# Patent

## Title
Conformation-stabilized TRAP antigens

## Abstract

This invention relates to compositions and methods for eliciting an immune response against a parasite of the genus Plasmodium in a mammal.

## Background
CLAIM OF PRIORITY
This application is a U.S. National Phase Application under 35 U.S.C. §371 of International Patent Application No. PCT/US2013/026461, filed on Feb. 15, 2013, which claims the benefit of U.S. Provisional Application Ser. Nos. 61/600,567 and Ser. No. 61/600,570, both filed on Feb. 17, 2012. The entire contents of the foregoing are incorporated herein by reference.


FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with Government support under Grant No. AI095686 awarded by the National Institutes of Health. The Government has certain rights in the invention.


TECHNICAL FIELD
This invention relates to compositions and methods for eliciting an immune response against a parasite of the genus Plasmodium in a mammal.
BACKGROUND
Malaria is caused by a eukaryotic protist parasite of the genus Plasmodium. Transmission is typically by the bite of infected female Anopheles mosquitoes, which carry Plasmodium sporozoites in their salivary glands, though congenital transmission and transmission by blood transfusion is also possible. Within minutes after infection of a mammalian host, the sporozoites enter the blood stream and migrate to the liver, where they infect hepatocytes, mature and release thousands of merozoites. The parasites then enter the bloodstream, infecting red blood cells.
Malaria is a major health problem to residents and visitors in much of the tropics and subtropics, with 250 million cases of fever and approximately one million deaths annually (2005 WHO World Malaria Report 2008).
SUMMARY
The present invention is based, at least in part, on the discovery of new vaccines (i.e., compositions that elicit an immune response in an animal, e.g., a mammal, e.g., a human) against malaria-causing parasites for use in subjects who may be, or who have been, exposed to such parasites. Thus described herein are antigens, nucleic acids encoding those antigens, host cells and transgenic animals expressing the antigens, and methods of using the antigens as vaccines to elicit an immune response in mammalian subjects.
Thus the invention provides Plasmodium TRAP proteins that include one or more mutations described herein.
In a first aspect, the invention provides Plasmodium falciparum Thrombospondin-Related Anonymous Protein (TRAP) antigens, wherein the antigen sequence includes one or more of the following (numbering relative to SEQ ID NO:5): Mutation at Cysteine 55 to a non-cysteine amino acid, e.g., Glycine, Serine, or Alanine; Mutation of N-linked glycosylation sites, e.g., mutation of N or (S/T) in the carbohydrate-encoding N-X-(S/T), e.g., N132S, S477N, and/or N483S; Mutation of Ala-216/Asn-222 or Lys-224/Gln-78 to cysteine to create a TRAP that is stabilized in the open conformation; Mutation of Asn-213/Ala-233, Ala-216/Phe-230, or Met-231/Gln-78 to cysteine to create a TRAP that is stabilized in the closed conformation; Deletion of N-terminal and/or C-terminal residues to create a TRAP fragment that is stabilized in the closed conformation comprising V47-V238; and/or Deletion of N-terminal and/or C-terminal residues to create a TRAP fragment that is stabilized in the open conformation comprising V47-M231.
In some embodiments, the falciparum or vivax deletion mutants include additional amino acids on one or both ends, e.g., one, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or thirty additional amino acids; the deletion mutants can include all of the beta-ribbon as shown in FIGS. 6A-6B.
In some embodiments, the sequence is a mutated P. falciparum sequence comprising a sequence that is at least 80% identical to SEQ ID NO:5, e.g., at least 85%, 90%, or 95% identical to SEQ ID NO:5. In some embodiments, the sequence lacks the signal sequence, e.g., lacks amino acids 1-24 of SEQ ID NO:5, e.g., is at least 80% identical to amino acids 25-574 of SEQ ID NO:5, e.g., at least 85%, 90%, or 95% identical to amino acids 25-574 of SEQ ID NO:5.
In another aspect, the invention provides Plasmodium vivax Thrombospondin-Related Anonymous Protein (TRAP) antigens wherein the antigen sequence comprises one or more of the following (numbering relative to SEQ ID NO:6): Mutation of N-linked glycosylation sites, e.g., mutation of N or (S/T) in the carbohydrate-encoding N-X-(S/T), e.g., S42Q, N91S, N128S, and/or S180R; Mutation of Ser-212/Glu-218, Val-220/Ser-74 to cysteine to create a TRAP that is stabilized in the open conformation; Mutation of Ser-212/Phe-226, Ile-223/Met-67, Ile-227/Ser-74 to cysteine to create a TRAP that is stabilized in the closed conformation; Deletion of N-terminal and/or C-terminal residues to create a TRAP fragment that is stabilized in the closed conformation comprising amino acids V43-V234; and/or Deletion of N-terminal and/or C-terminal residues to create a TRAP fragment that is stabilized in the open conformation comprising amino acids V43-I227.
In some embodiments, the falciparum or vivax deletion mutants include additional amino acids on one or both ends, e.g., one, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or thirty additional amino acids; the deletion mutants can include all of the beta-ribbon as shown in FIGS. 6A-6B.
In some embodiments, the sequence is a mutated P. vivax sequence comprising a sequence that is at least 80% identical to SEQ ID NO:6, e.g., at least 85%, 90%, or 95% identical to SEQ ID NO:6. In some embodiments, the sequence lacks the signal sequence, e.g., lacks amino acids 1-25 of SEQ ID NO:5, e.g., is at least 80% identical to SEQ ID NO:6, e.g., at least 85%, 90%, or 95% identical to amino acids 26-556 of SEQ ID NO:6.
In another aspect, the invention also provides fusion proteins include a first portion consisting essentially of a TRAP antigen protein as described herein, and at least a second portion comprising one or more of an adjuvant, carrier, or protein purification sequence, e.g., a FLAG sequence or a 6His sequence. In some embodiments, the carrier comprises a hepatitis B surface protein.
In another aspect the invention provides nucleic acids encoding an antigen or fusion protein of any of claims; vectors comprising the nucleic acids; and host cells expressing the nucleic acids or vectors.
In a further aspect, the invention provides compositions comprising one or more of the antigens, fusion proteins, or nucleic acids described herein, and pharmaceutical compositions comprising one or more of the antigens, fusion proteins, or nucleic acids described herein, and a physiologically acceptable carrier. In some embodiments, the compositions include an adjuvant.
In yet another aspect, the invention provides methods of inducing an immune response in a mammal The methods include administering to the subject a therapeutically effective amount of one or more of the antigens, fusion proteins, or nucleic acids described herein, e.g., a pharmaceutical composition comprising one or more of the antigens, fusion proteins, or nucleic acids described herein. In some embodiments, the pharmaceutical composition further comprises an adjuvant.
Unless otherwise defined, 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. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.
Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.



DESCRIPTION OF DRAWINGS
FIG. 1 is a schematic illustration of the structure of TRAP.
FIG. 2A is an illustration of the N-terminal portion of an exemplary P. falciparum TRAP sequence (amino acids 1-263 of SEQ ID NO:1). Disulfide bonds are illustrated by shaded bars.
FIG. 2B shows an alignment of the N-terminal portion of the mature ectodomain (without the signal sequence) of exemplary TRAP sequences, i.e., up to the end of the TSR domain shown in FIG. 1, of sequences from Plasmodium species Vivax (SEQ ID NO:17); falciparum (SEQ ID NO:18); cynomolgi (SEQ ID NO:19); knowlesi (SEQ ID NO:20); berghei (SEQ ID NO:21); yoelii (SEQ ID NO:22); gallinaceum (SEQ ID NO:23); and relictum(SEQ ID NO:24).
FIG. 3 is an illustration of the overall structure of P. falciparum TRAP VWA domain. The MIDAS residues are shown as sticks. The cysteine side chain bonds are labeled. Secondary structure elements are also labeled.
FIG. 4A is a ribbon diagram of two molecules of P. vivax TRAP in an asymmetric unit.
FIG. 4B is a ribbon diagram of P. vivax TRAP showing three domains: VWA, elastic beta-ribbon and TSR domains. The metal ions are shown as spheres. The O-linked glycans are shown as sticks and labeled.
FIGS. 5A-D show an exemplary alignment of reference Plasmodium TRAP sequences, as follows:












GenBank

SEQ ID


Acc No.
Title
NO:

















XP_001350088.1
Thrombospondin-related anonymous protein,
5



TRAP [Plasmodium falciparum 3D7]



>gi|160691|gb|AAA29767.1|


XP_001614147.1
sporozoite surface protein 2
6



[Plasmodium vivax SaI-1]



>gi|148803021|gb|EDL44420.1|


XP_002259987.1
sporozoite surface protein 2 [Plasmodium
7



knowlesi strain H]



>gi|193810060|emb|CAQ41254.1|


PCHAS_135440
hypothetical protein [Plasmodium chabaudi
8


(plasmodb))
chabaudi]



>gi|56520404|emb|CAH78071.1|


CAA73140.1
thrombospondin related adhesive protein
9



[Plasmodium cynomolgi]


EAA22580.1
sporozoite surface protein 2 precursor
10



[Plasmodium yoelii yoelii 17XNL]



>gi|45645179|sp|Q01443.2|


CAH99602.1
sporozoite surface protein 2 [Plasmodium
11



berghei strain ANKA]



>gi|56497475|emb|CAH99602.1|


AAC47461.1
thrombospondin-related anonymous protein
12



[Plasmodium gallinaceum]


AAF00021.2
thrombospondin-related anonymous protein
13



TRAP [Plasmodium relictum]









In FIGS. 5A-D, the fragments of falciparum and vivax TRAP that were used in the crystallization assays described herein are underlined. The triangle indicates the nonconserved cysteine (C55) in falciparum. Asterisks above sequences indicate potential N-linked glycosylation sites. The O marks a Thr glycosylation which is present in the Vivax structure and is expected to be present in all TRAP structures.
FIGS. 6A and 6B show the N-terminal sequences of vivax (6A, SEQ ID NO:16) and falciparum (6B, SEQ ID NO:17) TRAP, with the elastic b-ribbon underlined, and the VWA region (which is included within the elastic b-ribbon) double underlined.
FIG. 7 is a set of four ribbon diagrams of two molecules of P. falciparum TRAP in the open (left column) and closed (right column) configurations, with the wild type (top row) and conformation-stabilizing disulfide mutations (bottom row).
FIG. 8 is an image showing the results of PAGE analysis of the indicated TRAP disulfide mutants.



DETAILED DESCRIPTION
The goal of anti-sporozoite, or pre-erythrocytic vaccines is the development of sterilizing immunity that kills sporozoites (e.g., in mammals, either before infection of the liver, or during development in liver cells), before merozoites are released and begin the erythrocytic stage of the plasmodium life cycle (Vekemans and Ballou, 2008). The numbers of sporozoites released by a mosquito bite and the numbers of infected liver cells are very small. Perhaps for this reason, this phase of infection is asymptomatic, sterilizing immunity is never seen to develop in natural infections, and immune responses to pre-erythrocytic antigens are usually weak, if detectable at all. However, the pre-erythrocytic stage is extremely attractive as a vaccine candidate, because usually only one gene is present for each protein (albeit with variation between strains). In contrast, the erythrocytic stage often has cassettes with 50 or more variant proteins for each important antigenic target, so once immunity develops to one, parasites with expression of a different gene in the cassette can be selected.
Animal studies have emphasized the importance of T cells in pre-erythrocytic immunity. Lysis of infected liver cells before merozoites can mature and be released appears to be the key step; however, antibodies also contribute to pre-erythrocytic immunity (Overstreet et al., 2008; Schofield et al., 1987).
Thrombospondin-related Anonymous Protein (TRAP)
TRAP (also known as sporozoite surface protein 2 or SSP2) is one of the major surface components of sporozoites, the form of malaria parasite that mosquitoes transfer to humans. Intracellular TRAP localizes to the micronemes, a set of organelles that secrete their contents to the apical surface of the parasite during cell invasion. TRAP is also found in a patchy distribution on the plasma membrane of sporozoites, where it is translocated to the posterior surface of the parasite during host cell penetration (Kappe et al.). TRAP is responsible for binding to the extracellular environment, and by also connecting to the parasite cytoskeleton, mediates parasite gliding motility and host cell invasion (Sultan et al., 1997). TRAP is required for movement of parasites through host tissues, through cells, and in forming the moving junction required for the formation of the parasitophorous vacuole as the malaria parasite invades the liver cell it infects. TRAP is a transmembrane protein with two extracellular folded domains, a von Willebrand factor A (VWA) or integrin I domain and a TSR domain (FIG. 1). Conformational changes in VWA domains, including in integrin alphaI and betaI domains, and in complement components, regulate their affinity for ligand (Luo et al., 2007; Springer, 2006).
TRAP also has a predicted metal ion dependent adhesion site (MIDAS), which as shown herein indeed binds a metal in the structure. Mutation of MIDAS residues greatly decreases infection, showing the importance of the MIDAS. In integrin I domains, ligand binding occurs to a metal held in the MIDAS. The cytoplasmic tail domain (CTD) of TRAP connects to the actin cytoskeleton through aldolase, permitting functional cooperation between the extracellular adhesive domains and the intracellular actin/myosin motor during gliding and invasion (Buscaglia et al., 2003; Jewett and Sibley, 2003; Kappe et al., 1999).
As described herein, the structure of TRAP has been determined in two different conformational states, termed closed and open. The open conformation binds a metal at its MIDAS. It is likely that the closed conformation binds a metal ion also, although in the particular crystal lattices studied here no metal is bound. It is likely that the open conformation would bind to host receptors that enable sporozoite migration and invasion. However, the open conformation might exist only transiently on the sporozoite surface, and the closed conformation is likely to predominate in the absence of binding to a host ligand. Thus, described herein are antigens that allow the production of antibodies to either conformation, and the antigens can be used singly or in combination to evoke neutralizing, protective antibodies.
Immunity to parasite proteins in general, and also to TRAP, is important both at the antibody and cellular level. Antibodies can neutralize sporozoites before they reach their target cells in the liver. After infection of liver cells, T lymphocytes can kill liver cells before they burst and release many thousands of parasites that start the next step of infection of red blood cells, for which TRAP is irrelevant. The designed protein and DNA/RNA TRAP vaccines disclosed here can be useful in both types of immunity. Conformation is less important for cellular (T cell) immunity, but knowing the portion of the protein that constitutes the folding unit is important, because expression of this unit in vivo greatly boosts net synthesis by stabilizing the protein and preventing degradation, including degradation by the quality control apparatus in the endoplasmic reticulum. Thus by increasing the amount of protein that is made in vivo, much TRAP protein is available for association with major histocompatibility type I and II molecules for stimulation of cellular immunity.
Disclosed herein are malaria vaccines to thrombospondin-related anonymous protein (TRAP), and methods for making and using them. The species of Plasmodium may be the most clinically relevant species, i.e., falciparum or vivax (for which specific examples are given herein), or other species such as malariae or ovale, for which sequence alignments may be used to guide construct design (see, e.g., FIG. 2B and FIG. 5). As polymorphisms exist among different vivax and falciparum strains, variants with these polymorphisms can also be made; see, e.g., Robson et al., Am J Trop Med Hyg 58, 81-89 (1998); Robson et al., Proc Biol Sci 242, 205-216 (1990).
TRAP Vaccines
Described herein are genetically engineered TRAP antigens that are useful in eliciting an immune response in an immunized animal. The TRAP proteins described herein may be optimized in a number of ways, including by mutation and truncation, to enhance expression, conformational homogeneity, and/or antigenicity. As shown herein, immunization with TRAP proteins lacking N-linked glycans and encoding the VWA, elastic ribbon, and TSR domains, or the entire extracellular domain, elicits high-titer antibodies in mice and rabbits. Titers extend at least to dilutions of 125,000 in rabbits and 25,000 in mice. This contrasts with previous studies using TRAP peptides that had shown poor titers and did not provide protection against infection (Gantt et al. Infect Immun 68, 3667-3673 (2000)).
Optimized TRAP Protein Antigens
The TRAP protein antigens described herein can include optimized versions of the TRAP proteins from any of the known Plasmodium species, e.g., vivax; falciparum; chabaudi; cynomolgi; knowlesi; berghei; yoelii; gallinaceum; reichenowi; and relictum. For use in humans, the antigens can be based on P. vivax, P. falciparum, or P. knowlesi. P. knowlesi-based antigens are useful in immunizing monkeys. A vaccine composition can include more than one, e.g., a combination of antigens based on P. vivax and P. falciparum. Since polymorphic forms of these proteins exist, a vaccine composition can also include combinations of antigens based on more than one polymorphic form of P. vivax or P. falciparum. Reference sequences for falciparum TRAP proteins include GenBank Acc. No. XP_001350088.1 (falciparum 3D7); other sequences can also be used, including GenBank Acc. Nos. XP_001350088.1; AAA29775.1; AAA29771.1; AAQ11895.1; AAQ11894.1; AAQ11892.1; AAA29774.1; AAG12328.1; BAA31173.1; AAA29776.1; BAA31174.1; BAA31188.1; AAA29770.1; AAA29777.1; BAA31181.1; BAA31193.1; BAA31171.1; BAA31187.1; BAA31189.1; BAA31186.1; BAA31170.1; BAA31190.1; BAA31172.1; BAA31191.1; BAA31192.1; AAQ11891.1; BAA31167.1; BAA31177.1; AAA29772.1; BAA31169.1; BAA31180.1; CAA63617.1; P16893.1; BAA31178.1; 1411304A; 1708291A; BAA31182.1; BAA31183.1; AAA29778.1; AAW78134.1; BAA31168.1; AAW78143.1; BAA31194.1; BAA31176.1; BAA31175.1; AAW78169.1; AAA29773.1; AAW78167.1; AAW78171.1; AAC18657.1; AAW78131.1; AAW78160.1; AAW78142.1; AAW78139.1; AAW78172.1; AAW78164.1; AAW78159.1; AAW78155.1; AAW78132.1; AAW78133.1; AAW78130.1; AAW78148.1; AAW78168.1; AAW78144.1; AAW78170.1; AAW78149.1; AAW78165.1; AAW78146.1; AAW78147.1; AAW78151.1; AAW78137.1; AAW78152.1; AAW78138.1; AAW78140.1; AAW78175.1; AAW78135.1; AAW78153.1; AAW78162.1; AAW78141.1; AAW78166.1; AAW78161.1; AAW78163.1; AAW78158.1; AAW78136.1; AAW78157.1; BAA31195.1; AAW78176.1; AAW78150.1; AAW72737.1; CAE46494.1; CAE46496.1; CAE46497.1; CAE46493.1; CAE46626.1; CAE46492.1; CAE46498.1; and CAE46495.1, as well as sequences having at least 80% identity to any of these sequences, e.g., at least 85%, 90%, or 95% identity. See, e.g., Robson et al., Am J Trop Med Hyg 58, 81-89 (1998); Robson et al., Proc Biol Sci 242, 205-216 (1990).
Reference sequences for vivax TRAP proteins include GenBank Acc. No. XP_001614147.1 (vivax SaI-1); other sequences can also be used, including GenBank Acc. Nos. AAC97485.1; AAC97484.1; AAK57632.1; AAK57600.1; AAK57621.1; AAK57620.1; AAK57634.1; AAK57628.1; AAK57630.1; AAK57623.1; AAK57637.1; AAK57639.1; AAK57629.1; AAK57636.1; AAK57631.1; AAK57624.1; AAK57612.1; AAK57608.1; AAK57619.1; AAK57595.1; AAK57610.1; AAK57601.1; AAK57599.1; AAK57611.1; AAK57607.1; AAK57598.1; AAK57618.1; AAK57617.1; AAK57597.1; AAK57592.1; AAK57603.1; AAK57638.1; AAK57585.1; AAK57590.1; AEC32940.1; AEC32935.1; AEC32934.1; AAC47463.1; AAK57593.1; AAK57580.1; AAK57578.1; AAK57588.1; AAK57570.1; AAK57567.1; AAK57573.1; and AAK57591.1; as well as sequences having at least 80% identity to any of these sequences, e.g., at least 85%, 90%, or 95%. see, e.g., Robson et al., Am J Trop Med Hyg 58, 81-89 (1998); Robson et al., Proc Biol Sci 242, 205-216 (1990).
Reference sequences for knowlesi TRAP proteins include GenBank Acc. No. XP_002259987.1 (knowlesi strain H); other sequences can also be used, including GenBank Acc. Nos. XP_002261881.1; XP_002261881.1; CAQ41254.1; CAQ39045.1; AAG24613.1 and AAC47462.1; as well as sequences having at least 80% identity to any of these sequences, e.g., at least 85%, 90%, or 95% identity to any of these sequences.
Reference sequences for chabaudi TRAP proteins include PlasmoDB Acc. No. PCHAS_135440 (Plasmodium chabaudi chabaudi); other sequences can also be used, including GenBank Acc. Nos. XP_741796.1, XP_744771.1 and sequences having at least 80% identity to any of these sequences, e.g., at least 85%, 90%, or 95% identity.
Reference sequences for cynomolgi TRAP proteins include GenBank Acc. No. CAA73140.1 (Plasmodium cynomolgi); other sequences can also be used, including sequences having at least 80% identity to that sequence, e.g., at least 85%, 90%, or 95% identity.
Reference sequences for yoelii TRAP proteins include GenBank Acc. No. EAA22580.1 (Plasmodium yoelii yoelii str. 17XNL); other sequences can also be used, including AAA29768.1, XP_731015.1 and sequences having at least 80% identity to any of these sequences, e.g., at least 85%, 90%, or 95% identity.
Reference sequences for berghei TRAP proteins include GenBank Acc. No. CAH99602.1 (Plasmodium berghei str ANKA); other sequences can also be used, including AAB63302.1, XP_731015.1 and sequences having at least 80% identity to these sequences, e.g., at least 85%, 90%, or 95% identity.
Reference sequences for gallinaceum TRAP proteins include GenBank Acc. No. AAC47461.1 (Plasmodium gallinaceum); other sequences can also be used, including AAB63302.1, XP_731015.1 and sequences having at least 80% identity to these sequences, e.g., at least 85%, 90%, or 95% identity.
Reference sequences for relictum TRAP proteins include GenBank Acc. No. AAF00021.2 (Plasmodium relictum); other sequences can also be used, including AAF00021.2; ACJ24571.1; ACJ24583.1; ACJ24580.1; ACJ24578.1; ACJ24581.1; ACJ24577.1; ACJ61773.1; ACJ61772.1; ACJ24586.1; ACJ24584.1; ACJ61774.1; ACJ24582.1; AAR24260.1; ACJ24579.1; ACJ24574.1; ACJ24572.1; ACJ24576.1; ACJ24591.1; ACJ24588.1; ACJ61769.1; ACJ61770.1; ACJ61771.1; ACJ24570.1; ACJ61767.1; ACJ24575.1; ACJ24569.1; ACJ24573.1; ACJ61768.1; 1 and sequences having at least 80% identity to any of these sequences, e.g., at least 85%, 90%, or 95% identity.
Additional sequences can be identified bioinformatically, e.g., by searching databases such as GenBank, EMBL (e.g., the pathogen genome database), P. falciparum Genome Project Consortium; and PlasmoDB (Aurrecoechea et al. Nucleic Acids Res. 37(Database issue):D539-43 (2009); available on the internet at PlasmoDB.org).
To identify corresponding regions to a protein described herein, or to determine the percent identity of two amino acid sequences, or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In preferred embodiments, the length of a reference sequence aligned for comparison purposes is at least 80% of the length of the reference sequence, and in some embodiments is at least 90% or 100%. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. For example, the percent identity between two amino acid sequences can determined using the Needleman and Wunsch ((1970) J. Mol. Biol. 48:444-453) algorithm which has been incorporated into the GAP program in the GCG software package (available on the world wide web at gcg.com), using the default parameters, e.g., a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5. An exemplary alignment of a number of Plasmodim TRAP sequences is shown in FIG. 5. This alignment was created using the Cobalt Constraint-based Multiple Protein Alignment Tool (Papadopoulos J S and Agarwala R (2007) COBALT: constraint-based alignment tool for multiple protein sequences, Bioinformatics 23:1073-79) with the following parameters:












Exemplary Alignment Parameters










Gap penalties
−11, −1



End-Gap penalties
−5, −1







CDD Parameters










Use RPS BLAST
on



Blast E-value
0.01



Find Conserved columns and
on



Recompute







Query Clustering Parameters










Use query clusters
on



Word Size
4



Max cluster distance
0.8



Alphabet
Regular










The antigens useful in the present application can include one or more alterations, including C55G (when using falciparum TRAP); removal of N-linked glycosylation sites; introduction of one or more disulfide bridges; truncation of the molecule to favor an open or closed conformation; and addition of a GPI anchor sequence to improve expression in mammalian, e.g., human, cells.
The P. falciparum TRAP VWA domain contains a unique cysteine residue (Cys-55) at the MIDAS region, which differs from that of all other plasmodium homologs that contain a conserved glycine residue at that position (see FIG. 2B). With the Cys-55 present, the falciparum TRAP expressed well yet easily aggregated, however, when mutated to the conserved glycine no aggregation was observed. Thus mutation of the Cys-55, e.g., to C55G, is therefore advantageous for producing falciparum TRAP antigen for vaccination. Other mutations can also be used, preferably conservative substitutions such as C55A and C55S. (All sequence numbering here refers to the proTRAP sequence, before cleavage of its N-terminal signal sequence).
Alternatively or in addition, it may be desirable to stabilize the TRAP protein in the closed or open state, since protective antibodies may preferentially recognize one of these 2 states. Stabilization may be obtained by one of two methods. The first method is to express a VWA domain sequence the length of which is chosen to favor the open or closed conformation. The crystal structures show that the length for the closed conformation extends from approximately residue Glu-41 to residue Lys-240 (in falciparum sequence) and the length for the open conformation extends from approximately residue Asn-40 to residue Val-230 (in vivax sequence). Thus fragments (deletion mutants) stabilized in the open or closed conformation include deletion of N-terminal and/or C-terminal residues in a falciparum sequence to create a TRAP fragment that is stabilized in the closed conformation comprising V47-V238; and/or deletion of N-terminal and/or C-terminal residues in a falciparum sequence to create a TRAP fragment that is stabilized in the open conformation comprising V47-M231; deletion of N-terminal and/or C-terminal residues in a vivax sequence to create a TRAP fragment that is stabilized in the closed conformation comprising amino acids V43-V234; and/or deletion of N-terminal and/or C-terminal residues in a vivax sequence to create a TRAP fragment that is stabilized in the open conformation comprising amino acids V43-I227. These deletion mutants can include additional amino acids on one or both ends, e.g., one, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or thirty additional amino acids; for example, the deletion mutants can include all of the beta-ribbon as shown in FIGS. 6A-6B. Additional exemplary deletion mutants include open conformation deletion mutants that start at amino acid 38, 39, 40, 41, 42, or 43, and end at amino acid 227, 228, 229, 230, 231, 232, 233, 234, 235, or 236 in a vivax sequence (or the corresponding amino acids in the falciparum sequence), e.g., 40-230 (or the corresponding amino acids in the falciparum sequence); and closed conformation deletion mutants that start at amino acids 37, 38, 39, 40, 41, 42, or 43, and end at amino acids 234, 235, 236, 237, 238, 239, 240, 241, 242, or 243 (or the corresponding amino acids in the falciparum sequence), e.g., 37-234, 38-235 (or the corresponding amino acids in the falciparum sequence, e.g., 42-239).
The second method is to introduce a stabilizing disulfide bond into the VWA domain. To stabilize the open conformation, the disulfide is chosen to link residues that are close in the open conformation and distant in the closed conformation. Conversely, to stabilize the closed conformation, the disulfide is chosen to link residues that are distant in the open conformation and close in the closed conformation. Examples of stabilizing disulfide bonds in the open conformation are introduced by mutating to cysteine pairs of either Ser-212/Glu-218, Val-220/Ser-74 in vivax and Ala-216/Asn-222 or Lys-224/Gln-78 in falciparum. Examples of stabilizing disulfide bonds in the closed conformation are introduced by mutating to cysteine pairs of either Ser-212/Phe-226, Ile-223/Met-67, or Ile-227/Ser-74 in vivax and Asn-213/Ala-233, Ala-216/Phe-230, or Met-231/Gln-78 in falciparum. A stabilizing disulfide bond may be used with any length of protein ranging from the VWA domain to the entire TRAP protein. 
TRAP protein used for immunization may be expressed in E. coli, other bacteria, yeast, or higher organisms. However, yeast and higher organisms add N-linked carbohydrates that obscure epitopes; such carbohydrates are not added by Plasmodium. Therefore, proteins expressed in the latter organisms must be mutated to remove carbohydrate addition signals. This may be achieved by mutating the N or the S/T in the carbohydrate-encoding N-X-(S/T) sequence. In a preferred embodiment, the particular mutation is chosen based on amino acids present in other Plasmodium species at the same position in the amino acid sequence alignment. Such mutations should also be introduced in DNA prime-boost or RNA vaccines, since these are expressed in a mammalian host. As shown herein, when the carbohydrate encoding sequence is not removed, carbohydrate addition occurs in higher organisms. Carbohydrate addition is believed to obscure important epitopes on TRAP, including the MIDAS region that is thought to be important for infection of the host.
In contrast, fucosylation on a specific Thr residue in the TSR domain marked in FIG. 5 is expected to occur in Plasmodium. It occurred in mammalian cells in which TRAP was expressed as shown by the crystal structure of the vivax form. The Thr or Ser in a CXX(S/T)CXXG sequence in TSR domains is fucosylated by POFUT2 in humans (Hofsteenge, et al., J Biol Chem. 276(9):6485-98 (2001); Tan, et al., J Cell Biol 159:373-82 (2002)). The CSVTCG(K/R)G sequence in falciparum and vivax TRAP TSR is almost identical to the CSVTCGDG sequence in TSR domain 1 of thrombospondin. The fucose is modified by addition of β1-3 glucose, by a recently identified β1-3 Glc transferase (Kozma et al., J Biol Chem. 281(48):36742-51 (2006); Sato et al., Glycobiology. 16(12):1194-206 (2006)). PSI-BLAST searches strongly suggest POFUT2 (and not POFUT1, a homologue involved in Notch fucosylation) is conserved in P. falciparum. Therefore, it is believed that the Thr in the TRAP TSR domain should be fucosylated in Plasmodium, as has been found in mammalian cells. Database searches on the α1-3 Glc transferase are not revealing; at least a β1-3 Gal or β1-3 Glc transferase is present in Plasmodium. 
Of particular importance for DNA/RNA vaccines, which use full-length TRAP; i.e. TRAP containing its native transmembrane and cytoplasmic domains, DNA encoding full-length TRAP, even with the N-linked site mutations and Cys-55 mutation described above, expressed poorly in human cells. However, when the transmembrane and cytoplasmic domains were exchanged for a glycosylphosphatidylinositol (GPI) anchor attachment signal sequence, the TRAP ectodomain was highly expressed on the cell surface. This has been determined using transfection of 293T cells and immunofluorescent detection of a FLAG tag attached to the N-terminus of TRAP, which has been well characterized and generally does not to influence properties of proteins to which the tag is attached.
Thus, the TRAP antigens described herein can be fusion proteins, e.g., comprising one or more mutated TRAP antigens as described herein fused to at least one non-TRAP sequence. A “non-TRAP sequence” refers to an amino acid sequence encoding a protein (or portion thereof) that is not substantially homologous to a TRAP protein, e.g., is less than 35% identical. For example, the fusion protein can include a moiety which has a high affinity for a ligand, also known as an affinity tag. For example, the fusion protein can be a GST-TRAP antigen fusion protein in which the TRAP sequence is fused to the C-terminus of the GST sequences; a polyhistidine-, e.g., 6His-, TRAP antigen in which the TRAP sequence is fused to the N- or C-terminus of a sequence encoding a polyhistidine tag; or a FLAG-TRAP fusion protein in which the TRAP sequence is fused to one or more FLAG sequences (e.g., N-AspTyrLysAspAspAspAsp-Lys-C; SEQ ID NO:14). Such fusion proteins can facilitate the purification of recombinant TRAP antigen.
In some embodiments, the non-TRAP sequence can be a carrier or adjuvant. These can include FLAGELLIN proteins (see, e.g., Bargieri et al., Journal of Parasitology Research Volume 2011 (2011), Article ID 965369; doi:10.1155/2011/965369), a Hepatitis B virus-derived surface antigen, e.g., core antigen (see, e.g., Francis et al., Proc. Natl. Acad. Sci. USA 87:2545-2549 (1990)) or small hepatitis B virus surface protein (HBs) (see, e.g., Wunderlich et al., Infection and Immunity 68 (10): 5839 (2000); Stoute et al., N Engl J Med. 336:86-91 (1997); Bojang et al., Lancet, 358(9297) 1927-1934(2001)). In some embodiments, the non-TRAP sequence comprises one or more CpG motifs (e.g, Krieg et al., Trends Microbiol. 1998 January; 6(1):23-7; Sato et al., Science. 1996 Jul. 19; 273(5273):352-4).
Alternatively or in addition, the fusion protein can be a TRAP protein containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression and/or secretion of TRAP can be increased through use of a heterologous signal sequence that is from the same species as the host cell.
Fusion proteins can also include all or a part of a serum protein, e.g., an IgG constant region, or human serum albumin.
In some embodiments, the fusion protein further comprises a sequence that allows cleavage and thus removal of the non-TRAP sequences, e.g., a protease recognition site (proteolytic cleavage site) that would allow removal of any non-TRAP sequences, e.g., after purification. Alternatively, proteases such as DAPase, which removes dipeptides sequentially from the N-terminus of purified His-tagged proteins until it reaches an engineered or intrinsic stop point (i.e., a glutamine residue acts as a DAPase stop point), can be used.
Purified TRAP antigen proteins can be used in a number of clinical and research settings. For example, the proteins can be used in Plasmodium infectivity assays, (e.g., as known in the art), or to generate antibodies specific for TRAP antigens; such antibodies can then be administered as therapeutics, e.g., to subjects who have or are at risk of contracting malaria. In addition, a TRAP antigen can be administered to a subject who has or is at risk of contracting malaria, e.g., a subject who resides in or may visit a geographic area in which malaria is endemic, or who is in contact with an individual who has malaria or who resides in or may visit a geographic area in which malaria is endemic, e.g., health care workers, to elicit an anti-TRAP immune response, e.g., the production of anti-TRAP antibodies, that is expected to result in immunity to, or reduced risk of, malarial infection.
Nucleic Acids, Recombinant Expression Vectors, Host Cells and Genetically Engineered Cells
In one aspect, the invention provides nucleic acid molecules that encode a TRAP antigen or fusion protein as described herein.
In another aspect, the invention includes vectors, preferably expression vectors, containing a nucleic acid encoding a polypeptide described herein. As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked and can include a plasmid, cosmid or viral vector. The vector can be capable of autonomous replication or it can integrate into a host DNA. Viral vectors include, e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses.
A vector can include a TRAP antigen nucleic acid in a form suitable for expression of the nucleic acid in a host cell. Preferably the recombinant expression vector includes one or more regulatory sequences operatively linked to the nucleic acid sequence to be expressed. The term “regulatory sequence” includes promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence, as well as tissue-specific regulatory and/or inducible sequences. The design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or polypeptides, including fusion proteins or polypeptides, encoded by nucleic acids as described herein (e.g., TRAP antigens and fusion proteins, and the like).
The recombinant expression vectors of the invention can be designed for expression of TRAP antigens in prokaryotic or eukaryotic cells. For example, polypeptides of the invention can be expressed in E. coli, insect cells (e.g., using baculovirus expression vectors), yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, (1990) Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
Expression of proteins in prokaryotes is often carried out in E. coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein. Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) that fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.
One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., (1990) Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. 119-128). Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al., (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
The TRAP antigen expression vector can be, e.g., a yeast expression vector; a vector for expression in insect cells, e.g., a baculovirus expression vector; or a vector suitable for expression in a mammalian host or mammalian cells, e.g., a viral or plasmid vector.
When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40.
In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J. 8:729-733) and immunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Mammary-gland specific promoters are particularly useful for producing the TRAP antigens in the milk of a transgenic animal, e.g., a goat or cow.
In another aspect the invention provides a host cell which includes a nucleic acid molecule described herein, e.g., a TRAP antigen nucleic acid molecule within a recombinant expression vector or a TRAP antigen nucleic acid molecule containing sequences which allow it to homologously recombine into a specific site of the host cell's genome. The terms “host cell” and “recombinant host cell” are used interchangeably herein. Such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
A host cell can be any prokaryotic or eukaryotic cell. For example, a TRAP antigen can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.
Vector DNA can be introduced into host cells via conventional transformation or transfection techniques. As used herein, the terms “transformation” and “transfection” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation.
A host cell of the invention can be used to produce (i.e., express) a TRAP antigen. Accordingly, the invention further provides methods for producing a TRAP antigen using the host cells of the invention. In one embodiment, the method includes culturing the host cell of the invention (into which a recombinant expression vector encoding a TRAP antigen has been introduced) in a suitable medium such that a TRAP antigen is produced. In another embodiment, the method further includes isolating a TRAP antigen from the medium or the host cell using methods known in the art.
The invention also provides non-human transgenic animals. Such animals are useful, e.g., for studying the function and/or activity of a TRAP antigen and for producing TRAP antigen, e.g., in the milk of the animal. As used herein, a “transgenic animal” is a non-human animal, preferably a mammal, e.g., a rodent (such as a rat or mouse) or a ruminant such as a cow, goat or sheep, in which one or more of the cells of the animal includes a transgene expressing a TRAP antigen as described herein, which preferably is integrated into or occurs in the genome of the cells of a transgenic animal. A TRAP antigen transgene directs the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. Thus, a transgenic animal can be one in which a TRAP antigen transgene DNA molecule has been introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.
Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. A tissue-specific regulatory sequence(s) can be operably linked to a TRAP antigen transgene to direct expression of the TRAP antigen to particular cells. A transgenic founder animal can be identified based upon the presence of a TRAP antigen transgene in its genome and/or expression of TRAP antigen mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene encoding a TRAP antigen can further be bred to other transgenic animals carrying other transgenes.
In some embodiments the TRAP antigen transgene is under the control of a tissue specific promoter, e.g., a milk or egg specific promoter, and recovered from the milk or eggs produced by the animal. Suitable animals are mice, chickens, pigs, cows, goats, and sheep.
The invention also includes a population of cells from a transgenic animal expressing a TRAP antigen transgene.
The TRAP antigen-encoding nucleic acid can be a nucleic acid vaccine, e.g., as described in Hoffman et al., “Using DNA based vaccine technology and the Malaria Genome Project to overcome obstacles to Malaria vaccine development.” In: Sherman, editor. Malaria: parasite biology, pathogenesis and protection. Washington, D.C.: ASM Press; 1998. pp. 73-91; Krieg et al., Trends Microbiol. 1998 January; 6(1):23-7;
Methods of Eliciting an Immune Response
Also provided herein are methods of eliciting an immune response, i.e., the production of anti-TRAP antibodies, in a subject, e.g., a subject who has or is at risk of contracting malaria, e.g., a subject who resides in or may visit a geographic area in which malaria is endemic, or who is in contact with an individual who has malaria or who resides in or may visit a geographic area in which malaria is endemic, e.g., health care workers. Although human subjects can be treated by the methods described herein, other subjects can also include veterinary or livestock subjects who are susceptible to malaria, e.g., primates.
The methods of eliciting an immune response (also referred to herein as immunization) include administering a TRAP antigen protein or TRAP antigen-encoding nucleic acid as described herein.
Methods of immunizing with proteins and nucleic acids are well known in the field. For example, methods for prime and boost vaccines against TRAP have been disclosed in which TRAP is encoded as a DNA sequence in vectors such as adenovirus for the prime and a different vector such as a poxvirus for the boost (Hill et al. Hum Vaccin 6:78-83 (2010)). As described herein, immunization with TRAP proteins lacking N-linked glycans and encoding either the VWA, elastic ribbon, and/or TSR domains, or the entire extracellular domain, elicits high—titer antibodies in mice and rabbits.
The methods can include administering one or more doses of the TRAP antigen or TRAP antigen-encoding nucleic acid, e.g., a prime dose and one or more booster doses. The methods can further include administration of an adjuvant, e.g., a compound that enhances the longevity, potency, and/or quality of the specific immune response to TRAP antigen, and preferably has no or minimal toxicity or long-lasting immune effects on its own. Adjuvants can include, for example, mineral salt adjuvants (e.g., alum-based); tensoactive adjuvants (e.g., saponins); polymeric microspheres (e.g., poly (DL-lactide-coglycolide) microspheres); bacteria-derived adjuvants (e.g., N-acetyl muramyl-L-alanyl-D-isoglutamine (MDP)); liposome adjuvants; adjuvant emulsions (e.g., oil in water or water in oil emulsions such as FIA, Montanide, Adjuvant 65, and Lipovant); cytokines (e.g., IFN-gamma or GM-CSF); and carbohydrate adjuvants (e.g., inulin), among others. The choice of adjuvant can be determined by the nature of the antigen (e.g., protein or nucleic acid) and the route of administration (e.g., parenteral or mucosal). See, e.g., Petrovsky and Aguilar, Immunology and Cell Biology (2004) 82, 488-496; Kenney and Edelman, Expert Rev Vaccines. 2003 April; 2(2):167-88; Coler et al., Parasite Immunol. 2009 September; 31(9):520-8; and Reed et al., Trends Immunol. 2009 January; 30(1):23-32. In some embodiments, the adjuvants include an oil in water emulsion, monophosphoryl lipid A and the saponin derivative QS21 (Stoute et al., J Infect Dis. 178 (4):1139-1144 (1998)).
In some embodiments, the methods described herein elicit sterilizing immunity in a mammal that kills sporozoites either before infection of the liver, or during development in liver cells, before merozoites are released and begin the erythrocytic stage of the Plasmodium life cycle.
In some embodiments, the methods described herein elicit antibody titers of over 1,000, e.g., over 10,000, or over 100,000, in an immunized subject.
Pharmaceutical Compositions and Methods of Administration
The TRAP antigens and TRAP antigen-encoding nucleic acids described herein can be incorporated into pharmaceutical compositions. Such compositions typically include the antigen or nucleic acid (i.e., as an active agent) and a pharmaceutically acceptable carrier. As used herein, “pharmaceutically acceptable carriers” includes saline, solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. In some embodiments, the pharmaceutical compositions include an adjuvant as known in the art and/or described herein.
Pharmaceutical compositions are typically formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfate; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
For administration by inhalation, the compounds are typically delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer. Such methods include those described in U.S. Pat. No. 6,468,798.
Pharmaceutical compositions comprising TRAP antigen-encoding nucleic acids can be administered by any method suitable for administration of nucleic acid agents, such as DNA vaccines. These methods include gene guns, bio injectors, and skin patches as well as needle-free methods such as the micro-particle DNA vaccine technology disclosed in U.S. Pat. No. 6,194,389, and the mammalian transdermal needle-free vaccination with powder-form vaccine as disclosed in U.S. Pat. No. 6,168,587. Additionally, intranasal delivery is possible, as described in, inter alia, Hamajima et al., Clin. Immunol. Immunopathol., 88(2), 205-10 (1998). Liposomes (e.g., as described in U.S. Pat. No. 6,472,375) and microencapsulation can also be used. Biodegradable targetable microparticle delivery systems can also be used (e.g., as described in U.S. Pat. No. 6,471,996).
In one embodiment, the pharmaceutical compositions include carriers that will protect the therapeutic compounds against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Such formulations can be prepared using standard techniques, or obtained commercially, e.g., from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to selected cells with monoclonal antibodies to cellular antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.
Dosage, toxicity and therapeutic efficacy of the TRAP antigens can be determined by standard vaccine testing procedures in experimental animals or clinical trials, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The methods generally include administering at least one dose of the TRAP antigen to a subject (e.g., test animal or human clinical trial subject), optionally followed after a period of time by one or more boost doses, and then protection from challenge by an appropriate Plasmodium organism is measured. The organism challenge can be performed by injecting sporozoites collected from the salivary gland of mosquitoes, or by letting infected mosquitoes bite animals. This (biting) is also done routinely with humans in clinical trials; a well-defined strain of falciparum such as 3D7 is typically used, which gives a chloroquine-treatable infection in case protection is not achieved.
The data obtained from the animal studies can be used in formulating a range of dosage for use in humans, which is then confirmed in clinical trials, e.g., as described above. The dosage will lie preferably within a range of concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed (e.g., TRAP antigen protein or nucleic acid) and the route of administration utilized. A dose may be formulated in animal models to achieve a desired level of protection without significant toxicity. Such information can be used to determine useful starting doses in humans for clinical trials.
A therapeutically effective amount of a TRAP antigen (i.e., an effective dosage) as described herein depends on the form selected, e.g., whether TRAP antigen protein or TRAP-antigen-encoding nucleic acid (e.g., a DNA vaccine) is used. The skilled artisan will appreciate that certain factors may influence the dosage and timing required to effectively elicit an immune response in a subject, including but not limited to previous treatments and the general health and/or age of the subject. Moreover, treatment of a subject with a therapeutically effective amount of the TRAP antigens described herein can include a single dose or a series of treatments (i.e., a priming dose and one or more boosts).
The TRAP antigens can be included in a kit, container, pack, or dispenser, optionally with instructions for administration, for use in a method described herein.
EXAMPLES
The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
Example 1
Structural Features of TRAP Domains
Both the TSR and VWA domains are responsible for TRAP's adhesion to liver cells, but the exact mechanism is not clear. Both adhesive domains show affinity for heparin, and the TSR domain binds to heparin sulfate proteoglycans on the hepatocyte surface. However, the VWA domain has at least one other unidentified hepatocyte ligand (Akhouri et al., 2004; McCormick et al., 1999; Muller et al., 1993). Interestingly, surface plasmon resonance analysis of TRAP-heparin binding suggests a two-state reaction with conformational change (Akhouri et al., 2004). Although there is a solution NMR structure for the TSR domain, this does not show how it might fold in tandem with the VWA domain on the parasite surface (Tossavainen et al., 2006). Recently, a crystal structure was solved for the VWA domain of Toxoplasma gondii Micronemal protein 2 (MIC2), a member of the TRAP protein family (Tonkin et al., 2010). However, the VWA domain used for that structure had substantial truncation at the C-terminus, including two predicted alpha-helices and one predicted beta-strand. Several subfamilies of VWA domains undergo conformational change that regulates affinity for ligand (Springer, 2006).
In the sequence of TRAP, one cysteine each is present in two short segments between the signal sequence and the VWA domain, and between the VWA and TSR domains (FIG. 2A). It was hypothesized that these cysteines are linked in a disulfide bond (shaded in light gray in FIG. 2A), and that the insertion of the VWA domain between these short, disulfide-linked segments creates a similar linkage as in integrins and selectins, enabling similar pivoting and mechanochemical activation of ligand binding by the sporozoite's cytoskeleton. Mechanochemical transmission of information between the ligand binding site and the cytoplasmic domain could thus guide gliding motility. The structure of the two adhesive domains in TRAP should also reveal the basis for ligand recognition by the VWA domain.
The cysteines that are hypothesized to link the segments N and C-terminal of the VWA domain are conserved in all Plasmodium species (FIG. 2B). The DXSXS motif, which binds to a Mg2+ ion in other VWA domains where the Mg2+ coordinates an acidic residue in the ligand, is also conserved (FIGS. 2A-2B). A cysteine in the DXSXS motif in P. falciparum is not conserved in other Plasmodium species and thus was not expected to be disulfide-bonded (FIG. 2B).
Based on the above considerations, a DNA segment encoding the murine Ig chain signal peptide, falciparum TRAP adhesive domains (26-299 with unconserved Cys in the MIDAS mutated to Ala and N-link site mutated to Ser) and a HHHHHHA sequence was cloned into the EcoR I and NotI sites of plasmid pLEXm (Aricescu et al., Acta Crystallogr D Biol Crystallogr 62, 1243-1250 (2006)); this construct was termed “TRAP6”, and includes the sequence of TRAP from the predicted N-terminal residue after signal-peptide cleavage to after the TSR domain. Site-directed mutagenesis was used to mutate the unconserved cysteine in the DXSXS motif to glycine and remove the potential N-linked glycosylation site. The nucleic acid sequence was as follows:








TRAP-6



(SEQ ID NO: 16)



ATGGATATGAGAGTTCCTGCTCAATTGCTGGGGTTGCTCTTGCTCTGGTTCAGTGGGGTGTTGGGG



 


AGGGATGTGCAGAATAACATTGTGGACGAGATCAAGTACCGCGAGGAGGTATGCAATGACGAGGTGGATTTGTATCTCTTG


 


ATGGATGGCTCCGGATCGATCAGGAGGCACAACTGGGTCAATCATGCGGTCCCCCTGGCCATGAAGCTGATCCAGCAGCTG


 


AATCTCAACGACAATGCCATTCACCTCTATGCCAGCGTGTTCTCAAACAACGCGAGAGAGATCATCCGCTTGCACAGCGAC


 


GCTTCGAAGAACAAGGAAAAGGCACTCATCATTATCAAATCGTTGCTCTCAACGAATCTTCCGTACGGTAAAACGTCATTG


 


ACCGACGCACTGTTGCAAGTCCGCAAACATCTGAACGATAGAATCAACCGCGAGAATGCGAATCAGCTTGTAGTAATCCTG


 


ACGGACGGTATTCCCGATTCGATTCAAGATTCACTCAAGGAAAGCAGGAAACTTTCAGACAGAGGCGTGAAAATCGCTGTG


 


TTTGGAATTGGTCAGGGAATCAACGTGGCATTCAACAGGTTCCTGGTCGGTTGTCACCCCTCCGATGGAAAATGCAATCTC


 


TACGCGGACTCAGCGTGGGAAAACGTCAAGAACGTGATCGGACCCTTTATGAAAGCCGTCTGTGTCGAGGTAGAGAAAACC


 


GCGTCGTGTGGAGTGTGGGATGAGTGGTCACCGTGCTCCGTCACGTGCGGAAAAGGAACTAGGAGCCGCAAGAGGGAGATC


 


CTTCACGAAGGCTGCACATCGGAGTTGCAAGAGCAGTGTGAAGAAGAGAGGTGCCTCCCGAAGCGCGAACCTCTTGACG


 


TACCGGATGAACCAGCGCATCACCATCACCATCACGCG






The underlined sequence is a murine Ig chain signal peptide, and the double underlined sequence encodes the 6His tag. The protein sequence is as follows; mutated residues are bold and double underlined, and the TSR domain is underlined.








TRAP6


SEQ ID NO: 1


RDVQNNIVDEIKYREEVCNDEVDLYLLMDGSGSIRRHNWVNHAVPLA


 


MKLIQQLNLNDNAIHLYASVFSNNAREIIRLHSDASKNKEKALIIIK


 


SLLSTNLPYGKTSLTDALLQVRKHLNDRINRENANQLVVILTDGIPD


 


SIQDSLKESRKLSDRGVKIAVFGIGQGINVAFNRFLVGCHPSDGKCN


 


LYADSAWENVKNVIGPFMKAVCVEVEKTASCGVWDEWSPCSVTCGKG


 


TRSRKREILHEGCTSELQEQCEEERCLPKREPLDVPDEP






The sequence also included a 6His tag (AHHHHHHA; SEQ ID NO:3) at the N terminus HEK293S GnTI− cells (Reeves et al., Proceedings of the National Academy of Sciences of the United States of America 99, 13419-13424 (2002))) were transiently transfected by using polyethylenimine. Culture supernatants (1 L) were harvested after 5 days. Purification was performed with Ni-NTA affinity followed by Superdex 5200 column equilibrated with 20 mM HEPES 7.2 and 300 mM NaCl. The purified protein was concentrated to about 5 mg/ml and stored at −80° C. Crystallization screening was done with a Mosquito robot using commercially available sparse matrix screens. Diffraction-quality crystals were produced at 4° C. in a mother liquor solution containing 0.1 M Tris 8.5, 0.2 M Li2SO4, 25% PEG4000. Single crystals were frozen in liquid nitrogen prior to X-ray diffraction testing and data collection. Diffraction data were collected at 100 K at beamline 23-ID, Advanced Photon Source, Argonne National Laboratory. Early molecular replacement attempts using different VWA domains or TSR domains as models failed. The solution was obtained using molecular replacement with a modified VWA domain of human capillary morphogenesis protein 2 (pdb ID 1shu) as model. The crystal characteristics are shown in Table 1.








TABLE 1





TRAP crystal X-Ray diffraction data and refinement -


I4 spacegroup pfTRAP (26-299)


















Space group
I4



Cell dimensions



a, b, c (Å)
110.2, 110.2, 47.0



α, β, γ (°)
90.00, 90.00, 90.00



Resolution (Å)
43.27-2.20 (2.26-2.20) 



Rsym
 16.5% (112.3%)



//s/
11.26 (1.69) 



Completeness (%)
98.1% (97.5%)



Redundancy
2.89 (2.80)



No. reflections
14268



Rwork/Rfree
17.6%/22.3%



No. atoms



Protein
1584



Water
117



B-factors



Protein
50.37



Water
51.01



R.m.s deviations



Bond lengths (Å)
0.008



Bond angles (°)
1.10










TRAP VWA fold superficially resembles the typical VWA fold with 6β-strands surrounded by 6 α-helices (see FIG. 3), but differs from other VWA or integrin I domain structures in its unusual MIDAS. A long range disulfide links the sequence N-terminal to the VWA to the final C-terminal VWA domain α6-helix, and the α6-helix is longer than usual. The other disulfide bond residues, C205 and C212, are conserved within plasmodium species. However, they are absent in other VWA domains.
In addition, a construct comprising the P. vivax TRAP adhesive domains (25-283) was expressed and purified using similar procedures. That construct had the following sequence:







P. vivax TRAP


SEQ ID NO: 15


DEKVVDEVKYSEEVCNEQVDLYLLVDGSGSIGYPNWITKVIPMLNGLINS


 


LSLSRDTINLYMNLFGSYTTELIRLGSGQSIDKRQALSKVTELRKTYTPY


 


GTTSMTAALDEVQKHLNDRVNREKAIQLVILMTDGVPNSKYRALEVANKL


 


KQRNVRLAVIGIGQGINHQFNRLIAGCRPREPNCKFYSYADWNEAVALIK


 


PFIAKVCTEVERVANCGPWDPWTACSVTCGRGTHSRSRPSLHEKCTTHMV


 


SECEEGECP






The protein was crystallized with 15% PEG20000 and 0.1 M Tris 8.5. Crystals were harvested in their mother liquor supplemented with 20% glycerol as cryoprotectant, then flash frozen in liquid nitrogen. The data was collected and the structure was solved using the VWA domain of human capillary morphogenesis protein 2 as search model.

A model is shown in FIGS. 4A-B. Interestingly, the two short segments from the two ends of VWA domain form anti-parallel 13 strands, termed “Elastic β-ribbon” here. Partial residues in this Elastic ribbon were derived from the C-terminal α-helix in the falciparum VWA structure. The structure of the P. Vivax VWA domain showed that it was in an open conformation even in the absence of a metal ion or pseudo-ligand. Both Mg and Mn could be soaked into the crystal and bound to the MIDAS with no conformational change of the VWA domain. The structure of the TSR domain shows it belongs to the group 2 according the disulfide bond pattern. A disaccharide, Glcβ1,3 Fuc was O-linked to the Thr in the CSVTCG sequence motif on the TSR domain.
A comparison of the structures of the falciparum and vivax A domains was revealing. Comparison between the two TRAP structures, and to integrin I domains, showed that the falciparum protein crystallized in the closed conformation of the VWA or I domain, whereas the vivax protein crystallized in the open conformation. C-terminal, axial displacement of the α6-helix in the open compared to the closed conformation was coupled to reshaping of the b6-a7 loop, and movement of a Trp in this loop, similar to a Phe residue in integrins. N-C terminal disulfide bonds and position of terminal residues (K240 in falciparum and 8236 in vivax) were also shifted relative to each other.
The influence of lattice contact on the falciparum VWA structure was evaluated. In the the 14 space group pfTRAP, the unusual MIDAS is adjacent to the lattice contact area, and probably perturbed by lattice contact; this is not seen in the P4212 spacegroup pfTRAP. The MIDAS residues are conserved within species, and mutation of two of them has been found to inhibit TRAP function Matuschewski et al., EMBO J. 21, 1597-1606 (2002)). The specific binding of A domain to HepG2 cells is divalent cation dependent (Jethwaney et al., Infect Immun 73, 5883-5891 (2005)). In contrast, the β6-α6 loop and α6-helix in the closed TRAP conformation were not in lattice contacts, and thus their configuration, which is similar to that in closed integrin I domains, strongly suggests that the falciparum TRAP structure represents the closed conformation of TRAP (which should be accessible to TRAP in any Plasmodium species),
Superimposition of vivax TRAP with both open and closed conformations of integrin aM I domains showed marked similarity to the open conformation of integrin I domains, both in the b6-a6 loop and a6-helix, and in the loops surrounding the MIDAS. Furthermore, the TRAP MIDAS adopts the open conformation, with the Mg ion in direct coordination with the Thr and not the Asp of the MIDAS. Taken together these results indicate that the falciparum and vivax structures represent two different conformations: closed and open, respectively.
Example 2
Generation of Anti-Trap Antibodies
Immunization of mice with irradiated sporozoites results in production of antibodies and cytotoxic T-cells against TRAP Immunization with small fragments of TRAP alone provides no or at best partial protection (Gantt et al., Infect. Immun 68(6):3667-3673 (2000)), but complete protection has been documented in mice immunized with a mixture of transfectants expressing CSP and TRAP (Khusmith et al., 2001).
To determine whether immunization of animals with the TRAP peptides described would produce an immune response, falciparum TRAP6 (26-299, including the A domain and TSR and 12 residues extended at the C-terminus) and TRAPF (26-511, including the A domain, TSR, and repeats) were prepared for immunization. The nucleic acid and protein sequences of TRAPF, with the non-conserved cysteine in the DXSXS motif mutated to glycine and the potential N-linked glycosylation sites removed, is as follows:








TRAP-F



ATGGATATGAGAGTTCCTGCTCAATTGCTGGGGTTGCTCTTGCTCTGGTTCAGTGGGGTGTTGGGG


 


AGGGATGTGCAGAATAACATTGTGGACGAGATCAAGTACCGCGAGGAGGTATGCAATGACGAGGTGGATTTGTATCTCTTG


 


ATGGATGGCTCCGGATCGATCAGGAGGCACAACTGGGTCAATCATGCGGTCCCCCTGGCCATGAAGCTGATCCAGCAGCTG


 


AATCTCAACGACAATGCCATTCACCTCTATGCCAGCGTGTTCTCAAACAACGCGAGAGAGATCATCCGCTTGCACAGCGAC


 


GCTTCGAAGAACAAGGAAAAGGCACTCATCATTATCAAATCGTTGCTCTCAACGAATCTTCCGTACGGTAAAACGTCATTG


 


ACCGACGCACTGTTGCAAGTCCGCAAACATCTGAACGATAGAATCAACCGCGAGAATGCGAATCAGCTTGTAGTAATCCTG


 


ACGGACGGTATTCCCGATTCGATTCAAGATTCACTCAAGGAAAGCAGGAAACTTTCAGACAGAGGCGTGAAAATCGCTGTG


 


TTTGGAATTGGTCAGGGAATCAACGTGGCATTCAACAGGTTCCTGGTCGGTTGTCACCCCTCCGATGGAAAATGCAATCTC


 


TACGCGGACTCAGCGTGGGAAAACGTCAAGAACGTGATCGGACCCTTTATGAAAGCCGTCTGTGTCGAGGTAGAGAAAACC


 


GCGTCGTGTGGAGTGTGGGATGAGTGGTCACCGTGCTCCGTCACGTGCGGAAAAGGAACTAGGAGCCGCAAGAGGGAGATC


 


CTTCACGAAGGCTGCACATCGGAGTTGCAAGAGCAGTGTGAAGAAGAGAGGTGCCTCCCGAAGCGCGAACCTCTTGACGTA


 


CCGGATGAACCAGAGGACGACCAGCCAAGGCCCAGAGGAGACAACTTCGCCGTAGAAAAACCCAACGAGAACATCATTGAC


 


AACAACCCTCAAGAACCCTCGCCGAATCCCGAAGAGGGAAAGGGTGAAAATCCTAATGGTTTTGATTTGGATGAGAATCCC


 


GAGAATCCTCCGAACCCTCCCAACCCTCCGAATCCCCCGAATCCACCCAATCCACCTAATCCGGATATCCCGGAACAAGAG


 


CCGAACATTCCCGAAGATTCGGAGAAGGAAGTCCCCTCGGACGTCCCGAAGAATCCGGAGGACGATAGGGAGGAAAACTTT


 


GACATTCCCAAAAAGCCCGAGAACAAGCATGATAATCAGAACAACCTTCCAAATGACAAGTCCGATCGCTACATCCCCTAT


 


TCGCCGCTCAGCCCTAAAGTACTGGATAACGAGCGCAAACAGTCAGATCCCCAGAGCCAGGACAATAACGGCAATAGACAC


 


GTACCGAACTCGGAGGACAGAGAGACTAGGCCACACGGAAGAAACAATGAGAATAGAAACTACAATCGCAAGCATTCGAAT


 


ACACCGAAACATCCCGAAAGAGAAGAACACGAGAAACCGGACAACAACAAGAAGAAAGCGGGTAGCGATAACAAGTATAAG


 


GCGCATCACCATCACCATCACGCG






The underlined nucleic acid sequence encodes a murine Ig chain signal peptide, the dotted underlined region is the VWA domain, and the double underlined sequence encodes the 6His tag.








TRAPF (Full ectodomain)


SEQ ID NO: 2












The sequence also included a 6His tag (AHHHHHHA; SEQ ID NO: 3) at the N terminus The proteins were expressed in HEK 293S GnTI− cells, and purified by Ni-NTA affinity. The buffer was then changed to PBS, and proteins were concentrated to 1.46 mg/ml (TRAP6) and 2.2 mg/ml (TRAPF). Both rabbits and mice were used for immunization.

The rabbits were immunized by Cocalico Biological, Inc (Reamstown, Pa.) under an IACUC approved standard 90-day protocol, with 2 rabbits for each antigen given an initial inoculation and four boosts. A pre-bleed, two test bleeds, and a product bleed were taken (about 100 ml from each rabbit).
An ELISA assay was used to test the antisera. The TRAPF antigen was coated at 2 ug/ml, blocked with BSA, then incubated with the antisera. Binding was detected with HRP-anti-rabbit antibodies, developed with HRP substrate. Absorbance was read using an ELISA plate reader. The results are shown in Table 2.













TABLE 2





rabbit
Pre-
Test 1
Test 2

Test 1
Test 2


dilution
immune
(11/18)
(12/8)
Pre-immune
(11/18)
(12/8)


















IMDI3 (TRAP-
IMDI4 (TRAP-



FL ecto)
FL ecto)













1:125,000
0.000
0.363
0.634
0.000
0.220
0.605


1:25,000
0.000
1.003
1.334
0.000
0.738
1.446


1:5,000
0.015
1.619
1.689
0.006
1.528
1.768


1:1,000
0.071
1.662
1.713
0.024
1.860
1.882










IMDI5
IMDI6 (TRAP-



(TRAP-short)
short)













1:125,000
0.000
0.319
0.367
0.000
0.256
0.456


1:25,000
0.149
1.032
1.143
0.000
0.927
1.196


1:5,000
0.005
1.605
1.598
0.002
1.415
1.585


1:1,000
0.028
1.806
1.811
0.009
1.693
1.698









There were good titers in Elisa (at 1:125,000) for all 4 animals; an increase was observed in the second test bleeds. All 4 antisera worked in immunoprecipitation and Western blot experiments using cell lysate from TRAP-transfected cells.
Mice were also immunized with the same antigens to generate monoclonal antibodies. 3 CBF1 mice were immunized with each antigen (TRAP6 and TRAPF). Three IP immunizations were administered; the 1st injection was with complete Freund's adjuvant, the 2nd and 3rd with incomplete Freund's adjuvant. On day 38 tail bleeds were taken and tested by ELISA. The results are shown in Table 3.









TABLE 3









antigen











Irrelevant





protein
TRAP-F
TRAP-6 (short)









animal #

















1
2
3
4
5
6
7
8
9





















serum dilution
1:25,000
0
0
0
0.877
0.969
0.618
0.660
0.148
0.595



1:5,000
0
0
0
1.262
1.223
0.871
1.000
0.421
1.137



1:1000
0
0
0
1.471
1.550
1.289
1.206
0.960
1.440









Again, there were good titres (1:25,000).
These results demonstrate that administration of these antigens can elicit the production of TRAP-specific antibodies in mammals.
Example 3
Expression of Full-Length TRAP in Mammalian Cells
The following experiments describe methods to express full-length TRAP; i.e. TRAP containing its native transmembrane and cytoplasmic domains in mammalian cells. Full-length TRAP, even with the N-linked site mutations and Cys-55 mutation described above, cannot be expressed in human cells. Thus a construct was made wherein the transmembrane and cytoplasmic domains were exchanged for a glycosylphosphatidylinositol (GPI) anchor attachment signal sequence. The sequence of this construct was as follows:







Flag-TRAP-GPI


SEQ ID NO: 4












The construct includes a signal peptide derived from murine IgG kappa V leader sequences as in the ET vectors. The TSR domain is underlined, and the VWA domain is indicated with dotted underlining. A FLAG tag sequence (which has been well characterized not to influence properties of proteins to which the tag is attached) is in bold followed by GSG linker, and the C55G mutation and N-linked site mutations are shown double underlined. The GPI anchor attachment signal from decay accelerating factor (DAF), which replaces the TRAP transmembrane and cytoplasmic domains, is shown in italics.

The construct was transfected into human 293T cells and immunofluorescent detection was used to detect expression of the FLAG tag. This TRAP ectodomain construct was highly expressed on cell surface.
Example 4
Conformation-Stabilizing TRAP Disulfide Mutations
The following experiments were done to create TRAP disulfide mutants that are locked in either the open or closed conformation. Mutation sites were selected based on the structures of P. falciparum as shown in FIG. 7.
TRAP without its repeat region (res. 26-288) was cloned into the ET5 vector N-terminal to the human IgG1 Fc fragment. The crystal structures of TRAP provide evidence of two distinct conformations, namely open and closed. Pairs of cysteine mutants were designed in PfTRAP in order to stabilize the construct in its open and closed conformations by a covalent disulfide bond. Cysteine mutations were introduced by Quickchange mutagenesis (Agilent technologies) and include the following pairs for further testing: K224C with Q78C, M231C with Q78C, A216C with N222C, N213C with A233C, and A216C with F230C.
HEK293S GnT−/− cells in 6-well dishes were transfected with mock, wtTRAP-Fc, five single mutant controls (Q78C, N231C, N222C, A216C, N213C), five double mutants (K224C+Q78C, M231C+Q78C, A216C+N222C, N213C+A233C, and A216C+F230C), and a western positive control (GARP-Fc) using Lipofectamine 2000 following the manufacturer's protocol (Invitrogen).
After 2 days, the supernatants were collected. Expressed Fc-tagged protein was immunoprecipitated using protein G beads (GE Healthcare). The beads and supernatant were incubated at room temperature, washed in TBS-T three times and once in PBS and final beads were resuspended in 1×SDS loading buffer. Samples were incubated at 95° C. for 5 minutes before loading on a 10% SDS-PAGE gel.
Samples were then transferred to a PVDF membrane using a Bio-rad Trans-Blot semi-dry transfer cell. The membrane was blocked in 5% Dry milk-TBST for 2 hours at room temperature and probed with anti-human IgG-HRP conjugate (1:1000 dilution) for 1 hour at room temperature. Signal was detected with ECL detection reagents (GE Healthcare).
As seen in FIG. 8, the double cysteine mutants A216C+N222C and A216C+F230C express close to wild type levels and represent the open and closed TRAP conformations respectively. These were later transfected into HEK293S GnT−/− cells, expanded to thirty 15 cm plates and 450 mL of supernatants were collected after five days.
As shown in FIG. 8, some mutants expressed better than others, which had little to no expression. For example, the K224C+Q78C open conformation mutant and N213C+A233C closed conformation mutants were not detectable on the gel, but the A216C+N222C open conformation mutant and the A216C+F230C closed conformation mutant showed robust expression. Some of the single mutants had good to excellent expression levels (Q78C, A216C), while other single mutants showed little to no detectable expression (N231C, N222C, N213C).
Example 5
Vaccination with TRAP Mutants
The following experiments are done to determine the antibody titre produced after vaccination of mice with the TRAP mutants described herein, and to determine persistence of immunity in immunized mice after challenge with sporozoite infection.
All mouse experiments use Balb/cJ females (The Jackson Laboratory) at 5-6 weeks initial age; Anopheles stevensi mosquitoes are used for all insect-mediated infections. A recombinant form of Plasmodium berghei expressing GFP (Franke-Fayard et al., Mol. Biochem. Parasitol. 137 23-33 (2004)) is used for in vivo infections.
Mice are immunized with mutant TRAP constructs as follows. Groups of mice receive IP injections of the constructs described herein, in a series of three injections total, at 2-week intervals. Each injection is with 10-100 micrograms of purified protein in saline with adjuvant, 200 microliters total volume. One group receives each injection with protein in Freund's adjuvant (injection #1 complete Freund's, injections #2 and #3 in incomplete Freund's), and a duplicate group for each construct receives each injection with alum as adjuvant. Proteins may be pre-treated with endoglycosidase H (endoH).
Antisera is harvested for in vitro tests as follows. Titer is checked at one week and two weeks following third-round injections for immunization by tail nick and harvest of 50-100 microliters of blood per animal, and prior to infection for animals tested for persistence of immunity as described below. The persistence of high antibody titers to the various antigens described above is tested by sampling sera once per month. For terminal blood harvest, animals are euthanized by isoflurane anaesthesia and secondarily by thoracotomy and cardiac puncture.
To maintain a pool of infected mosquitoes for mouse infections, a group of mice are injected intraperitoneally (IP) with P. berghei-infected red blood cells from a frozen stock. Beginning 5 days post-injection, mice are assayed for infection by tail nick and blood smear. At 5-8 days post-injection, mice that have reached the expected titer of 3-7% infection of red blood cells will be used for feeding mosquitoes. For feeding, mice are anaesthetized with ketamine-xylazine and draped on a mesh covering a box of naïve mosquitoes for 15 minutes. Post-feeding, mice are euthanized. At 22 or more days post-feeding, infection in mosquitoes reaches the sporozoite stage; select mosquitoes are assayed for infectious load by examination of salivary glands. The infection cycle is maintained by using some of these infected mosquitoes to bite and infect another group of naïve mice.
Injection of immunized mice with P. berghei sporozoites/infection assays are performed as follows Immunized mice as described above are infected by intravenous injection (via tail vein) of P. berghei sporozoites as described above. 20,000 sporozoites in a volume of 200 microliters sterile saline are used for each mouse, following established parameters for sporozoite-based infection (Mauduit et al., Inf. Imm. 78 2182-2188 (2010)). Beginning 5 days post injection, animals are monitored every two days for development of infection by tail nick and blood smear; infection in controls is expected to develop between 5 and 8 days post injection. Upon detection of infection, animals are monitored by blood smear daily. Upon reaching 7% infection of red blood cells, animals are sacrificed by CO2 euthanasia; all animals will be sacrificed by 21 days post injection.
Challenge of immunized mice by mosquito-borne infection/infection assay is performed as follows. Separate cohorts of mice immunized as described above are subjected to mosquito-borne infection as described above. Mice are anaesthetized with ketamine (100 mg/kg)/xylazine (10 mg/kg) and exposed to infected mosquitoes for 15-minute feeding. For this procedure, mice are allowed to recover and are monitored by tail nick and blood smear at two-day intervals beginning on day 5 post-feeding. Controls in this series are expected to develop infection between 8 and 10 days post feeding Animals with detected infection are monitored daily by blood smear; animals reaching the threshold of 7% infected red blood cells will be euthanized. Animals in this series are euthanized by 21 days post feeding.
Persistence of immunity is tested at four weeks, three months, and one year following immunization, against infection via injected sporozoites and mosquito bite. Separate cohorts of mice in each immunization group described above have infection by either sporozoite injection or exposure to infected mosquitoes, with monitoring and euthanasia exactly as described above, beginning at 4 weeks, 3 months, and one year following their final immunization.
Example 6
Immunization of Mice with P. falciparum-based TRAP Constructs and Harvest of Antisera for In Vitro Infection Assays with Human Liver Cells
A separate set of cohorts of mice will receive immunizations with constructs paralleling the series described in Example 5, but with proteins based on the TRAP sequence of the human pathogen P. falciparum. Titers will be determined as described above, and all animals in this series will have blood harvested following the last titer determination, as described above, for in vitro analyses of infection of human liver cells, e.g., as described in Hollingdale et al., J. Immunol., 132(2):909-913 (1984); Sattabongkot et al., Am J Trop Med Hyg, 74(5):708-715 (2006); Brahimi et al., Infect Immun 2001 June; 69(6):3845-52; Meis et al., Cell Biol Int Rep. 1985 November; 9(11):976. Alternatively or in addition, immunity is analysed in an animal model, e.g., in mice with chimeric human livers. See, e.g., Sacci et al., International Journal for Parasitology 36:353-360 (2006); Vaughan et al., Clin Invest. 122(10):3618-3628 (2012).
Example 7
Screening and Production of Monoclonal Antibody Against TRAP
Separate mice were immunized with TRAPF and TRAP6 with three injections (i.p. with complete Freund's adjuvant) on day 1, day 14, and day 28. Tail bleed was done on day 38 and elisa assays were performed to determine response. Titers were significant up to and including a dilution of 1:25000, as described in Example 2 earlier.
Myeloma cells were passaged the day before cell hybridization so that they were confluent the next day. Spleens from mice were isolated into a 60 mm dish with 10 mL of DMEM media+heparin. The spleens were teased apart to release splenocytes. Myeloma cells were washed once in 50 mL of DMEM then resuspended in 10 mL DMEM and counted. Spleen and myeloma cells were mixed at a 4:1 ratio. The cells were washed once in 50 mL DMEM then the media was aspirated and the pellet was gently suspended by flicking. The tube was placed in 37° C. water bath and 1 mL 50% w/w PEG was gradually added over 30 seconds, while stirring the pellet with a sterile pipet tip. After PEG was added, the mixture was left to stand at 37° C. for 1.5 minutes with occasional stirring. Over the next 3 minutes, 5 mL of 37° C. DMEM was gradually added with stirring. Then 14 mL of 37° C. DMEM was added over 1 minute. 30 mL of DMEM with 20% FBS was added and the mixture was centrifuged. The pellet was resuspended to 1.5×106 cell/mL, based on the number of spleen cells used. 5% Hybridoma Cloning Factor (PAA Laboratories S05-HCF) was added to stimulate growth. The final mixture was aliquoted at 0.2 mL/well in 96 well plates and incubated at 37° C. with 10% CO2.
Cells were fed when the media turned from red to yellow 4 days after hybridization and every 2-3 days thereafter. To feed, about half of the media was removed by aspiration and replaced drop-wise using a 25 mL pipet. Cells were fed with DMEM 20% FBS+HAT (hypoxanthine aminopterin thymidine) media with L-gluatmine, gentamicin, pyruvate, 20% FBS. After two weeks, cells were fed with DMEM 20% FBS+HT (hypoxanthine thymidine). After 30 days total, cells were fed with DMEM 20% FBS.
Wells containing successfully fused hybridoma cells were identified by ELISA. ELISA was done by coating the ELISA plate surface with Donkey anti-human IgG and incubated with TRAP-Fc supernatants. Hybridoma supernatants were screened for anti-TRAP antibody production on these plates, probed with Sheep anti-mouse antibody conjugated to HRP and detected with ABTS reagent (Invitrogen). Positive wells were expanded to T25 and single-cell cloned by limiting dilution into 96-well plates. Again, positive wells were identified by ELISA and expanded to T25 then diluted to 1, 3, and 30 cell/well in 3, 96-well plates. Positive clones were identified by ELISA. The final clones isolated were: CL1/5.1.1, CL1/8.2.3, CL2/1.4.3, and CL2/4.2.1 (see Table 4).









TABLE 4









Screen



















P. vivax



Clones
FL
Short
Open
Closed
TRAP


















CL1/5.1.1
3.90
0.01
0
0
—



CL1/8.2.3
3.50
0.02
0
0
—



CL2/1.4.3
—
1.71
0.97
1.24
—



CL2/4.2.1
—
0
0
0
0.83










Other Embodiments
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

## Claims

1. A Plasmodium falciparum Thrombospondin-Related Anonymous Protein (TRAP) antigen that is at least 80% identical to amino acids 25-574 of SEQ ID NO:5, wherein the antigen sequence comprises one or more of the following mutations or deletions:
(a) Mutation at Cysteine 55 to a non-cysteine amino acid;
(b) Mutation of N-linked glycosylation sites;
(c) Mutation of Ala-216/Asn-222 or Lys-224/Gln-78 to cysteine to create a TRAP that is stabilized in the open conformation;
(d) Mutation of Asn-213/Ala-233, Ala-216/Phe-230, or Met-231/Gln-78 to cysteine to create a TRAP that is stabilized in the closed conformation;
(e) Deletion of N-terminal and/or C-terminal residues to create a TRAP fragment that is stabilized in the closed conformation comprising V47-V238;
(f) Deletion of N-terminal and/or C-terminal residues to create a TRAP fragment that is stabilized in the open conformation comprising V47-M231,

and wherein the antigen can elicit an immune response in a mammalian subject.

2. The antigen of claim 1, wherein the sequence is a mutated P. falciparum TRAP sequence that is at least 95% identical to SEQ ID NO:5.

3. The antigen of claim 1, wherein the mutation at Cys55 is to Glycine, Serine, or Alanine.

4. The antigen of claim 1, wherein the mutation of an N-linked glycosylation site is a mutation of N or (S/T) in the carbohydrate-encoding sequence N-X-(S/T).

5. The antigen of claim 4, wherein the mutation is N132S, S477N, and/or N483S.

6. A fusion protein comprising the antigen of claim 1 fused to one or more of an adjuvant, carrier, or protein purification sequence.

7. The fusion protein of claim 6, wherein the protein purification sequence comprises a FLAG sequence or a 6His sequence.

8. The fusion protein of claim 6, wherein the carrier comprises a hepatitis B surface protein.

9. A composition comprising one or more of the antigens or fusion proteins of claim 1.

10. A pharmaceutical composition comprising one or more of the antigens of claim 1 and a physiologically acceptable carrier.

11. The pharmaceutical composition of claim 10, further comprising an adjuvant.

12. A method of inducing an immune response in a mammal, the method comprising administering to the subject a pharmaceutical composition comprising one or more of the antigens of claim 1.

13. The method of claim 12, wherein the pharmaceutical composition further comprises an adjuvant.