# Patent

## Title
Compositions and methods for detecting microbial infections

## Abstract

Provided herein are vaccine compositions for control of Trypanosoma cruzi infection and Chagas disease. The compositions comprise plasmids encoding o GPI-anchored genes ASP-2, TcG-1, TcG2 and TcG4 from Trypanosoma cruzi; plasmids encoding cytokines IL12 and GM-CSF; and plasmids encoding a gene expression system. Certain vaccine compositions comprise recombinant proteins, selected from TcG-1, TcG2 and TcG4 from Trypanosoma cruzi. In another vaccination strategy, the recombinant proteins are replaced by lysates comprising Trypanosoma rangeli cells. Further provided herein are diagnosis compositions comprising 1) recombinant proteins, selected from TcG-1, TcG2 and TcG4 from Trypanosoma cruzi; 2) antibodies that specifically binds the TcG-1, TcG2 and TcG4 proteins; 3) sense and antisense polynucleotide sequences that encode the TcG-1, TcG2 and TcG4 proteins. Said compositions can be used in diagnosing and/or evaluating efficacy of treatments against Trypanosoma cruzi infection. A diagnosis kit, and methods of diagnosing and/or treating Trypanosoma cruzi infection are also provided.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a divisional application of U.S. application Ser. No. 13/135,621 filed Jul. 11, 2011 (pending), which is a continuation-in-part application claiming benefit of priority under 35 U.S.C. §120 of pending international application PCT/US2010/002465, filed Sep. 10, 2010 (expired), which claims benefit of priority under 35 U.S.C. §119(e) of provisional application U.S. Ser. No. 61/276,274, filed Sep. 10, 2009. Priority is claimed to each application described above and each application is hereby incorporated by reference in its entirety.


FEDERAL FUNDING
The invention was supported by Grant No. R03A1072538 awarded by the National Institutes of Health. Consequently, the Government has certain rights in the invention.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to the field of human and animal health and in particular to vaccination approaches for control of Trypanosoma cruzi infection and Chagas disease. The present invention also relates to diagnosis of Trypanosoma cruzi infection and provides composition and methods for detecting Trypanosoma cruzi infection and evaluating efficacy of treatments against T. cruzi. 
2. Description of the Related Art
American trypanosomiasis or Chagas disease caused by Trypanosoma cruzi infection is the prime cause of death in young adults in endemic areas of the American continent and results in over 50,000 deaths, 1 million new cases, and loss of 2.74 million disability-adjusted years per year.
The prevalence rate of T. cruzi infection in dogs may reach up to 84%, determined by serological procedures and xenodiagnosis, in endemic areas (e.g. rural Argentina, Chiapas state of Mexico) [1, 2]. Dogs are the most frequent blood meal source for the domestic triatomines (T. barberi and T. pallidipennis in Mexico [3], T. infestans in Argentina [2]). Likewise, a high prevalence of seropositive dogs [4-6] and infected triatomines is routinely noted in rural and urban developments in southern US states [4, 7, 8] and suggested to maintain T. cruzi transmission in the human habitat. Triatomines are several times more likely to take their blood meal from dogs than from humans. The ratio of dog blood meals to human blood meals in the engorged guts of triatomines is estimated to be 2.3-2.6 times the ratio of the number of dogs to the number of humans in a household [9]. Thus, the probability of infecting an insect in one blood meal from dogs is estimated to be 200 times higher compared to the probability from adult humans [2]. These studies conclude: a) dogs are important host blood sources for domiciliary triatomines, b) the risk of T. cruzi infection in humans is increased by the presence of infected dogs, and c) strategies that can limit T. cruzi infection in the reservoir host would be effective in interrupting the parasite transmission to the vector, and consequently, to the human host.
The mathematical models based on epidemiological data suggest that vector control would be the most effective strategy against T. cruzi transmission [10]. However, sustained vector control, followed by constant surveillance, requires large-scale insecticide spraying every year that is not cost-effective and affordable for developing countries. Concerns also remain that insecticide use in the long-term may not be efficacious in blocking T. cruzi transmission, owing to the development of drug resistance by triatomines and reinfestation of homes by secondary sylvatic vectors, e.g., Triatoma sordida, in Brazil and other South American countries [11]. The same epidemiological models indicate that dog vaccination would be the second most efficient approach.
The efforts towards vaccine development are numerous. Based upon numerous studies in animal models, a successful vaccine that can provide protection from T. cruzi infection is envisioned by the research community to be composed of defined antigens capable of inducing strong neutralizing and lytic antibody response and type 1-biased T cell responses. Yet currently no vaccine is available for control of T. cruzi infection and disease development in humans and dogs.
Another major concern is the >300,000 infected individuals that have migrated to the US [25] (or other developed countries [26-27]) who can potentially transfer infection through blood or organ donation [28-29]. It is important that the migrant workforce in the US and the 20 million infected individuals living in the endemic countries [30] are diagnosed so as to prevent contamination of the donor blood banks. In the U.S., Ortho T. Cruzi ELISA Test System is licensed and approved by FDA for screening the donor blood samples. The Ortho System utilizes crude antigen preparation and there is a concern that crude antigen may exhibit cross-reactivity with antibodies to other parasitic protozoans (e.g. Leishmania, Trypanosoma rangeli) due to significant homology in the genome.
Thus, there is a recognized need in the art for a vaccine, a diagnosis composition and a treatment for control of T. cruzi infection and disease development in humans and dogs. The present invention fulfills this long-standing need and desire in the art.
SUMMARY OF THE INVENTION
The present invention is directed to a DNA vaccine comprising at least one plasmid encoding one or more GPI-anchored genes from Trypanosoma cruzi; at least one plasmid encoding a cytokine; and a pharmaceutically acceptable carrier.
The present invention is further directed to a DNA-protein vaccine comprising at least one plasmid encoding one or more GPI-anchored genes from Trypanosoma cruzi; at least one plasmid encoding a cytokine; one or more recombinant GPI-anchored proteins from Trypanosoma cruzi; and a pharmaceutically acceptable adjuvant.
The present invention is directed further to a vaccine comprising at least one plasmid encoding one or more GPI-anchored genes from Trypanosoma cruzi; at least one plasmid encoding a cytokine; one or more lysates comprising cells from Trypanosoma rangeli or other protozoa that are non-infective to humans; and a pharmaceutically acceptable adjuvant.
The present invention is directed still further to immunogenic proteins encoded by genes from Trypanosoma cruzi; one or more than one of these proteins comprise a composition along with a pharmaceutically acceptable carrier. This composition can be used in a method to detect Trypanosoma cruzi infection.
The present invention is directed further to antibodies specific for immunogenic proteins encoded by genes from Trypanosoma cruzi. These antibodies can be used in a method to detect or treat Trypanosoma cruzi infection.
The present invention is directed further to sense polynucleotide sequences and antisense polynucleotide sequences from Trypanosoma cruzi. These polynucleotide sequences can be used in a method to detect or treat Trypanosoma cruzi infection.
The present invention is directed further to a kit comprising one or more than one of the following components: immunogenic protein(s) from Trypanosoma cruzi, antibodies specific for immunogenic protein(s) encoded by gene(s) from Trypanosoma cruzi, sense polynucleotide sequence(s) and antisense polynucleotide sequence(s) from Trypanosoma cruzi, and a detection reagent.
Other and further objects, features, and advantages will be apparent from the following description of the presently preferred embodiments of the invention, which are given for the purpose of disclosure.



BRIEF DESCRIPTIONS OF THE DRAWINGS
So that the matter in which the above-recited features, advantages and objects of the invention, as well as others which will become clear, are attained and can be understood in detail, more particular descriptions of the invention briefly summarized above may be had by reference to certain embodiments thereof which are illustrated in the appended drawings. These drawings form a part of the specification. It is to be noted, however, that the appended drawings illustrate preferred embodiments of the invention and therefore are not to be considered limiting in their scope.
FIG. 1 depicts the computational screening strategy used to screen the T. cruzi sequence database for the identification of potential vaccine candidates.
FIGS. 2A-2F depict expression plasmids used in the DNA vaccines. FIG. 2A depicts CMVI.UBF3/2 encoding ASP-2. The cDNA fragment of ASP-2 (GenBank accession no. U77951) encoding amino acid residues 61 to 705 (SEQ ID NO: 1) was cloned at BgIII and SmaI restriction sites of multiple cloning sequence (MCS) in eukaryotic expression plasmid pCMV.UBF3/2CMVI.UBF3/2 mammalian expression plasmid containing the cytomegalovirus (CMV) immediate-early gene promoter, a Synthetic 5′ intron, and a modified 3′ untranslated region from the human growth hormone. The cloned genes were fused to a ubiquitin-encoding gene at the 5′ end to promote targeting of the expressed protein to the proteosome and entry into the MHC class I pathway of antigen presentation. FIG. 2B shows pCDNA3 encoding TcG1-TcG8 cDNAs. The cDNA fragment of TcG1, TcG2, TcG3, TcG4, TcG5, TcG6, TcG7, and TcG8 were amplified using the oligonucleotides depicted in FIG. 2C, and cloned at indicated restriction sites in the eukaryotic expression plasmid pCDNA3.1. FIG. 2C depicts oligonucleotides used to amplify TcG1-TcG8 for cloning in pCDNA3. FIG. 2D depicts eukaryotic expression plasmids encoding murine granulocyte-macrophage colony-stimulating factor (GM-CSF; pCMVI.GM-CSF). FIG. 2E depicts eukaryotic expression plasmids encoding murine cytokine interleukin-12 (IL-12; pcDNA3.msp35 and pcDNA3.msp40). FIG. 2F depicts pCDNA3 encoding dog IL-12.
FIGS. 3A-3D depicts C57BL/6 mice immunized with pCDNA3 encoding TcG1, TcG2, and TcG4 plus IL-12 and GMCSF-expression plasmids (25 _g each plasmid/mouse, i.m., 3-week intervals) and then with recombinant protein cocktail (rTcG1, rTcG2, and rTcG4) with saponin adjuvant (25 _g each protein/mouse, i.d., 3-week intervals). Mice were challenged with T. cruzi 2-weeks after last immunization. FIG. 3A shows ab response after immunization and during acute (25 dpi) and chronic (>120 dpi) stages. FIGS. 3B-3C show Cytokine profile of splenocytes, in vitro activated with Tc lysate. FIG. 3D shows H&E staining, Controls+ were immunized with empty plasmid and saponin only (8 mice/group).
FIG. 4 depicts serological detection of anti-T. cruzi antibodies in vaccinated dogs. 96-well plates were coated with T. cruzi antigen (5×105 parasite equivalents/well) or recombinant antigen (10 μg/well) and sequentially incubated with sera samples (1:20 dilution, 100 _l/well) added in triplicate; 100 _l/well HRP-labeled goat anti-dog IgG+M (1:5000 dilution) (KOMA); and 100 _l/well of Sure Blue TMB substrate (K&P). Absorbance was measured at 650 nm. Background signal (without serum) was subtracted before the data were calculated.
FIGS. 5A-5C depicts dogs (n=6) immunized with TcVac3R and two weeks later, challenged with T. cruzi (2300 parasites/kg). Control+ Dogs given empty vector/saponin only followed by challenge infection. FIG. 5A shows Parasitemia determined at 2-day intervals, beginning day 7 pi. FIG. 5B shows heart pathology, displaying ventricle fibrosis and atrial dilation in control+ group. FIG. 5C shows that at 60 d post infection lab-reared triatomines were fed on vaccinated and control dogs (6 bugs/dog) Gut-parasitemia in triatomines was determined by light microscopic examination of diluted feces at 2 weeks-post feeding
FIGS. 6A-6B depict that the TcG1, TcG2, and TcG4 genes are expressed in T. cruzi. FIG. 6A shows TcG1, TcG2, and TcG4 are expressed in epimastigote and amastigote stages and TcG1 and TcG4 are also expressed in trypomastigote stage of T. cruzi. RT-PCR was performed to evaluate mRNA levels for TcG1, TcG2 and TcG4 in different stages of T. cruzi. Total RNA and cDNA from the epimastigote (E), trypomastigote (T), and amastigote (A) forms of T. cruzi was obtained. FIG. 6B shows TcG1, TcG2, and TcG4 are phylogenetically conserved in CL Brenner (CL), Sylvio X10 (S), Brazil (Br), Y strain of T. cruzi (P: plasmid DNA used as control). Genomic DNA was isolated from different T. cruzi strains obtained from endemic countries. PCR amplified products were resolved by agarose gel electrophoresis, and imaged.
FIGS. 7A-7B depict that TcG1, TcG2, and TcG4 elicit antigen-specific antibody in mice. FIG. 7A shows the sera levels of parasite- and antigen-specific antibodies, measured two-weeks after the last immunization. FIG. 7B shows that TcG1, TcG2, and TcG4 are immunogenic in mice, and immune system of mice recognizes these proteins and elicit antigen-specific antibody response. Sera levels (1:100 dilution) of antibody response in normal mice (NM), and mice injected with pCNDA3 vector only (Vector), or cytokine (cyt) adjuvants only are shown as control. TcTL stands for total cell lysate of T. cruzi. 
FIGS. 8A-8B depict that immunization with TcG1, TcG2, TcG4 elicits antigen-specific antibody response in dogs. FIG. 8 shows sera level of antibodies in dogs immunized with candidate antigens (FIG. 8A) and infected with T. cruzi (FIG. 8B), measured by ELISA.
FIGS. 9A-9B depict that TcG1, TcG2 and TcG4 are equally or more effective in diagnosing the exposure to T. cruzi, compared to total cell lysate of T. cruzi (TcTL). Shown is a box plot of ELISA data, graphically depicting the OD values for seronegative (gray box) and seropositive (white box) samples from Mexico, identified by ELISA. (FIG. 9A): IgG response, (FIG. 9B): IgM response.
FIG. 10 depicts that TcG1-, TcG2- and TcG4-specific IgG antibodies are detected in sera of chagasic patients from Argentina. Over 300 sera samples, which were diagnosed as seropositive by commercially available kits, were analyzed to evaluate the antibody response to TcG1, TcG2, and TcG4 antigens.



DETAILED DESCRIPTION OF THE INVENTION
The practice of the present invention will employ, unless otherwise indicated, conventional methods of chemistry, biochemistry, molecular biology, immunology and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Remington's Pharmaceutical Sciences, 18th Edition (Easton, Pa.: Mack Publishing Company, 1990); Methods In Enzymology (S. Colowick and N. Kaplan, eds., Academic Press, Inc.); and Handbook of Experimental Immunology, Vols. I-IV (D. M. Weir and C. C. Blackwell, eds., 1986, Blackwell Scientific Publications); Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Handbook of Surface and Colloidal Chemistry (Birdi, K. S. ed., CRC Press, 1997); Short Protocols in Molecular Biology, 4th ed. (Ausubel et al. eds., 1999, John Wiley & Sons); Molecular Biology Techniques: An Intensive Laboratory Course (Ream et al., eds., 1998, Academic Press); PCR (Introduction to Biotechniques Series), 2nd ed. (Newton & Graham eds., 1997, Springer Verlag); Peters and Dalrymple, Fields Virology, 2nd ed., Fields et al. (eds.) (B.N. Raven Press, New York, N.Y.).
As used herein the specification, “a” or “an” may mean one or more. As used herein in the claim(s), when used in conjunction with the word “comprising”, the words “a” or “an” may mean one or more than one. As used herein “another” or “other” may mean at least a second or more of the same or different claim element or components thereof. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. “Comprise” means “include.” It is further to be understood that all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for description. Although methods and materials similar or equivalents to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. Furthermore, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.
The term “antigen” as used herein is defined as a compound, composition, or substance that can stimulate the production of antibodies or a T cell response in an animal, including compositions that are injected or absorbed into an animal. An antigen reacts with the products of specific humoral or cellular immunity, including those induced by heterologous immunogens. The term “antigen” includes all related antigenic epitopes. “Epitope” or “antigenic determinant” refers to a site on an antigen to which B and/or T cells respond. Epitopes can be formed both from contiguous amino acids or noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained on exposure to denaturing solvents whereas epitopes formed by tertiary folding are typically lost on treatment with denaturing solvents. An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation. Methods of determining spatial conformation of epitopes include, for example, x-ray crystallography and 2-dimensional nuclear magnetic resonance.
An “antigen” can be a tissue-specific antigen, or a disease-specific antigen. These terms are not exclusive, as a tissue-specific antigen can also be a disease specific antigen. A tissue-specific antigen is expressed in a limited number of tissues, such as a single tissue. Specific, non-limiting examples of a tissue specific antigen are a prostate specific antigen. A disease-specific antigen is expressed coincidentally with a disease process. Specific non-limiting examples of a disease-specific antigen are an antigen whose expression correlates with, or is predictive of, tumor formation, such as prostate cancer. A disease specific antigen may be an antigen recognized by T cells or B cells.
The term “amplification” of a nucleic acid molecule (e.g., a DNA or RNA molecule) refers to use of a technique that increases the number of copies of a nucleic acid molecule in a specimen. An example of amplification is the polymerase chain reaction, in which a biological sample collected from a subject is contacted with a pair of oligonucleotide primers, under conditions that allow for the hybridization of the primers to a nucleic acid template in the sample. The primers are extended under suitable conditions, dissociated from the template, and then re-annealed, extended, and dissociated to amplify the number of copies of the nucleic acid. The product of amplification may be characterized by electrophoresis, restriction endonuclease cleavage patterns, oligonucleotide hybridization or ligation, and/or nucleic acid sequencing using standard techniques. Other examples of amplification include strand displacement amplification, as disclosed in U.S. Pat. No. 5,744,311; transcription-free isothermal amplification, as disclosed in U.S. Pat. No. 6,033,881; repair chain reaction amplification, as disclosed in WO 90/01069; ligase chain reaction amplification, as disclosed in EP-A-320 308; gap filling ligase chain reaction amplification, as disclosed in U.S. Pat. No. 5,427,930; and NASBATM RNA transcription-free amplification, as disclosed in U.S. Pat. No. 6,025,134.
The term “antibody” as used herein includes immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen. A naturally occurring antibody (e.g., IgG, IgM, IgD) includes four polypeptide chains, two heavy (H) chains and two light (L) chains interconnected by disulfide bonds. However, it has been shown that the antigen-binding function of an antibody can be performed by fragments of a naturally occurring antibody. Thus, these antigen-binding fragments are also intended to be designated by the term “antibody.” Specific, non-limiting examples of binding fragments encompassed within the term antibody include (i) a Fab fragment consisting of the VL, VH, CL and CH1 domains; (ii) an Fd fragment consisting of the VH and CH1 domains; (iii) an Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (iv) a dAb fragment (Ward et al., Nature 341:544-546, 1989) which consists of a VH domain; (v) an isolated complimentarily determining region (CDR); and (vi) a F(ab′)2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region.
Immunoglobulins and certain variants thereof are known and many have been prepared in recombinant cell culture (e.g., see U.S. Pat. No. 4,745,055; U.S. Pat. No. 4,444,487; WO 88/03565; EP 256,654; EP 120,694; EP 125,023; Faoulkner et al., Nature 298:286, 1982; Morrison, J. Immunol. 123:793, 1979; Morrison et al., Ann Rev. Immunol 2:239, 1984).
The term “animal” as used herein refers to living multi-cellular vertebrate organisms, a category that includes, for example, mammals and birds. The term mammal includes both human and non-human mammals. Similarly, the term “subject” includes both human and veterinary subjects.
The term conservative variation includes the use of a substituted amino acid in place of an unsubstituted parent amino acid, provided that antibodies raised to the substituted polypeptide also immunoreact with the unsubstituted polypeptide. Non-conservative substitutions are those that reduce an activity or antigenicity.
The term “cDNA” (complementary DNA) refers to a piece of DNA lacking internal, non-coding segments (introns) and regulatory sequences that determine transcription. cDNA is synthesized in the laboratory by reverse transcription from messenger RNA extracted from cells.
The term “diagnostic” refers to identifying the presence or nature of a pathologic condition, such as, but not limited to, prostate cancer. Diagnostic methods differ in their sensitivity and specificity. The “sensitivity” of a diagnostic assay is the percentage of diseased individuals who test positive (percent of true positives). The “specificity” of a diagnostic assay is 1 minus the false positive rate, where the false positive rate is defined as the proportion of those without the disease who test positive. While a particular diagnostic method may not provide a definitive diagnosis of a condition, it suffices if the method provides a positive indication that aids in diagnosis. “Prognostic” is the probability of development (e.g., severity) of a pathologic condition, such as prostate cancer, or metastasis.
An “epitope” as used herein, is an antigenic determinant. These are particular chemical groups or peptide sequences on a molecule that are antigenic, i.e. that elicit a specific immune response. An antibody specifically binds a particular antigenic epitope on a polypeptide. Epitopes can be formed both from contiguous amino acids or noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained on exposure to denaturing solvents whereas epitopes formed by tertiary folding are typically lost on treatment with denaturing solvents. An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation. Methods of determining spatial conformation of epitopes include, for example, x-ray crystallography and 2-dimensional nuclear magnetic resonance. See, e.g., Epitope Mapping Protocols in Methods in Molecular Biology, Vol. 66, Glenn E. Morris, Ed (1996).
The term “expression control sequence” refers to Nucleic acid sequences that regulate the expression of a heterologous nucleic acid sequence to which it is operatively linked. Expression control sequences are operatively linked to a nucleic acid sequence when the expression control sequences control and regulate the transcription and, as appropriate, translation of the nucleic acid sequence. Thus expression control sequences can include appropriate promoters, enhancers, transcription terminators, a start codon (i.e. ATG) in front of a protein-encoding gene, splicing signal for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons. The term “control sequences” is intended to include, at a minimum, components whose presence can influence expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. Expression control sequences can include a promoter.
The term “promoter” refers to a minimal sequence sufficient to direct transcription. Also included are those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue-specific, or inducible by external signals or agents; such elements may be located in the 5′ or 3′ regions of the gene. Both constitutive and inducible promoters are included (see e.g., Bitter et al., Methods in Enzymology 153:516-544, 1987). For example, when cloning in bacterial systems, inducible promoters such as pL of bacteriophage lambda, plac, ptrp, ptac (ptrp-lac hybrid promoter) and the like may be used. In one embodiment, when cloning in mammalian cell systems, promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter) can be used. Promoters produced by recombinant DNA or synthetic techniques may also be used to provide for transcription of the nucleic acid sequences.
As defined herein, the term “host cell” refers to cells in which a vector can be propagated and its DNA expressed. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. However, such progeny are included when the term “host cell” is used.
The term “immune response” refers to a response of a cell of the immune system, such as a B cell, T cell, or monocyte, to a stimulus. In one embodiment, the response is specific for a particular antigen (an “antigen-specific response”). In one embodiment, an immune response is a T cell response, such as a CD4+ response or a CD8+ response. In another embodiment, the response is a B cell response, and results in the production of specific antibodies.
An “isolated” biological component (such as a nucleic acid or protein or organelle) as defined herein, has been substantially separated or purified away from other biological components in the cell of the organism in which the component naturally occurs, i.e., other chromosomal and extra-chromosomal DNA and RNA, proteins and organelles. Nucleic acids and proteins that have been “isolated” include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
A “label” as defined herein, is a detectable compound or composition that is conjugated directly or indirectly to another molecule to facilitate detection of that molecule. Specific, non-limiting examples of labels include fluorescent tags, enzymatic linkages, and radioactive isotopes.
Lymphocytes as defined herein are a type of white blood cell that is involved in the immune defenses of the body. There are two main types of lymphocytes: B cells and T cells.
Open reading frame (ORF) is defined as a series of nucleotide triplets (codons) coding for amino acids without any internal termination codons. These sequences are usually translatable into a peptide.
The term “operably linked” refers to a first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.
As used herein, the term “vector” refers to a nucleic acid molecule as introduced into a host cell, thereby producing a transformed host cell. A vector may include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication. A vector may also include one or more selectable marker genes and other genetic elements known in the art.
As used herein, the term “transduction” encompasses all techniques by which a nucleic acid molecule might be introduced into such a cell, including transfection with viral vectors, transformation with plasmid vectors, and introduction of naked DNA by electroporation, lipofection, and particle gun acceleration. A transduced cell is a cell into which has been introduced a nucleic acid molecule by molecular biology techniques.
As used herein, the term “T Cell” refers to a white blood cell critical to the immune response. T cells include, but are not limited to, CD4+ T cells and CD8+ T cells. A CD4+ T lymphocyte is an immune cell that carries a marker on its surface known as “cluster of differentiation 4” (CD4). These cells, also known as helper T cells, help orchestrate the immune response, including antibody responses as well as killer T cell responses. CD8+ T cells carry the “cluster of differentiation 8” (CD8) marker. In one embodiment, a CD8 T cell is a cytotoxic T lymphocyte. In another embodiment, a CD8 cell is a suppressor T cell.
The term “purified” as used herein, does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified nucleic acid is one in which the nucleic acid is more enriched than the nucleic acid in its natural environment within a cell. Similarly, a purified peptide preparation is one in which the peptide or protein is more enriched than the peptide or protein is in its natural environment within a cell. In one embodiment, a preparation is purified such that the protein or peptide represents at least 50% (such as, but not limited to, 70%, 80%, 90%, 95%, 98% or 99%) of the total peptide or protein content of the preparation.
A “recombinant nucleic acid” is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.
As used herein, the term “selectively hybridize” refers to hybridization under moderately or highly stringent conditions that excludes non-related nucleotide sequences. In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA versus DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter. One of skill in the art can readily determine these conditions (e.g., Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, ed. Sambrook et al., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989). As mentioned above, optimal conditions will vary, depending on the particular hybridization reaction involved, and can be determined empirically.
The term “polynucleotide” or “nucleic acid sequence” refers to a polymeric form of nucleotide at least 10 bases in length. A recombinant polynucleotide includes a polynucleotide that is not immediately contiguous with both of the coding sequences with which it is immediately contiguous (one on the 5′ end and one on the 3′ end) in the naturally occurring genome of the organism from which it is derived. The term therefore includes, for example, a recombinant DNA which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA) independent of other sequences. The nucleotides can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide. The term includes single- and double-stranded forms of DNA.
The term peptide, as used herein refers to any chain of amino acids, regardless of length or post-translational modification (e.g., glycosylation or phosphorylation).
The term “probe” comprises an isolated nucleic acid attached to a detectable label or reporter molecule. The term “primer” includes short nucleic acids, preferably DNA oligonucleotides, 15 nucleotides or more in length. Primers may be annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, and then extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR) or other nucleic-acid amplification methods known in the art. One of skill in the art will appreciate that the specificity of a particular probe or primer increases with its length. Thus, for example, a primer comprising 20 consecutive nucleotides will anneal to a target with a higher specificity than a corresponding primer of only 15 nucleotides. Thus, in order to obtain greater specificity, probes and primers may be selected that comprise 20, 25, 30, 35, 40, 50 or more consecutive nucleotides.
The term “promoter” as described herein, is an array of nucleic acid control sequences that directs transcription of a nucleic acid. A promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element. A promoter also optionally includes distal enhancer or repressor elements which can be located as much as several thousand base pairs from the start site of transcription. Both constitutive and inducible promoters are included (see e.g., Bitter et al., Methods in Enzymology 153:516-544, 1987). Specific, non-limiting examples of promoters include promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter) may be used. Promoters produced by recombinant DNA or synthetic techniques may also be used. A polynucleotide can be inserted into an expression vector that contains a promoter sequence which facilitates the efficient transcription of the inserted genetic sequence of the host. The expression vector typically contains an origin of replication, a promoter, as well as specific nucleic acid sequences that allow phenotypic selection of the transformed cells.
The pharmaceutically acceptable carriers of use are conventional. Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 15th Edition (1975), describes compositions and formulations suitable for pharmaceutical delivery of the vaccines herein disclosed.
In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (e.g., powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
As used herein, the term “subject” refers to any target of the treatment. Preferably, the subject is a mammal, more preferably, the subject is a canine or a human.
In some embodiments of the present invention there is provided a DNA vaccine comprising at least one plasmid encoding one or more GPI-anchored genes from Trypanosoma cruzi; at least one plasmid encoding a cytokine; and a pharmaceutically acceptable carrier.
Further to these embodiments, representative GPI-anchored genes are ASP-2, TcG-1, TcG2, TcG3, TcG4, TcG5, TcG6, TcG7 and TcG8. These GPI-anchored genes encode proteins with sequences shown in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID NO: 9. Additionally, in some embodiments, representative cytokines are selected from the group comprising IL12, GM-CSF, CD40L, Flt3L and RANTES. In some embodiments, GPI-anchored genes are selected from ASP-2 encoding a protein with a sequence shown in SEQ ID NO: 1, TcG-1 encoding a protein with a sequence shown in SEQ ID NO: 2, TcG-2 encoding a protein with a sequence shown in SEQ ID NO: 3, and TcG4 encoding a protein with a sequence shown in SEQ ID NO: 5; and the cytokines are IL-12 and GM-CSF. In some embodiments, the DNA vaccine comprises 100 μg of each plasmid.
In some embodiments of the present invention, there is provided a DNA-protein vaccine comprising at least one plasmid encoding one or more GPI-anchored genes from Trypanosoma cruzi; at least one plasmid encoding a cytokine; one or more recombinant GPI-anchored proteins from Trypanosoma cruzi; and a pharmaceutically acceptable adjuvant. In some of these embodiments, representative GPI-anchored genes include but are not limited to ASP-2, TcG-1, TcG2, TcG3, TcG4, TcG5, TcG6, TcG7 and TcG8. These GPI-anchored genes encode proteins with sequences shown in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID NO: 9. Further to these embodiments, representative recombinant GPI-anchored proteins may be ASP-2, TcG-1, TcG2, TcG3, TcG4, TcG5, TcG6, TcG7 and TcG8. In some of these embodiments, recombinant GPI-anchored proteins have sequences of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID NO: 9. In some embodiments, the adjuvant is a saponin adjuvant.
In another embodiment of the present invention, there is provided a vaccine comprising at least one plasmid encoding one or more GPI-anchored genes from Trypanosoma cruzi; at least one plasmid encoding a cytokine; one or more lysates comprising cells from Trypanosoma rangeli or other protozoa that are non-infective to humans; and a pharmaceutically acceptable adjuvant.
Certain embodiments of the invention comprise methods of vaccination comprising one or more of the vaccines described supra. In certain embodiments, these methods are used in vaccinating dogs. In certain embodiments, the vaccines comprise from about 50 μg to about 500 μg of each plasmid. In other embodiments, the vaccines may comprise from about 50 μg to about 500 μg of each recombinant GPI-anchored protein. In certain embodiments, the vaccines comprise from about 50 μg up to about 900 μg of the bacterial cell lysates comprising Trypanosoma rangeli cells.
In yet another embodiment of the present invention, there is provided an isolated protein or protein fragment with at least 90% sequence identity to a protein having the sequence shown in SEQ ID NO: 2 encoded by a TcG-1 gene Trypanosoma cruzi; or a protein with a sequence shown in SEQ ID NO: 3 encoded by a TcG-2 gene Trypanosoma cruzi; or a protein with a sequence shown in SEQ ID NO: 5 encoded by a TcG-4 gene of Trypanosoma cruzi. Further to these embodiments, the protein or protein fragment is a synthetic or a recombinant protein or protein fragment.
In yet another embodiment of the present invention, there is provided an immunogenic composition, comprising one or more of the isolated protein or protein fragment of the TcG-1, TcG-2 or TcG-4 proteins and a pharmaceutically acceptable carrier. Further to these embodiments, immunogenic composition exhibits reactivity with sera from a subject infected with Trypanosoma cruzi. 
In yet another embodiment of the present invention, there is provided an isolated or purified antibody or antibody fragment thereof that specifically binds the protein or protein fragment of the TcG-1, TcG-2 or TcG-4 protein. In yet another embodiment of the present invention, there is provided a synthetic polynucleotide sequence encoding the protein or protein fragment of the TcG-1, TcG-2 or TcG-4 protein. In yet another embodiment of the present invention, there is provided a synthetic antisense polynucleotide sequence that is complementary to at least part of the synthetic polynucleotide sequence that encodes the TcG-1, TcG-2 or TcG-4 protein.
In yet another embodiment of the present invention, there is provided a method for detecting Trypanosoma cruzi infection in subject. This method comprising the steps of: contacting a sample isolated from a subject with the composition comprising one or more than one of the TcG-1, TcG-2 or TcG-4 proteins; detecting the specific antibody response from the isolated sample to said composition, wherein an increase of the antibody response indicates that the subject is infected with Trypanosoma cruzi. Representative antibody responses include but are not limited to an IgG antibody response and an IgM antibody response. Representative isolated samples include but are not limited to serum or blood.
Further to these embodiments, the isolated sample is contacted with: a protein with a sequence shown in SEQ ID NO: 2 encoded by a TcG-1 gene Trypanosoma cruzi; a protein with a sequence shown in SEQ ID NO: 3 encoded by a TcG-2 gene Trypanosoma cruzi; and a protein with a sequence shown in SEQ ID NO: 5 encoded by a TcG-4 gene of Trypanosoma cruzi, wherein an increase of the antibody responses in said isolated sample to all three antigens indicates that the subject is infected with Trypanosoma cruzi. 
In yet another embodiment of the present invention, there is provided a method for detecting Trypanosoma cruzi infection in a subject, said method comprising the steps of: labeling an antibody or antibody fragment that binds the TcG-1, TcG-2 or TcG-4 protein, with a detectable substrate; contacting a sample isolated from a subject with the labeled antibody or antibody fragment; detecting the binding of the labeled antibody or antibody fragment to the sample, wherein an increase of binding of the labeled antibody to the isolated sample indicates that the subject is infected with Trypanosoma cruzi. 
In yet another embodiment of the present invention, there is provided a method for detecting Trypanosoma cruzi infection in a subject, said method comprising the steps of: generating an antisense polynucleotide sequence that is complementary to at least part of the polynucleotide sequence encoding the protein or protein fragment of the TcG-1, TcG-2 or TcG-4 protein; labeling the antisense polynucleotide with a detectable substrate, isolating nucleic acids from a sample from a subject; amplifying the polynucleotide sequence encoding the protein or protein fragment of the TcG-1, TcG-2 or TcG-4 protein from the nucleic acids; contacting the amplified polynucleotide sequence with labeled antisense polynucleotide, wherein an increase of binding of the labeled antisense polynucleotide to the amplified polynucleotide sequence indicates that said subjected is infected with Trypanosoma cruzi. 
In yet another embodiment of the present invention, there is provided a method for treating Trypanosoma cruzi infection in subject, said method comprising the step of: administering the antibody or antibody fragment that binds the TcG-1, TcG-2 or TcG-4 protein to a subject infected with Trypanosoma cruzi, so as to decrease amount of Trypanosoma cruzi in the subject thereby treating the Trypanosoma cruzi infection.
In yet another embodiment of the present invention, there is provided a method for treating Trypanosoma cruzi infection in a subject, said method comprising the step of: administering the synthetic antisense polynucleotide sequence that encodes the TcG-1, TcG-2 or TcG-4 protein to a subject infected with Trypanosoma cruzi, so as to decrease Trypanosoma cruzi in the subject thereby treating the Trypanosoma cruzi infection.
In yet another embodiment of the present invention, there is provided a kit for detecting Trypanosoma cruzi infection in a sample, said kit comprising: (a) one or more of the isolated protein or protein fragment of the TcG-1, TcG-2 or TcG-4 protein; and (b) a detection reagent. Further to this embodiments, the kit contains: a protein with a sequence shown in SEQ ID NO: 2 encoded by a TcG-1 gene Trypanosoma cruzi; a protein with a sequence shown in SEQ ID NO: 3 encoded by a TcG-2 gene Trypanosoma cruzi; a protein with a sequence shown in SEQ ID NO: 5 encoded by a TcG-4 gene of Trypanosoma cruzi; and a detection reagent.
In yet another embodiment of the present invention, there is provided a kit for detecting Trypanosoma cruzi infection in a biological sample, said kit comprising: (a) one or more isolated or synthetic antibody or antibody fragment that specifically binds the protein or protein fragment of the TcG-1, TcG-2 or TcG-4 protein; and (b) a detection reagent. In this embodiment of the present invention, there is provided a kit for detecting Trypanosoma cruzi infection a biological sample, said kit comprising: (a) one or more of the isolated protein or protein fragment of the TcG-1, TcG-2 or TcG-4 protein; and (b) one or more isolated or synthetic antibody or antibody fragment that specifically binds the protein or protein fragment of the TcG-1, TcG-2 or TcG-4 protein; and (c) a detection reagent.
In yet another embodiment of the present invention, there is provided a kit for detecting Trypanosoma cruzi infection a biological sample, said kit comprising: (a) one or more of the synthetic antisense polynucleotide sequence that encodes the TcG-1, TcG-2 or TcG-4 protein; and (b) a detection reagent.
The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion.
Example 1
Vaccine Development
A transfection approach is employed to express ovalbumin (model antigen) in different cellular compartments of T. cruzi. Using these transfectants, it has been demonstrated that parasite secreted antigens and GPI-proteins (released by default in host cell cytoplasm) would be capable of entering the class I and II pathways of antigen presentation and elicit antibody and T cell responses, and, thus, would be the best choice as vaccine candidates [12].
Example 2
Computational Screening
An unbiased computational/bioinformatics approach was developed and the T. cruzi sequence database was screened for the identification of potential vaccine candidates [18] (FIG. 1). This strategy was chosen because testing of  ̃8,000 genes, estimated to be present in the haploid genome of T. cruzi (5-8×107 bp), as subunit vaccine candidates was not economically feasible. Strategic analysis of the database led to a selection of 71 candidate sequences of which eight (TcG1-TcG8, Table 1: SEQ ID NOs 2-9) were found to be phylogenetically conserved in clinically important strains of T. cruzi, and expressed in the infective and intracellular stages of the parasite [18]. When delivered as a DNA vaccine in mice, TcG1, TcG2, TcG4 elicited a significant trypanolytic antibody response and Th1 cytokine (IFN-γ), a property associated with immune control of T. cruzi [18] (Table 2). These vaccine candidates, thus, increased the pool of protective vaccine candidates against T. cruzi. 
Example 3
Protective Efficacy of TcG1, TcG2, and TcG4 in Mice
TcG1, TcG2, and TcG4 were cloned in eukaryotic expression vector pCDNA3.1 (for DNA vaccination) and in E. coli expression vector to generate recombinant proteins (for protein vaccination). One group of mice was immunized with four doses of DNA vaccine (pcDNA3 encoding TcG1, TcG2, and TcG4+ IL-12 and GM-CSF expression plasmids as illustrated in FIGS. 2A-2F, intramuscular delivery). Second group of mice was immunized with 2 doses of DNA vaccine and 2 doses of recombinant proteins with saponin adjuvant (intradermal). Both groups of mice immunized with DNA-DNA or DNA-protein vaccine elicited anti-parasite humoral and cellular immune responses (FIGS. 3A-3D) [19].
The DNA-protein vaccine of the present invention induced significantly higher levels of T. cruzi- and antigen-specific humoral responses that were maintained after challenge infection and during chronic disease phase. Likewise, the DNA-protein vaccine elicited a stronger, Th1 biased cellular response (IFN-_, TNF-_ cytokines, CD8+T cells) that was effective in controlling the acute parasitemia and tissue parasite burden during acute phase. Due to controlled acute infection, DNA-protein vaccinated mice exhibited remarkable reduction in immunopathology, a hallmark of chronic Chagas disease. Overall DNA-protein vaccine polarized the B & T cell immune response towards Th1 type that controlled parasites during acute phase and towards Th2 type after acute infection that reduced chronic inflammation during disease phase, respectively. These studies suggested that DNA/protein vaccination would be a better approach in eliciting protective immunity against T. cruzi infection and disease.







TABLE 1







Genes phylogenetically conserved in clinically 


important strains of T. cruzi.









Gene
SEQ ID
SEQUENCE





ASP-2
SEQ ID
PCEAADAVEGKSGAVQLPKWVDIFVPEKTHVLPKEGSESGVKKAFA



NO: 1
APSLVSAGGVMVAFAEGFSEYNAHENNPFGIRPYEILAGYIKAAESW




PSIVAEVNASTWRAHTVIGSRNGNDRLCFLYRPTAVARENKVFLLVG




SDTVGYDSDDDMWVKDGWDIQLVEGVATQSTDGKPSKTINWGEPK




SLLKHIPKHTQGHLRDVVTAGGSGIVMQNNTLVFPLVVNGKNYPFSS




ITYSTDNGNNWVFPESISPVGCLDPRITEWETGQILMIVDCGNGQSV




YESRDMGTTWTKAVRTLSGVWAISQRGVRSYEIFRVGAIITATIEGR




KVMLYTRRGYASGEKEANALYLWVTDNNRTFHVGPVAMDSAVNET




LSNALLYSDGNLHLLQQRANEKGSAISLARLTEELKEIESVLRTWAQL




DAFFSKSSTPTAGLVGFLSNTSSGGNTWIDEYRCVNATVTKASKVK




NGFKFTGPGPMATWLVNSREDNRQYSFVNHRFTLVATVTIHQVPKG




STPLLGAGLGDGHGAKIIGLSYSMNKTWETVFYGKKTTSNTTWELG




KEYQVTLMLQDGNKGSVYVDGVIVGSPAKIPKVGALGHEIAHFYFGG




GEGDSDSSVTVTNVFLYNRPLSVGELKMVRKSDDKKGNGGDQK


 


TcG1
SEQ ID
MVKANYIRAGRLVRIIRGPRQDRVGVVVDIIDGNRVLVENPADKKMW



NO: 2
RHVQNLKNVEPLKFSVELSRNCSTRTLKNVLAEKKILEKYAATKSAR




RIAAKRAFARSTDFERYQLRVAKRSRAFWTRKVFDENDQKKPVSW




HKVALKKLQKNAKKVDSKPAAKKRISN


 


TcG2
SEQ ID
MSLSFIESGFVPSDGMRRGVEAADTSAAAELLHLAVPPLMDAGGKT



NO: 3
RVCVAFYEAAQCPFDSRCEHAHHFSELNGYTQNKLLETVPVESIPK




HFVAPLNSNSSSGNNKNDRTFYATDGNAANYTATAAVDGGVAHRS




LGGEHGEKEKTSTNRRSKRTARLYDISGSNTNLCDNSLSSLASSTDT




LLLLGSVHDSKDVSPQKGTRRDEGMEAFRIRLPPLLG


 


TcG3
SEQ ID
MLQRTCSGSLYAVLEVARDATPQEIKKAYHRLALRLHPDKTGGTTTE



NO: 4
QFTLIQEAQSILGDPRQRRVYDTFGRMGIESLRQFGDGMVVMTTAGI




RCAFFIIAFWMLLWLLTLVLAIVRFDYNKGWPWAAVFAPVWVALVPL




LLIGGLLVFHGATRREIASTLLGLMCFLVTFAVAMFVVGLSGALTWTI




ALAPSAAIYVFQSCFILRYLLPFQFRNGFAEFIPPGSSVCLSRMYWGF




CWKQYLKSCVVSALLVLPCYRGANRRGRYIKTDLLLDSFYSSYFVL




WVHDVCFCRTKIFCGNSGGAVMSPEPTVPCADGRHRLRQSSFYGM




HVGGEVSS


 


TcG4
SEQ ID
MSAKAPPKTLHQVRNVAYIFAAWAGLQKGFAEKSANDKMWVEHQR



NO: 5
RLRQENAKRQHAAHALEELKQDEELERSIPTIVPKELHELVKALEK


 


TcG5
SEQ ID
MGKEKVHMNLVVVGHVDAGKSTATGHLIYKCGGIDKRTIEKFEKEA



NO: 6
AEIGKSSFKYAWVLDKLKAERERGITIDIALWKFESPKSVFTIIDAPG




HRDFIKNMITGTSQADAAVLVIASSQGEFEAGISKDGQTREHALLAF




TLGVKQMVVCCNKMDDKSVNFAQERYDEIVKEVSAYLKKVGYNVE




KVRFIPISGWQGDNMIDKSENMPWYKGPTLLEALDMLEPPVRPSD




KPLRLPLQDVYKIGGIGTVPVGRVETGTMKPGDVVTFAPANVTTEV




KSIEMHHEQLAEATPGDNVGFNVKNVSVKDIRRGNVCGNSKNDPP




KEAADFTAQVIILNHPGQIGNGYAPVLDCHTCHIACKFAEIESKIDRR




SGKELEKNPKSIKSGDAAMVRMVPQKPMCVEVFNDYAPLGRFAVR




DMRQTVAVGIIKAVTKKDGGAGKVTKAAAKAAKK


 


TcG6
SEQ ID
MQSELSGILSRIPAAVIGTILADESCKTVWFFNPKSREVISMDALRSL



NO: 7
PNPPSNSGADATERHLVYGMMRVRNQGVMFERDHIQRLYENCVL




AATSKPLTDEATLPFPVEGVTQSIREYILSEHKESGDINLKFVTWLPP




FSNSLTTAEAWQKFLSDFSYVVYFVKSFFPPKEWYTEGIRISLLYNA




RRHTPNAKIIQAPLRSRAKSLQDSSGAFEVFFVWDKEAHFLVPEGS




RSNYLLVTEDGHLCCSLAV


 


TcG7
SEQ ID
MLATHGRGRRVQGAVGAVFSFEEGKRGKTRRAPLTSQNARKKKT



NO: 8
VKSIAASCGADPDILHERNSTALLKEGDGVVYSAVPKYKQSRLGVL




LQHPLYSPHVVCCRFVCCVRLRRGWM


 


TcG8
SEQ ID
MSDNHQLEYKRGLEDARRHRSRTEDNWLRASVGPLLWFGVPFAV



NO: 9
AWLYLRRQAPASAKINPFGGMMEQMMPIKKRQFRVDVKGTKFEDV




IGIPEAKQEVQQYVEFLTNPNKFTRLGARLPKGRLLTGEPGTGKTLL




AKAVAGEADVPFFSCSGSDFIELMGGSGPKRVRELFEEARSSAPAI




VFIDEIDAIGSRAGKIGGSVSSEENRTINQLLAELDGLNTGTDAIIVIA




ATNFQDNIDKALLREGRFDRKVNIEMPDKAARVDIFKHYLNRVGTG




DPRGRKVDEEGEPLPTNEKVDNLELARELADLTPGVSPATIATIVNE




AALQSGIREKRLVDKESILEAVDNTLVGRKHRNRQSVTSLRRTAIHE




AGHALTAWMLPSVKQVLKVSVVPQ
















TABLE 2







Screening immunogenic potential of antigens as DNA vaccine in mice.












Elicitation of immune response 
Pathological parameters 




by vaccine
after challenge infection*













Immunization 

Antibodies
CTL
Th1 cytokine
Control of
Percent


with
Mice
(IgG + M)
activity
IFNγ, IL-12
Inflammation 
Survivala-c





None

−
−
−
−
 10c


ASP-1
C3H/HeSnJ,
+/−
+
+
+
 40b



C57BL/6







TSA-1
Balb/c, C3H/He,
+/−
+
+
+
 30b



C57B/6







ASP-2
C3H/HeSnJ,
+
++
++
++
 62b



C57BL/6







ASP-1 + ASP-2 + 
C3H/HeSnJ,
+
++
++
++
 68a


TSA-1
C57BL/6







ASP-2 + IL-12 + 
C3H/HeSnJ,
++
+++
+
+++
 80a


GM-CSFd
C57BL/6







TcG1 + IL-12 +
C57BL/6
++
ND
+
++
 90b


GM-CSFd








TcG2 + IL-12 + 
C57BL/6
++
ND
+
++
 92b


GMCSFd








TcG4 + IL-12 + 
C57BL/6
++
ND
+
+++
100b


GMCSFd








ASP-1 + ASP-2 +
C3H/HeSnJ,
+++
+++
++
+++
 83a


TSA-1 + IL-12 + 
C57BL/6







GM-CSFd





Mice were intra-muscularly immunized with antigen-encoding plasmids ± cytokine expression constructs (33 μg each DNA/mouse) twice at six-week intervals. Two week after 2nd immunization, mice were either used for measuring immune responses, or challenged with T. cruzi.


*Immunization protocol provided variable degree of protection in different mouse strains.


a-cUpon challenge infection, immunized animals exhibited very low (≦10%)a, moderate (~50%)b or similarc parasitemia as detected in un-immunized/infected animals (data presented are from the animal model that exhibited best protection).


dImmunization with these antigens was effective in decreasing the severity of chronic disease, evaluated by histopathological analysis of cardiac tissue biopsies..


A “+” or “−” sign indicates the effectiveness or limitation of the genetic vaccine in eliciting immune responses and protection from T. cruzi infection, respectively.


ND: not determined.






Example 4
Immunogenicity of Vaccine Candidates in Dogs
The protective efficacy of selected vaccine candidates in dogs was determined. The candidate antigens included in dog studies were those that have exhibited maximal protection in murine studies.
TcVac1R Vaccine
pCDNA3 encoding TcG1, TcG2 and TcG4+ IL-12 and GM-CSF expression plasmids. 100 μg each plasmid, total 600 μg DNA. Four doses, intramuscular delivery, 2-week intervals.
TcVac2R Vaccine
Two doses of TcVac1R followed by two doses of recombinant proteins (TcG1, TcG2, TcG4 with saponin adjuvant (DNA vaccine: im, 600-μg total DNA/dog; protein vaccine: id, 300 μg protein/dog, all doses at 2-week intervals). The recombinant proteins (TcG1, TcG2, and TcG4) were prepared in E. coli. No other study has demonstrated the protection afforded by this cocktail of antigens against T. cruzi in any model of disease.
Example 5
Antibody Response
T. cruzi and antigen-specific antibody response were determined in sera obtained from vaccinated dogs before each immunization, and 2 weeks after the last immunization. Negative control: sera from dogs immunized with vector only. Positive control: Sera from T. cruzi-infected dogs. It was found that after a second dose of DNA vaccine, antigen-specific antibody responses were elicited and these were enhanced by booster immunization with recombinant protein doses of TcVac2R. An antibody response to individual candidate genes was elicited in vaccinated dogs, and it was similar to that detected in chronically infected dogs. Shown in FIG. 4 are the parasite- and recombinant antigen-specific antibody response in sera collected after the last immunization.
Example 6
Trypanolytic Activity
Trypanolytic activity correlates with protection from T. cruzi infection as antibodies to surface proteins (plus complement) induce damage to infective trypomastigotes [20, 21]. Trypanocidal activity of the antibodies elicited was determined in dogs vaccinated with TcVac1R using procedures standardized in the lab [18]. The sera from vaccinated dogs, obtained after 4th immunization, provided ≧80% lytic efficiency (1:8 dilution). In comparison, sera from T. cruzi-infected dogs exposed to multiple parasite proteins exhibited 90% lytic activity. No parasite lysis was observed with negative control sera from dogs immunized with empty vector, or when heat-inactivated immune sera or heat-inactivated complement were used. Together, these data show that dogs immunized with TcVac1R elicit antigen-specific antibody responses that are trypanolytic in nature, and hence capable of providing protection from T. cruzi infection.







TABLE 3







Trypanolytic activity of antisera from vaccinated dogs











% lytic activity




Sera dilution












Antiserum from dogs immunized with
1:4
1:8
1:16
















Vector only
0
0
0



TcVac2R
90
81
62



T. cruzi-infected
100
92
81







Chronic serum was obtained from lab-infected dogs. Immune sera from vaccinated dogs were obtained after 4th immunization (as for FIG. 3). T. cruzi trypomastigotes (5 × 104/25 μl were incubated for 4 h at 37° C., 5% CO2 with 25 μl two-fold dilution of sera samples + 25 μl/well human complement (Sigma). The live, freely moving parasites were counted by light microscopy. Parasites that stained positively with 0.03% trypan blue were considered dead. All samples were analyzed in triplicate.



Percent trypanocidal efficiency: (Total parasites − free parasites after incubation/Total parasites) × 100



SD was ≦10%, n = 3/gp.






Example 7
TcVac3R Vaccine
Protective and Transmission Blocking Efficacy
To simplify vaccine composition and reduce the cost of production, TcVac3R was designed in which recombinant proteins were replaced by equivalent amount of protein lysate of T. rangeli (non-pathogenic in mammals and humans).
TcVac3R Vaccine
Two doses of DNA vaccine containing four expression plasmids+cytokine expression plasmids followed by two doses of T. rangeli lysates with saponin adjuvant (n=6, DNA vaccine: im, 600-μg DNA/dog; T. rangeli lysate: id, 400 μg protein/dog, all doses at 3-week intervals). Vaccinated dogs exhibited up to 8-fold decline in acute parasitemia (FIG. 5A), and a significant decline in myocardial pathology evidenced by decreased fibrosis in left ventricle and decreased dilation of right ventricle (FIG. 5B) when compared to controls that were immunized with empty vector only and infected with T. cruzi. Clinical exam (EKG analysis) of TcVac3R vaccinated dogs detected no alterations while control+ dogs exhibited symptoms of conduction problems, myocarditis and/or pericarditis (Table 4).







TABLE 4







Echocardiographic findings










TcVac1R
TcVac3R
CONTROL+
CONTROL−





1.-Ventricular dilatation
1.-No alterations 
1.-Repolarization problems
1.-No alterations




myocarditis



2.-Repolarization problems
2.-No alterations
2.-Myocarditis
2.-No alterations


myocarditis





3.-No alterations
3.-No alterations 
3.-Pericarditis
3.-No alterations









In the above experiments, the infectivity of the dogs to triatomines was determined by feeding the insects on abdomen skin using a membrane-feeding apparatus. Importantly, xenodiagnostic studies (FIG. 5C) showed that >88% of bugs (23/26) fed on control+ dogs were infected while only 50% bugs (15/30) bugs fed on TcVacR vaccinated dogs became infected, thus demonstrating at least 50% reduction in infectivity (Table 5).







TABLE 5







Transmission blocking efficiency.












# infected/Total bugs




Groups
fed on dogs
% Infectivity















TcVac1R
10/19
52.63



TcVac3R
15/30
50



CONTROL+
23/26
88.46



CONTROL−
0
0










Triatomines (6 per dog) were fed on vaccinated or control dogs (6 dogs per group) at day 60 pi. The infectivity of triatomines was determined by light microscopic examination for metacyclic trypomastigotes in diluted feces of bugs.

Example 8
Utilizing TcG1, TcG2, and TcG4 for Screening Sero-Prevalence and Diagnosis of Exposure to T. cruzi 
Three proteins, encoded respectively by TcG1, TcG2 and TcG4, are proposed herein for the diagnosis of exposure to T. cruzi infection. These proteins serve as diagnostic markers, are useful in screening blood banks, evaluating seroprevalence in humans, and animal population in domestic or non-domestic environments. An ELISA kit containing the three antigens together or a dip-stick coated with the three antigens together will provide >98% sensitivity and >98% specificity for diagnosis of exposure to T. cruzi. 
Example 9
TcG1, TcG2, TcG4 are Expressed in Infective Stage of T. cruzi 
To establish the diagnostic utility of TcG1, TcG2, and TcG4, it is important that these genes are expressed in infective stage of T. cruzi and expressed in diverse strains of T. cruzi. For this, RT-PCR was performed to evaluate mRNA levels for TcG1, TcG2 and TcG4 (along with other genes) in different stages of T. cruzi. Total RNA and cDNA from the epimastigote (E), trypomastigote (T), and amastigote (A) forms of T. cruzi was obtained. The cDNA (2 μl) from each stage was subsequently amplified by PCR in a 50 μl reaction volume using 2.5 U of Taq polymerase and 1 _l of 20 _M gene-specific forward and reverse primers. Individual amplicons were electrophoresed on 1% agarose gel, and imaged. GAPDH and GPI8 genes that are constitutively expressed in all three stages of T. cruzi were used as positive control (FIG. 6A). These data demonstrated that TcG1, TcG2, and TcG4 are expressed in epimastigote and amastigote stages and TcG1 and TcG4 are also expressed in trypomastigote stage of T. cruzi [31].
Example 10
TcG1, TcG2, and TcG4 Encoding Sequences are Present in Diverse Strains of T. cruzi 
Genomic DNA was isolated from different T. cruzi strains obtained from endemic countries. Briefly, parasites were lysed in lysis buffer (50 mM Tris-HCl, pH 8, 62.5 mM EDTA, 2.5 M LiCl, 4% (v/v) Triton X-100) (109 parasites/ml). Samples were extracted with an equal volume of phenol:chloroform:isoamylalcohol (24:24:1), centrifuged at 12,000 g for 5 min, and the total DNA in top aqueous phase purified by ethanol precipitation. PCR amplification was then carried out of the selected genes for 35 cycles in a 50 μl reaction volume with 100 ng of genomic DNA and 1 _l of 20 _M gene-specific forward and reverse primers. PCR amplified products were resolved by agarose gel electrophoresis, and imaged (FIG. 6B). These data demonstrate that TcG1, TcG2, and TcG4 are phylogenetically conserved in CL Brenner (CL), Sylvio X10 (S), Brazil (Br), Y strain of T. cruzi (P: plasmid DNA used as control). Genomic DNA from Leishmania major and Trypanosoma brucei were used as template in parallel reactions. TcG1, TcG2 and TcG4 were not amplified in genomic DNA of Leishmania and Trypanosoma brucei, thus establishing their specificity to T. cruzi [31].
Example 11
TcG1, TcG2, TcG4 Elicit Antigen-Specific Antibody Response in Mice
C57BL/6 mice (8/group) were immunized with pCDNA3 eukaryotic expression plasmids encoding TcG1, TcG2, and TcG4 followed by recombinant proteins generated in E. coli (named TcVac2). Sera were collected 2-weeks after second immunization, and an enzyme-linked immunosorbent assay (ELISA) was performed. Briefly, 96-well plates were coated with recombinant antigen (20 μg/ml, 50 μl/well) or T. cruzi lysate (TcTL) (50% trypomastigotes/50% amastigotes, 109/ml, 50 μl/well), blocked with 5% non-fat dry milk. Plates were then sequentially incubated at room temperature with sera samples (1:50-1:1000 dilution, 50 μl/well) in triplicate, followed by appropriate HRP-conjugated secondary antibody (1:5000 dilution). All dilutions were made in PBST-0.5% NFDM. Color was developed with 100-μl/well Sure Blue TMB substrate (Kirkegaard & Perry Labs), reaction was stopped with 2N sulfuric acid, and antibody response was monitored at 450 nm using a Spectramax microplate reader (FIG. 7).
FIG. 7A shows the sera levels of parasite- and antigen-specific antibodies, measured two-weeks after the last immunization. Various sera dilutions were tested (1:50-1:1000) to identify maximum signal/noise ratio. FIG. 7B shows sera levels (1:100 dilution) of antibody response in normal mice (NM), and mice injected with pCNDA3 vector only (Vector), or cytokine (cyt) adjuvants only as control. TcVac2 is defined above. All data are presented as mean value from triplicate observations/sample (n=at least 6). Standard deviation is shown in FIG. 7B (##p<0.001).
These data demonstrate that TcG1, TcG2, and TcG4 are immunogenic in mice, and immune system of mice recognizes these proteins and elicit antigen-specific antibody response. The antigen-specific response was additive, and co-delivery of these antigens did not inhibit the immunogenicity of other antigens. These data also demonstrate the specificity of the antibodies against the three antigens.
Example 8
Immunization with TcG1, TcG2, TcG4 Elicits Antigen-Specific Antibody Response in Dogs
As above, dogs (6/group) were immunized with TcG1, TcG2 and TcG4 (i.e., TcVac2). Sera were collected 2-weeks after immunization, and ELISA was performed using 1:50 dilution of sera samples (FIG. 8A). In some experiments, 2-weeks after immunization, dogs were infected with T. cruzi trypomastigotes and sera samples were collected at 60 days post-infection (FIG. 8B). Sera samples from naïve dogs and dogs experimentally or naturally infected with T. cruzi were used as controls. FIG. 8 shows sera level of antibodies in dogs immunized with candidate antigens (FIG. 8A) and infected with T. cruzi (FIG. 8B), measured by ELISA. The data demonstrate that TcG1, TcG2, and TcG4 are immunogenic in dogs, and antigen-specific antibody responses are elicited in dogs immunized with the candidate antigens (FIG. 8A). FIG. 8B shows that in response to infection with T. cruzi, both vaccinated and non-vaccinated dogs mount antibody response to T. cruzi antigenic lysate (TcTL) as well as to TcG1, TcG2 and TcG4 antigens. The detection of antigen-specific antibody responses in dogs infected by T. cruzi suggest the potential utility of these antigens in screening the prevalence of T. cruzi infection in dogs.
Example 9
Prevalence of Antibodies to TcG1, TcG2, and TcG4 in Sera Samples of Human Inhabitants
Mexico: All samples came from clinics located in areas where triatomine infestation and the prevalence of T. cruzi was earlier reported. Samples were obtained from randomly selected adults. A total of 1481 human sera samples, collected from Chiapas, Mexico, were first analyzed by ELISA using T. cruzi lysate (TcTL) as antigen for IgG response (FIG. 9A). The 121 samples identified as seropositive using TcTL and an equivalent number of seronegative samples (randomly chosen) were then tested for TcG1-, TcG2-, and TcG4-specific IgG and IgM antibody response by ELISA.
FIG. 9 shows a box plot of ELISA data, graphically depicting the OD values for seronegative (gray box) and seropositive (white box) samples from Mexico, identified by ELISA. (FIG. 9A): IgG response, (FIG. 9B): IgM response. The standard deviation for triplicate observations for each sample was <12%. The horizontal lines of the box (bottom to top) depict the lower quartile (Q1, cuts off lowest 25% of the data); median (Q2, middle value); and upper quartile (Q3, cuts off the highest 25% of the data). The lower and upper whiskers depict the smallest and largest non-outlier observations, respectively, and solid dots represent the outliers. The spacing between the different parts of the box indicates the degree of dispersion (spread). The mean S.D. optical density (O.D.) value for the seronegative and serpositive populations was 0.44±0.19 and 1.64±0.45, respectively. An 8.5% seroprevalence for T. cruzi-specific IgG antibodies was identified in the inhabitants of Chiapas (n=121 out of 1481) using TcTL antigen. The 121 samples identified as seropositive using TcTL and an equivalent number of seronegative samples (randomly chosen) were then tested for TcG1-, TcG2-, and TcG4-specific IgG and IgM antibody response by ELISA. These data demonstrate that TcG1, TcG2 and TcG4 are equally or more effective in diagnosing the exposure to T. cruzi (FIG. 9A). Importantly TcG1-specific IgM antibodies were found to be >3-fold higher than the TcTL-specific IgM antibodies in seropositive patients, suggesting that TcG1 antigen is useful in detecting the early antibody responses, and possibly distinguish acute exposure to T. cruzi. 
Argentina: Over 300 sera samples, which were diagnosed as seropositive by commercially available kits, were analyzed to evaluate the antibody response to TcG1, TcG2, and TcG4 antigens. ELISA was performed using plates coated with the T. cruzi lysate or TcG1, TcG2 and TcG4 antigens. FIG. 10 demonstrates that TcG1-, TcG2- and TcG4-specific IgG antibodies are detected in sera of chagasic patients from Argentina.
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Any patents or publications mentioned in this specification are indicative of the levels of those skilled in the art to which the invention pertains. These patents and publications are herein incorporated by reference to the same extent as if each individual publication was specifically and individually incorporated by reference.
One skilled in the art will readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. It will be apparent to those skilled in the art that various modifications and variations can be made in practicing the present invention without departing from the spirit or scope of the invention. Changes therein and other uses will occur to those skilled in the art which are encompassed within the spirit of the invention as defined by the scope of the claims.

## Claims

1. A method for detecting Trypanosoma cruzi infection in a subject, said method comprising the steps of:
contacting a sample from a subject that has not been administered a vaccine comprising a Trypanosoma cruzi TcG-1 protein, a Trypanosoma cruzi TcG-2 protein, or a Trypanosoma cruzi TcG-4 protein with a composition comprising an isolated Trypanosoma cruzi TcG-1 protein, an isolated Trypanosoma cruzi TcG-2 protein, or an isolated Trypanosoma cruzi TcG-4 protein; and
detecting binding of antibody in the sample to the isolated Trypanosoma cruzi TcG-1 protein, the isolated Trypanosoma cruzi TcG-2 protein, or the isolated Trypanosoma cruzi TcG-4 protein, wherein detection of antibody binding to the Trypanosoma cruzi protein(s) indicates that the subjected is infected with Trypanosoma cruzi.

2. The method of claim 1, wherein the antibody is IgG antibody.

3. The method of claim 1, wherein the antibody is IgM antibody.

4. The method of claim 1, wherein said sample is a serum or a blood sample.

5. The method of claim 1, wherein the sample is contacted with the Trypanosoma cruzi TcG-1 protein, the Trypanosoma cruzi TcG-2 protein, and the Trypanosoma cruzi TcG-4 protein.

6. A kit for detecting Trypanosoma cruzi infection comprising:
(a) an isolated Trypanosoma cruzi TcG-1 protein, Trypanosoma cruzi TcG-2 protein, or Trypanosoma cruzi TcG-4 protein coupled to a substrate; and
(b) a detection reagent.

7. The kit of claim 6, wherein
the Trypanosoma cruzi TcG-1 protein has the amino acid sequence of SEQ ID NO: 2;
the Trypanosoma cruzi TcG-2 protein has the amino acid sequence of SEQ ID NO: 3;
the Trypanosoma cruzi TcG-4 protein has the amino acid sequence of SEQ ID NO: 5.

8. The kit of claim 6, wherein the substrate is a dip stick.