunization, and declines to below protective levels (>10 IU/L) in up to 60% of vaccinated individuals. Fourth, escape mutations in the surface protein gene can produce virus that is resistant to the antibody response generated by the vaccine. Finally, as discussed above, although it elicits a protective antibody response that prevents infection, the current vaccine does not generate a strong CD8 T cell response, and it has not been effective in clinical trials to control virus replication in those who are already infected with HBV.
Current therapies for CHB. Current standard of care for CHB includes anti-viral and immune-enhancing drugs, such as tenofovir, entecavir and PEGylated IFN which are very effective at slowing down disease, are curative only 8-12% of the patients treated. Cessation of antiviral therapy is often accompanied by a rebound in the viral load; therefore, lifelong treatment is required. Although available antiviral drugs can lead to suppression of serum HBV viral load to undetectable levels efficiently, however, they usually fail to achieve sero-clearance of hepatitis B surface antigen (HBsAg), which indicates eradication of HBV infection, the ultimate goal of antiviral treatment for CHB. The failure to achieve HBsAg sero-clearance may be due to emerging drug-resistant HBV variants and the covalently closed circular DNA (cccDNA) in remaining infected hepatocytes. As none of these clinical therapies achieve long-term virological control in majority of patients with CHB, therefore, there is an urgent need to develop new therapies to improve HBsAg clearance and virological cure.
New Modalities for HBV Treatment. The failure of HBsAg sero-clearance requires the development of novel therapeutic strategies for achieving durable viral remission. One strategy is to target virus directly, by targeting viral entry, viral assembly/encapsidation, preS1 or hepatitis B surface antigen (HBsAg) secretion, envelopment- and cccDNA. Another strategy is to interfere with the host mechanisms, by using Toll-like receptor (TLR) agonists, cytokines and the blocking of PD-1/PD-L1. In addition, therapeutic vaccines based on recombinant HBV proteins or HBV-envelope subviral particles, DNA and T-cell peptide epitope resent another promising strategy for HBV eradication. Therapeutic vaccination is aimed at eliminating persistent viral infection by augmenting the patient's immune responses. Individuals who become acutely infected but ultimately clear the virus have a relatively strong, multi-specific T-cell response to HBV. However, in those who become chronically infected, the T-cell response is much weaker in magnitude and is directed toward fewer viral antigens. This suboptimal immune response persists in chronically infected individuals despite the continual presence of viral antigens in the liver and blood. Although the current HBV vaccines induce potent antibody responses that prevent infection, they do not elicit the virus-specific T cells needed to control an established infection. New technologies that generate an effective T cell-dependent immune response to HBV are urgently needed. One promising approach for treating CHB is a therapeutic vaccine capable of inducing virus-specific CD8 T cells to clear HBV infection.
Functional cure of HBV. The ultimate goal of HBV treatment is ‘functional cure’. According to the meeting of AASLD and EASL.), functional cure is defined as a sustained loss of HBsAg in serum. In this scenario, although HBV cccDNA remains at low levels, a functional adaptive immune response ensures suppression of viral replication without treatment, analogous to that which occurs in clearance of acute HBV. A strong HBV-specific CD8 T cell response is required for HBV clearance in acute infection, but in CHB the T cell response is dysfunctional and is not fully restored by NUCs. As functional cure is rarely achieved with current therapy, alternative treatments that can be given in shorter and finite courses are urgently required. CHB infection is the result of complex interactions between HBV and the host, and an impaired immune response to viral antigens is believed to be a key factor associated with the CHB carrier state. If this state of immune tolerance could be overcome, the loss of HBeAg or HBsAg from the serum (seroclearance) and sustained control of the HBV infection would be achieved.
Scientific Premise. Current standard-of-care therapies only rarely lead to a functional cure, characterized by sustained loss of HBsAg (with or without HBsAg antibody seroconversion). The goal for the next generation CHB therapies is to achieve a higher rate of functional cure with finite treatment duration. To address this urgent need, we developed targeted shRNA therapeutics for CHB based on VLV delivery platform. The shRNA can be developed as a stand-alone treatment or in combination with therapeutic vaccine to achieve a functional cure. Since the human immune system can control HBV but often fails to do so, immunotherapies including therapeutic vaccine represent a promising approach to cure CHB. However, the therapeutic immune responses generated in the persistent HBV infection are often weak due to CD8 T cell exhaustion. Exhaustion of virus-specific T cells may play an important role in HBV persistence. The interaction between programmed death-1 (PD-1) receptor on lymphocytes and its ligand PD-L1 plays a critical role in T-cell exhaustion by inducing T-cell inactivation indicating that the PD-1/PD-L1 pathway is a good therapeutic candidate for chronic HBV infection. Woodchucks infected with woodchuck hepatitis virus (WHV) can have increased hepatic expression of PD-1-ligand-1 (PD-L1), increased PD-1 on CD8+ T cells, and a limited number of virus-specific T cells. Others have shown that in these animals, combination therapy with aPD-L1 and entecavir (ETV) improved control of viremia and antigenemia compared to ETV treatment alone. In addition, others have shown that PD-L1 blockade synergistically augments HBV-specific CD4 T cells. Furthermore, there is accumulating evidence that immune checkpoint inhibitors can enhance ex vivo effector T-cell responses from patients with other chronic viral, bacterial, or parasitic infection, including HIV, tuberculosis, and malaria [64-66]. We have found that therapeutic shRNA intervention targeting exhausted T cells by blocking these suppressive pathways can restore the function of these impaired T cells and lead to a functional cure.
Platform immunotherapy technology. We have found that alphavirus replicons are excellent vaccine vectors because they are highly immunogenic and target dendritic cells. The virus-like vesicles (VLV) vaccine platform is a capsid-free, self-replicating, antigen expression system that represents an attractive alternative to other virus-based vectors. VLV encodes a Semliki Forest virus (SFV) replicon and an additional structural protein, the vesicular stomatitis virus glycoprotein (VSV-G). Following in vitro evolution by 50 passages in BHK-21 cells that led to 10 amino acid changes in SFV nsP1-4, the evolved SFV nonstructural proteins promote high-titer VLV replication in cell culture through increased efficiency of VLV release. VSV-G expression allows for robust and pantropic infectivity, as infectious vesicles composed of SFV replication spherules derived from bulb-shaped plasma membrane invaginations are coated with VSV-G protein and bud from infected cells, spread to uninfected cells, and undergo multiple rounds of infection. VLV are nonpathogenic in mice and rhesus macaques, have little risk of genome integration or reversion to pathogenesis, and are immunogenic in the absence of adjuvant. Recent improvements to the system allow the generation of high-titers of VLV particles as well as high gene expression until multiple subgenomic promoters. Although VLVs mimic the immune stimulating properties of viral vectors, they are safe and non-pathogenic when administered to mice or rhesus macaques, nor do they display neurovirulence when injected directly into mouse brain. These vectors are significant because of their potency, case of high-titer particle production, and predicted safety due to the lack of viral structural proteins. Furthermore, VLVs have a demonstrated large capacity to deliver nucleic acids for the expression of several antigens resulting in induction of T cell and antibody responses against multiple epitopes of multiple antigens and thus help to maximize the potential efficacy of the proposed immunotherapy in patients.
During the last 20 years multiple studies have assessed therapeutic vaccine candidates for CHB therapy using lipopeptide epitope-based vaccine; DNA-based vaccines and adenoviral vectored vaccines. Thus far, attempts at therapeutic vaccination for HBV have been ineffective in reliably inducing functional cure in people with CHB. The persistence of HBV-specific T cell hypo-responsiveness and high baseline HBsAg load of participants, together with limited T cell immunogenicity of the vaccine candidates themselves, are possible reasons that may have hampered the success of these vaccine candidates. Other possibilities for failure include the use of HBsAg which in healthy induces HBs antibodies which block viral entry and prevent infection, the effects on T cell induction and immune restoration in the chronic setting using protein vaccines alone are likely to be minimal. Large proportion of patients had HBeAg+ disease, associated with high HBV antigen levels. High antigen loads have been proposed as a barrier to the successful rescue of tolerized T cells by therapeutic vaccination.
Vectors of the present invention may generally be a plasmid or other vector encoding VLVs. The term “vector” is therefore inclusive of plasmids. The plasmids can generally comprise any required elements for VLV production. The vectors or plasmids can be defined by one or more sequence domains or components, or by one or more sequences. Generally, unless clear from the context, plasmids may comprise additional sequence domains or components as necessary or desirable. Sequences may be defined as polynucleotide sequences or corresponding amino acid sequences. Some sequence components (such as shRNAs) may not have corresponding amino acid sequences. Exemplary sequence domains are provided in Table 1 below:
In various embodiments, vectors or plasmids may comprise and/or encode one or more of SEQ ID NOs: 1-30. In various embodiments, vectors or plasmids may comprise and/or encode a sequence or sequence portion having more than 70%, or more than 75%, or more than 80%, or more than 85%, or more than 90%, or more than 95%, or more than 96%, or more than 97%, or more than 98%, or more than 99% homology to one or more of SEQ ID NOs: 1-30. In some embodiments, vectors or plasmids may comprise a sequence consisting of one or more of SEQ ID NOs: 1-30. Where a vector or plasmid comprises a sequence consisting of or encoding one or more of SEQ ID NOs: 1-30, it is intended that the vector or plasmid may comprise additional sequence domains.
In exemplary embodiments, plasmids may have a polynucleotide sequence corresponding to SEQ ID NO: 16 or SEQ ID NO: 17. In exemplary embodiments, plasmids may have a polynucleotide sequence having more than about 70%, or more than 75%, or more than 80%, or more than 85%, or more than 90%, or more than 95%, or more than 96%, or more than 97%, or more than 98%, or more than 99% homology to SEQ ID NO: 16 or SEQ ID NO: 17. In some embodiments, a plasmid may have a polynucleotide sequence consisting of SEQ ID NO: 16 or SEQ ID NO: 17. In some embodiments, a plasmid may have a polynucleotide sequence consisting essentially of SEQ ID NO: 16 or SEQ ID NO: 17. Where a plasmid has a polynucleotide sequence consisting essentially of SEQ ID NO: 16 or SEQ ID NO: 17, it is intended that the plasmid, having the same general sequence domains, may contain one or more nucleotide and/or amino acid substitutions, additions, or deletions in or between those domains which do not significantly impact the function of the plasmid.
Where a sequence “homology” or “identity” is contemplated, for a DNA sequence or an amino acid sequence, the same percentage “similarity” is also contemplated for the amino acid sequence or amino acid sequence corresponding to the DNA sequence. The term “similarity” is different from the term identity because it allows conservative substitutions of amino acid residues having similar physicochemical properties over a defined length of a given alignment. Generally, any reasonable similarity-scoring matrix known may be used to determine similarity.
In determining the sequence homology or identity of a first sequence compared to a second sequence, various identity calculations may be performed such as those implemented in the National Institute of Health's Basic Local Alignment Search Tool (BLAST). In some embodiments, the standard BLAST settings may be utilized. For example, a BLAST identity may be defined as the number of matching bases over the number of alignment positions.
VLVs can generally be produced by transfecting any appropriate cell line with appropriate plasmids or vectors. In an embodiment, VLVs are produced by transfecting BHK-21 or HEK293 T cells with a vector or plasmid, incubating the transfected BHK-21 or HEK293 T cells in a buffer solution for a suitable time and at a suitable temperature to propagate VLVs; and isolating the VLVs from the BHK-21 or HEK293 T cells and buffer solution by a technique selected from the group consisting of ultrafiltration, centrifugation, tangential flow filtration, affinity purification, ion exchange chromatography, and combinations thereof. In various embodiments, VLVs can be produced by any appropriate transduction, incubation, and isolation methods.
The produced VLVs are generally useful for therapeutic methods. The produced VLVs may be formulated as vaccine compositions for treatment of HBV with one or more diluents, excipients, or other ingredients. The compositions may generally be administered by any appropriate route, such as by oral, parenteral, intravenous, or other routes.
The figures are described in more detail as follows, with reference to the Examples presented herein.
The invention is now described with reference to the following Examples. These Examples are provided for the purpose of illustration only and the invention should in no way be construed as being limited to these Examples, but rather should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.
Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the compounds of the present invention and practice the claimed methods.
We have established that the treatment of mice chronically infected with AAV-HBV with CARG-101 (VLV harboring MHBs, only one HBV antigen) significantly reduces and, in some animals, eliminates serum HBsAg, a surrogate biomarker for viral persistence in the liver. The clearance of HBsAg in 40% of the AAV-HBV mice by only one immunization with CARG-101 is a superior outcome compared with other HBV immunotherapies being developed in the same animal model.
Remarkably, we have now attained a reduction in serum biomarker levels in >80% AAV-HBV mice (n=10) with high antigenemia, indicating that CARG-201 (HBcAg and MHBs: two HBV antigens) can break tolerance in highly tolerant models. To attain this reduction, we combined an enhanced gene expression strategy and a robust prime-boost regimen to achieve complete clearance of HBsAg in mice. We have therefore selected CARG-201 for advancement to the clinic based on the following results: (i) complete reduction of HBsAg in most of but not all treated animals in a mouse model of persistent HBV replication, (ii) reduction of HBV RNA in the liver to undetectable levels, and (iii) induction of multi-specific HBV T cells and antibodies. The reduction in intrahepatic HBV RNA may be the result of strong immune control under a high level of CD8+ and CD4+ T-cell responses, as observed in patients with resolution of acute HBV infection (
These data we have generated establish that (i) we can enhance the antigenic load with a concomitant increase in immunogenicity by modifying the VLV to harbor two or more subgenomic promoters and (ii) the VSV G serotype switch is an effective prime-boost strategy. An optimized single-antigen (MHBs) or double-antigen (MHBs and HBc) vector can drive complete clearance of HBsAg in mice (
CARG-201 drives HBsAg clearance in highly antigenemic mice (
As seen in
shRNA inhibits PD-L1 expression in stably transfected BHK21 cells in vitro (
CARG-201-mediated decrease of serum biomarker is correlated with decreasing population of PD-1+/CD8+ in high HBsAg AAV-HBV chronic model (
A CARG-2020 construct expressing both rIL-12 and PD-L1 shRNA down regulates the expression of multiple immune checkpoints (
As seen in Table 2, we have completed the generation of CARG-301 secreting all three antigens (secCARG-301). We have also engineered CARG-301 to incorporate shRNA alone (CARG-301. sh) or both secretion signals and shRNA (secCARG-301. shNA). We will now test the immunogenicity of these constructs and prioritize them for efficacy studies in a chronic mouse model of HBV infection. The availability of constructs in both serotypes will allow us to employ a prime boost regimen if necessary.
1.2 × 1010
To demonstrate the utility of the VLV platform for manufacturing at larger scale, we compared CARG-201 titers obtained with one protocol using BHK-21 cells transfected with Lipofectamine vs. a modified protocol using BHK-21 cells transfected with PEIPro transfection reagent (suitable for manufacturing under cGMP guidelines) and HEK293T cells transfected with either reagent. The main purpose was to demonstrate that CARG-201 may be produced in 293T cells, a substrate cell line used by industry for production of viral vectors. The table is divided into three sections, showing the titers and productivity at harvest, post-filtration, and post-concentration by ultrafiltration.
In embodiments, lipofectamine or PEIPro may be advantageous over other transfection agents. Lipofectamine is a transfection reagent containing lipid subunits that associate with a transfection construct, such as a DNA plasmid, to form liposomes. Nucleic acid molecules have a negative charge and the liposomes which are formed have a net positive surface charge which overcomes static repulsion by the negatively charged cell membrane. PEIPro is another transfection reagent which is a polymeric reagent (containing polyethylenimine) that condenses DNA into positively charged particles.
From the results in Table 3, it can be seen that transfection with PEIPro can be optimized to yield improved titer, yield, and productivity compared to lipofectamine protocols. Therefore, in some embodiments. PEIPro as a transfection reagent may be particularly advantageous in methods for producing VLVs such as CARG-201.
In D. Knipe and P. Howley (ed.), Fields& #39; Virology. Lippencott-Raven, Philadelphia
The entire disclosure of each of the patent documents, including certificates of correction, patent application documents, scientific articles, governmental reports, websites, and other references referred to herein is incorporated by reference herein in its entirety for all purposes. In case of a conflict in terminology, the present specification controls.
The invention can be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are to be considered in all respects illustrative rather than limiting on the invention described herein. In the various embodiments of the compositions and methods of the present invention, where the term comprises is used with respect to the compositions or recited steps of the methods, it is also contemplated that the compositions and methods consist essentially of, or consist of, the recited compositions or steps or components. Furthermore, it should be understood that the order of steps or order for performing certain actions is immaterial so long as the invention remains operable. Moreover, two or more steps or actions can be conducted simultaneously.
In the specification, the singular forms also include the plural forms, unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In the case of conflict, the present specification will control.
Furthermore, it should be recognized that in certain instances a composition can be described as being composed of the components prior to mixing, or prior to a further processing step such as drying, binder removal, heating, sintering, etc. It is recognized that certain components can further react or be transformed into new materials.
All percentages and ratios used herein are on a volume (volume/volume) or weight (weight/weight) basis as shown, or otherwise indicated.
This continuation application claims the benefit of and priority to International Patent Application No. PCT/US2023/062986, filed Feb. 22, 2023, which claims priority to U.S. Provisional Patent Application No. 63/312,816, filed Feb. 22, 2022, each of which are incorporated by reference in their entireties herein.
This invention was made with government support under Grant No. 2R44 DK113858 awarded by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), and under Grant No. 1R43AI149798-01A1 awarded by the National Institute of Allergy and Infectious Diseases (NIAID), each of which are institutes within the National Institutes of Health (NIH). The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 63312816 | Feb 2022 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US2023/062986 | Feb 2023 | WO |
| Child | 18802462 | US |
