Patent Application
20230173050
The material contained in the Sequence Listing provided herewith in ASCII compliant format in the text file entitled “220053-23_ST25.txt” created on Nov. 10, 2021 and containing 86,754 bytes, is hereby incorporated by reference herein.
The invention relates to immunogenic proteins or fragments thereof derived from Plasmodium falciparum and/or Plasmodium vivax for use in the treatment or prevention of malaria.
Malaria is a serious and life-threatening mosquito-borne infectious disease caused by parasitic protozoans of the genus Plasmodium. In 2018, there were approximately 500,000 deaths from malaria mainly caused by Plasmodium falciparum. Whilst preventive small molecule based medicines exist to prevent malaria, such as chloroquine, they can be associated with significant side-effects, they are unsuitable for long-term use, and drug resistance is increasingly problematic. Vaccination programs have proven to be effective in the reduction and eradication of various diseases worldwide. The aim is to develop an effective malaria vaccine, which is urgently needed. However, current single-component vaccines lack sufficient efficacy for deployment in the field. The two leading malaria vaccine candidates, RTS,S and ChAd63-MVA ME-TRAP, are both sub-unit vaccines targeting the pre-erythrocytic phase of malaria. Whilst neither vaccine currently provides optimal protective efficacy for deployment in endemic countries, they both demonstrate the strength of targeting the pre-erythrocytic phase, as no blood-stage vaccine has progressed as far as in clinical development.
The most advanced vaccine in clinical development, RTS,S/AS01, has completed a phase III trial in African infants and children, where efficacy in young infants was
<20% and in 5-17 month olds was 35%. This vaccine is based on a platform in which RTS,S has four molecules of unfused HBsAg (Hepatitis B surface antigen) for each fusion protein containing HBsAg fused to the C-terminal half of the circumsporozoite protein (CSP). The vaccine works by inducing production of a high titre of antibodies against the central four amino acid conserved repeat of the circumsporozoite protein (CSP) of the malaria sporozoites. But as antibody titres fall over time, protection is reduced and then lost. There have also been suggestions of possible safety issues in the phase III trial and also uncertainty about logistic
deployability which has led to a delay in WHO pre-qualification, licensure and deployment of this vaccine.
Vaccination with irradiated sporozoites delivered by mosquito bite has been considered the ‘gold-standard’ of malaria vaccines, as whilst it is impractical for deployment, this regimen has repeatedly shown sterile protection in vaccinated volunteers. The increased efficacy of irradiated sporozoite immunization over sub-unit vaccines is likely because immune responses are induced to a broad range of antigenic targets. However, perhaps not only multiple targets are needed to create an efficacious sub-unit vaccine, but also better targets than those traditionally focused on (e.g. CSP and TRAP). Over 5000 different proteins are expressed throughout the Plasmodium life-cycle, leading to a high probability that alternative target antigens other than CSP or TRAP may exist, or a target antigen to be used alongside CSP or TRAP in a multicomponent vaccination strategy.
Several approaches are being utilised to try and produce an improved or alternative vaccine. One such approach may be to target the pre-erythrocytic, liver stage of the life cycle of the parasite. This type of malaria vaccine, unlike those described above, targets not the sporozoites themselves but the liver-stage parasite that grows in hepatocytes for approximately seven days after sporozoites successfully infect the liver.
The second part of the pre-erythrocytic stage (the liver-stage) ends with the emergence of large numbers of merozoites from each hepatocyte seven days after infection of the hepatocyte. Typically about 20,000 parasites emerge from each hepatocyte and rapidly invade erythrocytes, to start the blood-stage of infection. If the blood-stage is not controlled rapidly, the infected individual develops malaria and may die from the disease. Clearly, pre-erythrocytic vaccines have the potential advantage of stopping the malaria infection before any blood-stage infection occurs and when the number of potentially infected host cells is small.
A particularly promising approach to malaria liver-stage vaccine development has been to use recombinant non-replication-competent viral vectors such as adenoviral vectors or attenuated vaccine vectors, for example simian or human adenoviruses and modified vaccinia Ankara (MVA). Plasma DNA vectors and RNA-based vectors have also been tested but have yet to show clear clinical efficacy when used alone, but may usefully be used in heterologous prime boost regimens with viral vectors. Viral vectors appear to be particularly effective against the liver-stage because of their ability in inducing a cellular immune response, specifically malaria-specific CD8+ T cells that can target and kill malaria-infected hepatocytes.
CD8+ T cells recognise peptide antigens that are displayed on the surface of major histocompatibility complex (MHC) class I molecules, also known as HLA class I molecules in humans, on the surface of infected cells. CD8+ T cells, which are highly cytolytic, are strongly implicated in anti-malaria immunity at the liver stage. In some vaccine trials, the number of vaccine-induced malaria-specific CD8+ T cells has been shown to correlate with liver stage vaccine efficacy in humans, consistent with many experimental animal vaccine studies which have demonstrated this protective mechanism.
Because of this correlation, a so-called heterologous prime-boost vaccination regime is frequently used. This involves sequential immunisation with two different viral vectors encoding the same malaria antigen(s) or epitope(s). The vectors may be replication competent but preferentially are non-replication competent. This generates higher numbers of circulating CD8+ T cells compared to use of a single vector alone or with repeated administrations and leads to much higher vaccine efficacy in many clinical trials. A recent further development of liver-stage immunisation approaches has been to use a so-called prime-target immunisation regime. This involves administering the last dose of viral vector by an intravenous route (or other route that leads to antigen deposition in the liver) and has been found to increase the number of malaria-specific CD8+ T cells amongst the resident memory T cell population in the liver. Importantly, this generally leads to substantially greater vaccine efficacy (see WO2017/178809).
However, a challenge in developing effective liver-stage vaccines against malaria has been in identifying suitable target antigens to induce strong protective effects.
Murine malaria models exist but these are not helpful for studying P. falciparum infection in humans, and many antigens in P. falciparum have no homologues in the rodent parasites. Furthermore, hundreds or perhaps thousands of the 5000 or so genes in the P. falciparum genome are likely expressed in the liver and there has been no way of finding out which of these is a good vaccine immunogen. However, it is likely that only a small number or minority of the many genes expressed in the liver by P. falciparum produce proteins that end up as peptides presented by MHC class 1 molecules on the infected liver cell surface. These are the potential targets of vaccine-induced T cells whereas antigens that do not reach the surface in MHC molecules cannot be protective when using a liver stage vaccine. Because parasite antigens in the liver are inside a parasitophorous vacuole, which is surrounded by a parasitophorous vacuole (PV) membrane, most parasite antigens will be unable to reach the liver cell cytoplasm where they can be degraded, loaded on the MHC molecules and transported to the hepatocyte surface. Due to various technical difficulties limiting the ability of identification of the MHC-peptide complexes on the liver-cell surface directly, it has not been possible to determine which P. falciparum antigens/immunogens would be suitable liver-stage vaccine antigens/immunogens. These difficulties include:
Further, as it has been possible to achieve higher efficacy in humans by immunizing with whole irradiated sporozoites, it is widely believed that there may well be other, more protective, immunogens yet to be identified that are expressed by the Plasmodium parasite inside liver cells, which when used as vaccines would be more suitable and effective.
Therefore, it would be desirable to provide alternative immunogens, and improved delivery and vaccination methods for eliciting a protective immune response against malaria.
The inventors have identified proteins and peptides which are presented on HLA class I molecules of Plasmodium infected cells. Surprisingly, a large proportion (approx. 57%) are derived from ribosomal proteins or ribosomal associated proteins of the parasite, many of which are highly conserved between Plasmodium species. The peptides have been shown to be effective immunogens capable of producing a protective cellular response against the Plasmodium parasite, and provide a new class of immunogens useful in vaccines, in particular against malaria.
The present invention provides novel immunogens which may be used in vaccine compositions; in particular the invention provides novel immunogens which may be used in vaccine compositions for use against malaria, preferably wherein the vaccine targets the CD8+ T cell immunological response, both at liver and blood stage.
According to a first aspect of the invention, there is provided one or more Plasmodium-derived proteins or immunogenic fragments thereof for use in eliciting an immune response in a subject. The one or more Plasmodium-derived protein or immunogenic fragment thereof may be, or may be derived from, a ribosomal protein or ribosomal associated protein. The one or more Plasmodium-derived protein or immunogenic fragment thereof may be, or may be derived from, a malarial early transcribed membrane protein (ETRAMP) or a histone. The one or more Plasmodium-derived protein or immunogenic fragment thereof may be, or may be derived from, a protein recited in
The one or more Plasmodium-derived protein or immunogenic fragment thereof may be derived from Plasmodium falciparum and/or from Plasmodium vivax.
The invention may provide one or more Plasmodium falciparum or Plasmodium vivax proteins or immunogenic fragments thereof for use in raising an immune response in a subject. The one or more Plasmodium-derived protein or immunogenic fragment thereof may be, or may be derived from, a ribosomal protein or ribosome associated protein. The one or more Plasmodium-derived protein or immunogenic fragment thereof may be, or may be derived from, a malarial early transcribed membrane protein (ETRAMP) or a histone. The one or more Plasmodium-derived protein or immunogenic fragment thereof may be, or may be derived from, a protein recited in
In a further aspect, the invention provides an immunogenic composition comprising:
The immunogenic composition may further comprise a pharmaceutically acceptable excipient or carrier. The one or more Plasmodium-derived protein or immunogenic fragment thereof may be derived from Plasmodium falciparum and/or from Plasmodium vivax. The immunogenic composition may be used as a vaccine to treat or prevent malaria.
In another aspect the invention provides a method of eliciting an immune response in a subject, the method comprising the step of administering an immunogenic composition according to the invention to the subject. Preferably the immune response elicited is sufficient to treat or prevent malaria.
In a further aspect of the invention, there is provided an immunogenic composition according to the invention for use in treating or preventing malaria.
In a further aspect of the invention, there is provided an immunogenic composition according to the invention for use in the preparation of a medicament for treating or preventing malaria.
The immune response elicited in a subject by a composition according to the invention may be against malaria. Suitably, the immune response elicited may be sufficient to treat or prevent malaria caused by infection with Plasmodium falciparum and/or Plasmodium vivax. The malaria may comprise liver-stage malaria. The malaria may comprise pre-erythrocytic-stage malaria. The malaria may comprise erythrocytic-stage malaria.
The immune response elicited by a composition of the invention may be a protective immune response. Suitably, the protective immune response induces the activation of CD8+ T-cells. Where the immunogen is or is derived from a ribosomal protein or a ribosomal associated protein, or an ETRAMP, or a histone, or a protein recited in
The term “protective immune response” used herein, may be understood to be a host immune response that can sterilise the Plasmodium infection in a subject or reduce the number of parasites emerging from the liver (so that they are more readily cleared by blood-stage immunity). The protective immune response may sterilise the Plasmodium infection in at least 20% of subjects treated. The protective immune response may sterilise the Plasmodium infection in at least 35% of subjects treated. The protective immune response may sterilise the Plasmodium infection in at least 40% of subjects treated. The protective immune response may sterilise the Plasmodium infection in at least 50% of subjects treated. The protective immune response may sterilise the Plasmodium infection in at least 60% of subjects treated.
The protective immune response may provide clinical benefit in a subject by preventing the development of clinical malaria of a chronic parasitaemia. A protective immune response may comprise at least 0.1% of CD8+ T cells being antigen/immunogen-specific as determined, for example, by flow cytometry staining, and/or at least 500 spot forming cells (SFU) per million peripheral blood mononuclear cells (PBMC). Spot forming cells (SFU) may be determined by an ELISpot assay (enzyme-linked immunosorbent spot assay (For example the ELISpot assay provided by Mabtech AB, Sweden, see: http://www.mabtech.com/Main/Page.asp?PageId=16).
A protective immune response may comprise at least 0.2% of CD8+ T cells being antigen/immunogen-specific. A protective immune response may comprise at least 0.4% of CD8+ T cells being antigen/immunogen-specific. A protective immune response may comprise at least 0.8% of CD8+ T cells being antigen/immunogen-specific. A protective immune response may comprise at least 1% of CD8+ T cells being antigen/immunogen-specific.
A protective immune response may comprise at least 100 spot forming cells (SFU) per million peripheral blood mononuclear cells (PBMC). A protective immune response may comprise at least 300 spot forming cells (SFU) per million peripheral blood mononuclear cells (PBMC). A protective immune response may comprise at least 1000 spot forming cells (SFU) per million peripheral blood mononuclear cells (PBMC). A protective immune response may comprise at least 2000 spot forming cells (SFU) per million peripheral blood mononuclear cells (PBMC).
The Plasmodium-derived protein or immunogenic fragment thereof may have a sequence which is 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to a protein or a fragment of a protein recited in
The Plasmodium-derived protein or immunogenic fragment thereof may have a sequence which is 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to a protein or a fragment of a protein recited in
The Plasmodium-derived protein or immunogenic fragment thereof may have a sequence which is 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to a 40S ribosomal protein, preferably the 40S ribosomal protein S20e or a fragment of the 40S ribosomal protein S20e. The 40S ribosomal protein S20e may be derived from P. falciparum (Accession Q8IK02) or P. vivax (Accession A5K757). Preferably, the 40S ribosomal protein S20e is derived from P. falciparum (Accession Q8IK02).
The Plasmodium-derived protein or immunogenic fragment thereof may have a sequence which is 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to an ETRAMP or a fragment of an ETRAMP. The ETRAMP may be derived from P. falciparum or P. Vivax. Preferably, the ETRAMP is derived from P. vivax (Accession A5KBH5 and A5K676).
The Plasmodium-derived protein or immunogenic fragment thereof may have a sequence which is 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to a protein or a fragment of a protein selected from:
Accession numbers, where given, relate to those identifiable using UniProt (Universal Protein Resource), a comprehensive catalogue of information on proteins (‘UniProt: a hub for protein information’ Nucleic Acids Res. 43: D204-D212 (2015)).
Due to a high level of sequence conservation across the Plasmodium species, a high level of sequence homology exists between many Plasmodium-derived proteins, including ribosomal proteins and ribosomal associated proteins, of Plasmodium falciparum and Plasmodium vivax. A Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
The term “fragment” encompasses immunogenic and/or antigenic fragments of a Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
Percentage sequence identity is defined as the percentage of amino acids in a sequence that are identical with the amino acids in a provided sequence after aligning the sequences and introducing gaps if necessary to achieve the maximum percent sequence identity. Alignment for the purpose of determining percent sequence identity can be achieved in many ways that are well known to the man skilled in the art, and include, for example, using BLAST (National Center for Biotechnology Information Basic Local Alignment Search Tool).
Variations in percent identity may be due, for example, to amino acid substitutions, insertions or deletions.
The Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
The skilled person will be readily able to determine the polynucleotide sequence that would be needed to encode the immunogen. Of course, one of skill will appreciate that the degeneracy of the genetic code permits substitution of one or more bases in a codon without changing the primary amino acid sequence encoded. The skilled person will also appreciate the existence of codon bias and may tailor any polynucleotide sequence to the organism in which it will be expressed, preferably a human.
A polynucleotide encoding the Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
The polynucleotide in the immunogenic composition may be provided in a vector. The vector may be a viral vector. Alternatively the polynucleotide may be provided in a plasmid DNA vector or as an RNA vector-based immunogen.
The polynucleotide may be expressed as a protein in a variety of cells that are known in the field (Pichia, human cell lines, simian cell lines, insect cell lines, bacterial host etc.). The expressed protein encoded by the polynucleotide may be delivered as a vaccine, typically in combination with an adjuvant. Adjuvants and adjuvant formulations are well known, such as alum, AS01, matrix-M, MF59, GLA, Hiltonol and others.
In an aspect, the invention may provide a vector comprising a polynucleotide encoding one or more Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone or a protein or peptide of
In a further aspect the invention may provide an immunogenic composition comprising a vector of the invention, and optionally a pharmaceutically acceptable carrier or excipient. The vector may be a viral vector.
In a yet further aspect the invention may provide an immunogenic composition comprising a vector according to the invention and a pharmaceutically acceptable carrier for use as a vaccine.
The vector may be a virus (viral vector) or a protozoa parasite capable of delivering a polynucleotide encoding one or more Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
The viral vector may comprise a Modified Vaccinia Ankara (MVA) virus. The viral vector may be selected from any of the group comprising, a poxvirus, such as Modified Vaccinia Ankara (MVA) virus, or an adenovirus. The adenovirus may comprise a simian or human adenovirus. The adenovirus may comprise a Group E adenovirus. The adenovirus may comprise ChAd63 or ChAd3 or ChAdOx1 or ChAdOx2 or gorilla-derived adenoviruses. The adenovirus may comprise ChAdOx1. The adenovirus may comprise a group A, B, C, D or E adenovirus. The adenovirus may comprise Ad35, Ad5, Ad6, Ad26, or Ad28. The adenovirus may be of simian (e.g. chimpanzee, gorilla or bonobo) origin. The adenovirus may comprise any of ChAd63, ChAdOx1, ChAdOx2, C6, C7, C9, PanAd3, or ChAd3. The protozoa vector may comprise a Trypanosoma cruzi. The viral vector may be selected from any of the group comprising, a Trypanosomatidae, such as Trypanosoma cruzi, or Leishmania. The Trypanosoma cruzi may comprise Trypanosoma cruzi CL-14. The composition may comprise two or more different vectors. One or more of the vectors may be live vectors. One or more of the vectors may be viral vectors.
The Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
In a single dose vaccination regime the Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
The administration may be part of a prime-boost vaccination regime in a subject, where a first/prime administration of the immunogenic composition of the invention is followed by a second/boost administration of the immunogenic composition of the invention.
The administration may be part of a prime-target vaccination regime in a subject, where a first/prime administration of the immunogenic composition of the invention is followed by a second/boost administration of the immunogenic composition of the invention, wherein the boost dose is administered by an intravenous route or other route that leads to antigen deposition in the liver.
Additional boost vaccinations may be provided. Alternatively only one of the prime and boosts may comprise a composition of the invention. Alternatively, only a single dose of the vaccine may be required to induce protective immunity.
Where the immunogenic composition is intended for a multiple administration regime, such as a prime-boost regime or prime-target regime, the different administration may comprise identical or different immunogenic compositions or vaccines or pharmaceutical compositions. Where the immunogenic composition is intended for a prime-boost or prime-target administration regime, the prime composition may comprise the same or different viral vector as the boost composition. The same immunogenic composition may be used for both prime and boost administrations. A different immunogenic composition or vaccine may be used for the prime and boost administrations.
The viral vector of the first/prime administration may comprise adenovirus. The viral vector of the second/boost administration may comprise poxvirus, such as MVA, or adenovirus.
The second/boost administration may be between about 1 day and about 30 days after the first/prime administration. The second/boost administration may be about 14 days after the first/prime administration.
Additional administrations of the immunogenic composition of the invention may be provided.
Suitable doses of adenoviral vectors for immunising humans are about 1×108 to about 1×1011 viral particles. Suitable doses of MVA for immunising humans are about 1×107 pfu to about 1×109 pfu. These vectors may be given by a range of immunisation routes, typically intramuscular and intravenous, but also for example subcutaneous, intradermal, intranasal and aerosol.
According to a yet further aspect, the invention provides a host cell comprising a vector, preferably a viral vector, according to the invention. The host cell may be in vitro. The host cell may be infected with the viral vector of the invention, or may comprise and express a polynucleotide of the invention.
Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator sequences, polyadenylation sequences, enhancer sequences, invariant chain sequences, marker genes and other sequences as appropriate. For further details see, for example, (Sambrook, J., E. F. Fritsch, and T. Maniatis. (1989), Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.). Many known techniques and protocols for manipulation of nucleic acid, for example in preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA into cells and gene expression, and analysis of proteins, are described in detail in (Ausubel et al., Current protocols in molecular biology. New York: Greene Publishing Association; Wiley-Interscience, 1992). A polynucleotide of the invention may be expressed using any suitable expression system, for example in a suitable host cell infected with a viral vector encoding a polynucleotide of the invention.
A composition of the invention can be formulated using established methods of preparation (Gennaro, A. L. and Gennaro, A. R. (2000) Remington: The Science and Practice of Pharmacy, 20th Ed., Lippincott Williams & Wilkins, Philadelphia, Pa.).
A composition of the invention may be administered via any parenteral or non-parenteral (enteral) route that is therapeutically effective. Parenteral application methods include, for example, intracutaneous, subcutaneous, intramuscular, intratracheal, intranasal, intravitreal or intravenous injection and infusion techniques, e.g. in the form of injection solutions, infusion solutions or mixtures, as well as aerosol installation and inhalation, e.g. in the form of aerosol mixtures, sprays or powders. In a preferred embodiment, a composition of the invention is administered intramuscularly or intravenously. A composition can be administered systemically in a formulation containing conventional non-toxic pharmaceutically acceptable excipients or carriers, additives and vehicles as desired. The composition may be an aqueous solution, an oil-in water emulsion or a water-in-oil emulsion.
To prepare the compositions, pharmaceutically inert inorganic or organic excipients can be used. To prepare for example pills, powders, gelatin capsules or suppositories, lactose, talc, stearic acid and its salts, fats, waxes, solid or liquid polyols, natural and hardened oils are examples of pharmaceutically acceptable excipients which can be used. Suitable excipients for the production of solutions, suspensions, emulsions, aerosol mixtures or powders for reconstitution into solutions or aerosol mixtures prior to use include water, alcohols, glycerol, polyols, and suitable mixtures thereof as well as vegetable oils.
For intravenous injection, the active ingredient will be in the form of a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection. Preservatives, stabilisers, buffers, antioxidants and/or other additives may be included, as required.
The compositions are preferably administered to an individual in a “therapeutically effective amount”, this being sufficient to show benefit to the individual. The optimal dosage will depend on, for example, the biodistribution of the active agent which induces immunogenicity, and the mode of administration.
The composition may also contain additives, such as, for example, fillers, binders, wetting agents, glidants, stabilizers, preservatives, emulsifiers, and furthermore solvents or solubilizers.
A pharmaceutically acceptable carrier can contain physiologically acceptable agents that act, for example, to stabilize, increase solubility or to increase the absorption of a composition. Such physiologically acceptable agents include, for example, carbohydrates, such as glucose, sucrose or dextrans, antioxidants, such as ascorbic acid or glutathione, chelating agents, low molecular weight proteins or other stabilizers or excipients. The choice of a pharmaceutically acceptable carrier, including a physiologically acceptable agent, depends, for example, on the route of administration of the composition. The compositions can be a self-emulsifying drug delivery system or a selfmicroemulsifying drug delivery system. The compositions can also be a liposome or other polymer matrix, which can have incorporated therein, for example, the compositions of the invention. Liposomes, for example, which comprise phospholipids or other lipids, are nontoxic, physiologically acceptable and metabolisable carriers that are relatively simple to make and administer.
The phrase “pharmaceutically acceptable” is employed herein to refer to those compounds, materials, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
A composition of the invention may further comprise, or be intended to be administered simultaneously, sequentially, or separately with an adjuvant. The adjuvant may comprise an oil emulsion. The adjuvant may be selected from any of the group comprising PEI; Alum; AS01 or AS02 (GlaxoSmithKline); inorganic compounds, such as aluminium hydroxide, aluminium phosphate, calcium phosphate hydroxide, or beryllium; mineral oil, such as paraffin oil; emulsions, such as MF59; bacterial products, such as killed bacteria Bordetella pertussis, or Mycobacterium bovis; toxoids; non-bacterial organics, such as squalene or thimerosal; the saponin adjuvant matrix M (Isconova/Novavax) or other ISCOM-type adjuvants; detergents, such as Quil A; cytokines, such as IL-1, IL-2, or IL-12; Freund's complete adjuvant; and Freund's incomplete adjuvant; or combinations thereof.
In another aspect, there is provided a method of treatment or prevention of malaria, said method comprising administering to a subject at risk of or suffering from malaria one or more Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
In another aspect, there is provided one or more Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
Thus, in another aspect of the invention, there is provided a method of prevention or treatment of malaria in a subject, comprising:
In another aspect, there is provided a kit for a vaccination regime against malaria in a subject, comprising:
The kit may further comprise directions to administer the prime composition prior to the boost composition in a subject. The nucleic acid of the viral vector of the kit may further encode one or more other Plasmodium-derived protein or immunogenic fragment thereof, such as a ribosomal protein or ribosomal associated protein, or an ETRAMP, or a histone, or a protein or peptide of
The kit, prime, and/or boost composition may further comprise an adjuvant.
According to another aspect of the invention, there is provided a method of manufacturing a viral vector of the invention, comprising:
Suitable cell lines for production of adenoviral vectors include HEK293 cells and Per.C6 cells. Suitable cells for production of MVA include chicken embryo fibroblast, DF1 cells, AGE1.CR.pIX and EB66.
The skilled person will understand that optional features of one embodiment or aspect of the invention may be applicable, where appropriate, to other embodiments or aspects of the invention.
There now follows by way of example only a detailed description of the present invention with reference to the accompanying drawings, in which;
peptides identified the majority come from plasmodial ribosomal proteins. Non-ribosomal associated proteins are marked with an asterix (*)
1. Humanised Mice Infected with P. falciparum
TK-NOG mice were transplanted/engrafted with human primary hepatocytes, which repopulate the damaged liver (repopulation (60-80%) as described in Soulard, V. et al. Nat Commun 6 (2015). This model allows the complete hepatic development of P. falciparum and the transition to erythrocytic stages, including the appearance of mature gametocytes. This mouse model closely mimics the physiological complexity and specificity of an in vivo infection in the human environment and is also a source of fresh human hepatocytes. Every mouse received hepatocytes from the same donor. The donor HLA alleles were HLA-A*03:01, HLA-A*11:01, HLA-B*40:01, HLA-B*50:01, HLA-C*03:02 and HLA-C*06:02. Thirteen TK-NOG mice were used in three independent experiments and infected with P. falciparum sporozoites in the tail vein as described in the Table 1.
Mice were infected sporozoites from P. falciparum, NF54 or NF135 strains, in the tail vein, and livers were harvested at discreet time points post-infection as described in Table 1 below.
P.
P. falciparum
falciparum
50 μm thick liver sections were obtained and histology was performed to determine the rate of infection. The rate of infection was determined by staining the parasites with an anti-HSP70 antibody and by calculating the average of schizonts counted, divided by the total number of human hepatocytes in each liver. The total number of human hepatocytes infected (rate of infection multiplied by the total number of human hepatocytes) was also calculated. The rate of infection in these mice varied from 30,000 to 60,000 per liver.
Starting from 200 mg of liver material, cells were lysed and total proteins were collected for mass spectrometry (MS) analysis. See section 3 for details.
2. Human Reticulocytes Infected with P. vivax
Human reticulocytes from patients infected with P. vivax were purified as described in Junqueira, C. et al. Nature medicine 24, 1330-1336 (2018). Seven samples containing >99% P. vivax-infected reticulocytes varying from 4.3×107 to 7×108 cells (Table 2), were lysed and total proteins were collected for mass spectrometry analysis. See section 3 for details.
5 × 107
7 × 108
Parasitemia was determined at the site of sample collection following local clinical protocols.
3. Peptide Identification by Immunopeptidomics
3.1 Mass Spectrometry
Cells were lysed in 1 ml lysis buffer (0.5% Igepal, 150 mM NaCl, 50 mM Tris, pH 8.0, supplemented with Complete™ protease inhibitor cocktail (Roche)). HLA complexes were immunoprecipitated using 1 mg monoclonal antibody W6/32 against HLA-ABC complexes (GE healthcare) cross-linked to Protein A Sepharose beads using dimethyl pimelimidate (DMP, Sigma). Lysates were incubated overnight. Beads were subsequently washed with 10 column volumes of 2×150 mM NaCl in 50 mM Tris, 1×450 mM NaCl in 50 mM Tris and 50 mM Tris buffer without salt. Peptides bound to the HLA groove are released after mild acid elution with 5 mL 10% acetic acid to denaturate of the alpha-chains and beta-2-microglobulin. The HLA-bound peptides were further purified from beta-2-microglobulin and alpha-chains by HPLC (Ultimate 3000) on a ProSwift RP-IS 4.6×50 mm column (Thermo Scientific) by applying a linear gradient of 2-35% (v/v) acetonitrile in 0.1% (v/v) formic acid in water over 10 min. Alternating fractions that did not contain beta-2-microglobulin or alpha-chains were pooled into two final fractions, concentrated and kept at −80° C. prior to MS analysis.
Peptides were suspended in 20 μL buffer A (1% acetonitrile, 0.1% TFA in water) and analyzed by nUPLC-MS/MS using an Ultimate 3000 RSLCnano System coupled with an Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Scientific). 9 μl of each sampled was injected and trapped onto a 3 μm particle size 0.075 mm×150 mm Acclaim PepMap RSLC column at 8 μl/min flowrate. Peptide separation was performed at 40° C. by applying a 1 h linear gradient of 3-25% (v/v) acetonitrile in 0.1% (v/v) formic acid, 5% DMSO in water at a flow rate of 250 μl/min on a 2 μm particle size, 75 μm×50 cm Acclaim PepMap RSLC column. For HLA class II samples, a linear gradient of 5-30% (v/v) acetonitrile was applied. Peptides were introduced to a Fusion Lumos mass spectrometer (Thermo Scientific) via an Easy-Spray source at 2000 V. The ion transfer tube temperature was set to 305° C. Measurement of precursor peptides was performed with a resolution of 120,000 for full MS (300-1500 m/z scan range) at an AGC target of 400,000. Precursor ion selection and fragmentation by high-energy collisional dissociation (HCD at 28% collision energy for charge state 2-4, 35% for charge state 1) was performed in TopSpeed mode at an isolation window of 1.2 Da for singly to quarterly charged ions at a resolution of 30,000 and an AGC target of 300,000 in the Orbitrap for a cycle duration of 2 s. Singly charged ions were acquired with lower priority.
3.2 Peptide Identification
MS data was analyzed with Peaks 8 (Bioinformatics Solutions and Tran, N. H. et al. Nature methods 16, 63-66 (2019)) for identification of peptide sequences. Spectra were matched to all reviewed human proteins combined with Plasmodium falciparum (isolate 3D7) or Plasmodium vivax (Salvador I), produced based on UniProt proteomes (UniProt, C. UniProt: a worldwide hub of protein knowledge. Nucleic acids research 47, (2019)). The results were filtered using a score cut-off of −1g10P=15. The searches were performed with the following parameters: no enzyme specificity, no static and variable modifications, peptide tolerance: ±5 ppm and fragment tolerance: ±0.03 Da.
Human sequences were disregarded from the analysis. The peptide spectrum matches (PSMs) of plasmodial origin obtained were analysed following a pipeline consisting of: 1) Size exclusion: MHC-I peptides longer than 15 amino were excluded. Peptides smaller than 8 amino acid long were excluded; 2) A Peaks score cut-off of 15 was applied to all samples; 3) False positive peptides, that is, peptides with incorrect identification were removed from the samples; 4) A stringent blast analysis was performed in every peptides sequence using the DeBosT script (see section 3.3). Peptides with two or more amino acid different from human sequences were considered non-human and therefore identified as plasmodial peptides. Peptides with higher netMHC rank were prioritized. The amino acids leucine (L) and isoleucine (I) are isomers, which are indistinguishable from each other through the mass spectrometry protocol. All peptides were blasted for all possible combinations of I and L, and when a combination matched a human peptide, the sequence was excluded. Applying these four-step data analysis criteria, a list of Plasmodium peptides were identified, see
3.3 DeBosT Script
Blast searches (National Library of Medicine, https.//blast.ncbi.nlm.nih.gov) of putative plasmodial sequences were performed using a batch script. Sequences that have less than two amino acid differences compared to human sequences were excluded from downstream analysis (Bettencourt, P. et al. Identification of antigens presented by MHC for vaccines against tuberculosis. npj Vaccines 5, 2 (2020)).
3.4 Peptide Validation
Malaria infected patients and healthy donors. P. vivax infected patients were recruited in the Tropical Medicine Research Center (Porto Velho-Brazil) along with healthy donors from the same endemic region and from a non-endemic region (Belo Horizonte-Brazil). All participants provided written informed consent for participation in the study, which has a protocol approved by the Institutional Review Boards of the Oswaldo Cruz Foundation and National Ethical Council (CAAE: 59902816.7.0000.5091). Samples were collected at three different times. Firstly, 7 samples from P. vivax infected patients were obtained for the mass spec experiments. Twenty two samples from P. vivax infected patients, eighteen healthy donors from the endemic region and 6 from a non-endemic region posteriorly were collected for the Elispot assay.
PBMC and P. vivax infected reticulocytes obtention. 100 mL of blood was collected from infected individuals and controls. First, mononuclear cells were separated from peripheral blood (PBMCs). For this, the blood was diluted in a 1:1 ratio, was gently added to a tube containing 15 mL of Ficoll (GE Healthcare, USA). Red blood cell pellet resulting from PBMC purification was resuspended in RPMI culture medium in a 1:4 ratio. Diluted blood was added carefully into a 50 mL tube containing Percoll 45% (GE Healthcare, USA), 5× the volume of the red blood cell pellet. Samples were centrifuged for 15 minutes at 2000 rpm. After centrifugation, the reticulocyte interface was collected. Reticulocyte purified samples had 99% purity.
ELISPOT assay. The ex vivo IFN-γ ELISpot assays were performed using 5×105 fresh PBMCs from P. vivax infected patients, endemic and non-endemic healthy donors. Cells were plated in duplicates into 96-well ELISpot plates (Merck Millipore) precoated with 4 μg/ml anti-human-IFN-γ (clone 1-D1K; Mabtech). Peptides of Table 3 (
3.5 Spectral Match Validation
To further confirm the identity of the peptide sequences identified, a spectral match validation experiment will be performed. Synthetic peptides will be produced and compared to a selection of PSMs obtained from the experiments (the biological peptides). Synthetic peptides will be run in the same experimental conditions as biological peptides. The mass over charge [m/z] for each peptide, the charge state, the intensity and distribution of each peak within each peptide sequences, as well as the peptide specific retention time (RT) on the Liquid Chromatography will be compared between synthetic and biological peptides.
3.6 CD8+ T-Cell Response
The CD8+ T-cell responses from healthy patients from endemic and non-endemic areas for malaria, and those of P. falciparum and P. vivax-infected patients were analysed against peptides identified by immunopeptidomics (Table 3), using IFN-gamma ELISpot. Several peptides, including ribosomal protein peptides were shown to be recognised in ex vivo ELISPOT assays. This demonstrated that peptides displayed on MHC-1 molecules on reticulocytes, including those derived from ribosomal proteins, are naturally immunogenic in human infections and thus are good immunogens for vaccination.
3.7 Efficacy and Immunogenicity of New Vaccine Candidates
The immunogens described here may be cloned into viral vectors for use as vaccines. The platform of subunit vaccines has proved to be very safe and is very powerful in inducing CD8+ T-cell responses against the antigen that is being expressed. Generation of ChAdOx1, AdHu5 and/or MVA expressing each antigen may be cloned using GeneArt Technology (ThermoFisher Scientific, UK). Subunit vaccines expressing liver stage antigens may be produced. Immunogens may be mammalian codon-optimized flanked by a Kozak consensus sequence, a tPA leader sequence and a GS linker at the 5′-end and at the 3′ end, cloned into a GeneArt entry vector and then recombined into an ChAdOx1, AdHu5 and/or MVA destination plasmid as previously described in Dicks, M. D. et al. PloS one 7 (2012) and McConkey, S. J. et al. Nature medicine 9, 729-735 (2003). Efficacy and immunogenicity of the viral vectors will be evaluated in a malaria challenge mouse model.
Plasmodium vivax is the most widespread cause of human malaria and the second most lethal after P. falciparum. Unusually, P. vivax preferentially infects reticulocytes and recently it has been demonstrated that P. vivax-infected patients have circulating CD8+ T cells that recognize and form immunological synapses with P. vivax-infected reticulocytes in an HLA-dependent manner, releasing their cytotoxic granules to kill both host cell and intracellular parasite, preventing reinvasion. 50 and 700 million reticulocytes per subject were obtained from seven Brazilian subjects infected with P. vivax, as described in section of the materials and methods.
453 unique peptides were identified by tandem mass spectrometry sequencing and these were from 176 distinct P. vivax antigens. There was significant overlap in immunogens identified in the six subjects, with peptides from 29 antigens found in at least 50% of the subjects and peptides from two antigens found in all six subjects, with high quality data. A most striking and unexpected finding was that over half of the peptides (57%) came from a single class of proteins, plasmodial ribosomal or ribosome associated proteins. A list of peptides identified and the protein they are derived from is provided in
Ribosomal proteins are species-specific and between humans and Plasmodia, most ribosomal proteins share approximately 60% sequence identity on average. This divergence provides adequate differences for regions on non-identify between human/mammalian ribosomal and parasite ribosomal sequences to avoid self-tolerance and be suitably immunogenic. However, proteins with less homology to humans are preferred so as to potentially maximise immunogenicity. Furthermore proteins with identify or greater similarity between P. falciparum and P. vivax are preferred because they are more likely to provide a cross-species protective effect.
Further, ribosomes are required for protein production and their structure and mechanism of polypeptide generation are well understood. Cells and microbes that are rapidly dividing or very metabolically active may need a lot of ribosomes and ribosomal proteins to engage in the required protein synthesis. This is likely to be true of parasitized reticulocytes in which P. vivax grows very rapidly. Similarly, within hepatocytes, malaria parasites generally grow very rapidly. For example, in the case of P. falciparum, one sporozoite infects a liver cell and seven days later 20,000 parasites with a largely different antigenic composition, malaria merozoites, emerge from the same liver cell. Therefore, the findings of the mass spectrometry analysis support the fact the parasite will need to generate a lot of ribosomal proteins intracellularly, which are capable of ending up on the HLA class I molecules in parasitized cells.
In addition to the vast majority of ribosomal proteins identified in the mass spectrometry analysis of peptides eluted from HLA-I expressed on infected reticulocytes, two Pv ETRAMPs peptides that are expressed both in hepatocyte and reticulocyte stages were also identified. The ETRAMPs compose a family of polymorphic, small, highly-charged transmembrane proteins unique to malaria parasites, they localize in the parasitophorous vacuole membrane (PVM) with the C-terminal region exposed to the RBC cytosol and are also exported to the host cell cytoplasm. Therefore, the ETRAMPs are accessible to the protein machinery that processes and presents endogenous antigens. Furthermore, they are expressed in the first hours of invasion and, thus, the infected reticulocytes may become targets to CTLs at the early stages of infection. In addition, the ETRAMPs are recognized by antibodies from Plasmodium falciparum and Plasmodium vivax malaria patients and CD4+ T cells from P. berghei-infected mice. In conclusion, the HLA-I binding and biology of ETRAMPs suggest that they could be key targets for protective CD8+ T cell-mediated immunity against malaria. Like ribosomal proteins, ETRAMPs have not been employed or evaluated for CD8+ T cell mediated immunity.
As a proof of concept, one plasmodial ribosomal protein gene was selected and expressed to test the concept that plasmodial ribosomal proteins could be suitable immunogens for developing immunogenic, protective malaria vaccines.
The P. falciparum 40S ribosomal protein S20e was selected, which is 118 amino acids in length (sequence: MSKLMKGAIDNEKYRLRRIRIALTSKNLRAIEKVCSDIMKG AKEKNLNVSGPVRLPVKTLRITTRKSPCGEGTNTWDRFELRIYKRLIDLYSQCE VVTQMTSINIDPVVEVEVIITDS, Uniprot accession: PF3D7_1003500.1). The protein was expressed in both a simian adenoviral vector ChAdOx1 and in MVA. BALB/c Mice were immunised with a single shot of 1×108 infectious units of the ChAd recombinant and boosted with the MVA three weeks later with a dose of 1×108 pfu and challenged intravenously three weeks later with 1000 P. berghei sporozoites transgenic for P. falciparum 40S ribosomal protein S20e (expressed under a Pbuis4 promoter). There was highly significant protective efficacy with 2 of 8 mice sterilely protected and the remaining six delayed in time to parasitaemia reflecting a substantial reduction of liver parasite load, P=0.0001 (
CD-1 mice were immunised with a single shot of 1×108 infectious units of the ChAd recombinant and boosted with the MVA eight weeks later with a dose of 1×108 pfu and challenged intravenously three weeks later with 1000 P. berghei sporozoites transgenic for P. falciparum 40S ribosomal protein S20e (expressed under a Pbuis4 promoter). There was highly significant protective efficacy with 3 of 10 mice sterilely protected and the remaining six delayed in time to parasitaemia reflecting a substantial reduction of liver parasite load, P=0.0001 (
Using prime-target vaccination regime in CD-1 mice, there was highly significant protective efficacy with 5 of 10 mice sterilely protected and the remaining 5 delayed in time to parasitaemia reflecting a substantial reduction of liver parasite load, P=0.0001 (
This efficacy with a Plasmodium falciparum ribosomal protein immunogen demonstrates that ribosomal protein immunogens are a new class of antigens for malaria vaccination, especially to target the liver-stage of infection.
To allow analysis of larger numbers of P. falciparum-infected human hepatocytes, a recently described mouse strain (TK-NOG) in which most of the mouse liver has been replaced by human hepatocytes was utilised (which unlike mouse hepatocytes will support invasion and growth of P. falciparum).
The TK-NOG mice (Soulard et al Nature Communications 2015) express the HSVtk transgene under the albumin promoter onto the NOD SCID IL2Rg/background. In this mouse strain, the loss of endogenous hepatocytes is inducible by a brief exposure to a non-toxic dose of ganciclovir, a method that is rapid and temporally restricted, and routinely leads to substantial repopulation (60-80%) with human hepatocytes. The human herpes simplex virus thymidine kinase type 1 gene (HSVtk) acts as a conditional lethal marker in mammalian cells. The HSVtk-encoded enzyme is able to phosphorylate certain nucleoside analogs (e.g. ganciclovir, an antiherpetic drug), thus converting them to toxic DNA replication inhibitors. The utility of HSVtk is a conditional negative-selection marker.
These TK-NOG mice were infected with 1×107 P. falciparum sporozoites of a rapidly growing strain (e.g. P. falciparum NF135) and livers were removed at 3-5 days post-infection. After applying the immunopeptidomics pipeline to identify peptides bound to MHC molecules, Table 4 was obtained. Remarkably, the peptide sequence VITDVGDSDIIKTNE that is part of the protein W4IGC0 form P. falciparum NF135 (Ribosomal_L7Ae domain-containing protein) (
Finding two antigens in a short list of few confirmed eluted peptides from this type of experiment using human hepatocytes, provides clear evidence that ribosomal protein peptides can be presented on the HLA class I molecules of P. falciparum-infected liver cells. This further supports the concept that vaccines based on ribosomal proteins would be effective malaria vaccines.
falciparum NF135/5.C10 OX = 1036726 GN = PFNF135_05644 PE = 3 SV = 1
Peptide Validation by ELIspot Assay
48 peptides were tested by ex vivo IFN-γ ELIspot assay. The peptides are detailed in
All ribosomal peptides were immunogenic in the P. vivax tested samples and twelve were positive in at least 70% of the patients (
All the ETRAMP peptides tested were immunogenic in the P. vivax samples, ranging from 47.8 to 82.6% positivity in the tested patients (
All the histone peptides tested were immunogenic in all P. vivax and all P. falciparum tested samples. In P. vivax the rate of responder patients ranged between 40% and 71.4% (
The Uncharacterized proteins or Don Juan peptides showed a rate of patients with positive responses between 45 and 63.6% (
| Number | Date | Country | Kind |
|---|---|---|---|
| 1906641.4 | May 2019 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/GB2020/051146 | 5/11/2020 | WO |
