# Patent

## Title
Fusion proteins and their use in the diagnosis and treatment of leishmaniasis

## Abstract

The present invention relates generally to a fusion protein made from a synthetic gene construct comprising of elements derived from the Leishmania antigens K26, K39, and K9. The fusion protein is particularly useful in the diagnosis of leishmaniasis, particularly visceral leishmaniasis in animals such as humans and dogs.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation application of U.S. patent application Ser. No. 13/560,565, filed Jul. 27, 2012 now U.S. Pat. No. 8,771,710 issued Jul. 8, 2015, which is a continuation application of U.S. patent application Ser. No. 12/497,178, filed Jul. 2, 2009, now U.S. Pat. No. 8,231,881, which claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Patent Application No. 61/078,255, filed Jul. 3, 2008, the contents of which are hereby incorporated by reference in their entirety.


SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE
The content of the following submission on ASCII text file is incorporated herein by reference in its entirety: a computer readable form (CRF) of the Sequence Listing (file name: 712192001802_Sequence_Listing.txt, date recorded: May 22, 2014, size: 57,239 bytes).
BACKGROUND
1. Technical Field
The present invention relates generally to fusion proteins made from a synthetic chimeric gene construct comprising sequences from K26, K39, and K9 and their use in the diagnosis and treatment of leishmaniasis.
2. Description of the Related Art
Leishmania organisms are intracellular protozoan parasites of macrophages that cause a wide range of clinical diseases in humans and domestic animals, primarily dogs. In some infections, the parasite may lie dormant for many years. In other cases, the host may develop one of a variety of forms of leishmaniasis. For example, the disease may be asymptomatic or may be manifested as sub-clinical visceral leishmaniasis, which is characterized by mild symptoms of malaise, diarrhea and intermittent hepatomegaly. Patients with sub-clinical or asymptomatic disease usually have low antibody titers, making the disease difficult to detect with standard techniques. Alternatively, leishmaniasis may be manifested as a cutaneous disease, which is a severe medical problem but is generally self-limiting, or as a highly destructive mucosal disease, which is not self-limiting. Finally, and most seriously, the disease may be manifested as an acute visceral infection involving the spleen, liver and lymph nodes, which, if left untreated, is generally a fatal disease. Symptoms of acute visceral leishmaniasis include hepatosplenomegaly, fever, leukopenia, anemia and hypergamma-globulinemia.
Three main clinical variants of this disease are known: cutaneous, mucocutaneous, and visceral. Cutaneous leishmaniasis can manifest itself as a single skin ulceration at the site of the sandfly bite appearing soon after infection or months later as disseminated lesions. Mucocutaneous syndrome develops as the cutaneous form, but progresses months or years later to lesions of the mouth, nose, or pharynx. The major long-term effects of cutaneous and mucocutaneous disease are scarring. Visceral leishmaniasis has an incubation period of 3-6 months and involves the reticuloendothelial system.
Clinical manifestations of visceral leishmaniasis include enlargement of the liver and spleen, fever, anemia, and weight loss. In the absence of treatment, symptomatic visceral disease often ends in death. In recent years, the coexistence of HIV and Leishmania species causing visceral disease has resulted in several hundreds of cases of dually infected individuals (Berman, J. D., (1997) Clin. Infect. Dis. 24:684). The World Health Organization recently estimated in 2000 that leishmaniasis affects people in 88 countries, with 350 million at risk of contracting the disease and about two million new cases each year. The devastating impact of this disease is exemplified by the recent epidemic of visceral leishmaniasis in the Sudan, which claimed an estimated 100,000 lives (Seaman, J., et al. (1996) Int. J. Epidemiol. 25:862). This disease is frequently a threat in military operations, as demonstrated by the outbreak of viscerotropic leishmaniasis during the Gulf War (Magill, J., et al. (1993) N Engl J Med 328:1383).
Leishmaniasis is a serious problem in much of the world, including Brazil, China, East Africa, India and areas of the Middle East. The disease is also endemic in the Mediterranean region, including southern France, Italy, Greece, Spain, Portugal and North Africa. The number of cases of leishmaniasis has increased dramatically in the last 20 years, and millions of cases of this disease now exist worldwide. About 2 million new cases are diagnosed each year, 25% of which are visceral leishmaniasis. There are, however, no vaccines or effective treatments currently available.
Leishmaniasis is caused by several species of Leishmania. These unicellular organisms of the order Kinetoplastida are related to trypanosomes, the causative organisms of Sleeping Sickness in Africa and Chagas' disease in South America. Leishmania parasites commonly exist in two distinct forms, the motile promastigote of the insect vector and the sessile amastigote present in the mammalian host. Promastigotes are transmitted to humans by the bite of infected phlebotomine sandflies, which are found throughout the world's inter-tropical and temperate regions. Upon delivery into the mammalian host, promastigotes infect macrophages of the reticuloendothelial system and transform into amastigotes.
Accurate diagnosis of leishmaniasis is frequently difficult to achieve. There are 20 species of Leishmania that infect humans, including L. donovani, L. chagasi, L. infantum, L. major, L. amazonensis, L. braziliensis, L. panamensis, L. mexicana, L. tropica, and L. guyanensis, and there are no distinctive signs or symptoms that unambiguously indicate the presence of Leishmania infection. Parasite detection methods have been used, but such methods are neither sensitive nor clinically practical. Current skin tests typically use whole or lysed parasites. Such tests are generally insensitive, irreproducible and prone to cross-reaction with a variety of other diseases. In addition, the preparations employed in such tests are often unstable.
Thus, there is a need for improved methods for the detection of Leishmania infection. For example, there is a need in the art for more sensitive and specific methods for detecting Leishmania infection, and for identifying those asymptomatic Leishmania infections that are likely to progress to acute visceral infections. The present invention fulfills these needs and further provides other related advantages.
BRIEF SUMMARY
The present invention relates generally to compositions comprising at least two heterologous Leishmania antigens, fusion polypeptides comprising the antigens, and polynucleotides encoding the antigens and fusions, wherein the Leishmania antigens are selected from K39, K26, and/or K9. The present invention also relates methods of using the polypeptides and polynucleotides of the invention in the diagnosis, treatment, and prevention of leishmaniasis. The antigens of the invention, when employed in combination and/or as fusion polypeptides or polynucleotides as described herein, offer improved and unexpected advantages, and are particularly useful in the context of leishmaniasis diagnostics and vaccine development.
Therefore, according to one embodiment, the present invention provides an isolated fusion polypeptide comprising two or more Leishmania antigens selected from the group consisting of K26, K39, and K9, or immunogenic portions or variants thereof. In a related embodiment, an isolated fusion polypeptide comprises at least all three of the above Leishmania antigens, wherein at least one of the antigens is isolated from Leishmania donovani. 
In particular embodiments, fusion polypeptides of the invention comprise a first immunogenic portion comprising at least residues 142-267 of K26 (SEQ ID NO: 5); a second immunogenic portion comprising at least residues 2110-2343 of K39 (SEQ ID NO: 6); and a third immunogenic portion comprising at least residues 1-399 of K9 (SEQ ID NO: 7). In more particular embodiments, a fusion polypeptide of the present invention comprises an amino acid sequence as set forth in amino acid residues 10-262 of SEQ ID NO: 8. In certain embodiments, the fusion polypeptide comprises an N-terminal amino acid sequence of MHHHHHHTS (SEQ ID NO: 21). In certain other embodiments, the fusion polypeptide comprises an amino acid sequence as set forth in SEQ ID NO: 8.
In various embodiments, the present invention provides isolated polynucleotides encoding a fusion polypeptide of the present invention.
The present invention also provides an isolated antibody, or antigen binding fragment that specifically bind a fusion polypeptide as described herein throughout.
In another embodiment, the invention contemplates, pharmaceutical composition comprising a fusion polypeptide of the present invention, or an isolated antibody or antigen binding fragment recognizing a fusion polypeptide of the present invention, or a polynucleotide encoding a fusion polypeptide of the present invention, in combination with a physiologically acceptable carrier.
In a related embodiment, the present invention contemplates vaccine compositions comprising a fusion polypeptide of the present invention, or an isolated antibody or antigen binding fragment recognizing a fusion polypeptide of the present invention, or a polynucleotide encoding a fusion polypeptide of the present invention, in combination with a non-specific immune response enhancer.
In particular embodiments, the present invention provides methods to detect asymptomatic or sub-clinical Leishmania infection in a biological sample selected from the group consisting of sera, blood, and saliva, comprising: contacting a biological sample with a fusion polypeptide comprising two or more Leishmania antigens selected from the group consisting of K26, K39, and K9, or immunogenic portions thereof; and detecting in the biological sample the presence of antibodies that bind to the fusion polypeptide, thereby detecting asymptomatic sub-clinical or active Leishmania infection in the biological sample. In more particular embodiments, a method to detect asymptomatic or sub-clinical Leishmania infection in a biological sample employs a fusion polypeptide comprising: a first immunogenic portion comprising at least residues 142-267 of K26 (SEQ ID NO: 5); a second immunogenic portion comprising at least residues 2110-2343 of K39 (SEQ ID NO: 6); and a third immunogenic portion comprising at least residues 1-399 of K9 (SEQ ID NO: 7). In yet more particular embodiments, the fusion polypeptide comprises an amino acid sequence as set forth in residues 10-262 of SEQ ID NO: 8. In yet more particular related embodiments, the fusion polypeptide further comprises an N-terminal amino acid sequence of MHHHHHHTS (SEQ ID NO: 21).
In related embodiments, methods for detecting asymptomatic or sub-clinical Leishmania infection in a biological sample use a fusion polypeptide bound to a solid support, wherein the solid support may comprise, for example, nitrocellulose, latex or a plastic material. In certain embodiments, the methods further comprise i) removing unbound sample from a solid support; ii) adding a detection reagent to the solid support; and iii) determining the level of detection reagent bound to the solid support, relative to a predetermined cutoff value, thereby detecting asymptomatic or sub-clinical Leishmania infection in the biological sample.
In various embodiments, the present invention provides methods of identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis, comprising: contacting a biological sample obtained from a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis with a first polypeptide that is a fusion polypeptide comprising two or more Leishmania antigens selected from the group consisting of K26, K39, and K9, or immunogenic portions thereof, the biological sample being selected from the group consisting of sera, blood, and saliva; and independently contacting the biological sample with a second polypeptide comprising an amino acid sequence as set forth in SEQ ID NOs: 6, 10 or 11; and detecting in the sample the presence of antibodies that bind to at least one of the first and second polypeptides, thereby identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis.
In particular embodiments, the methods of identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis employ a fusion polypeptide comprising a first immunogenic portion comprising at least residues 142-267 of K26 (SEQ ID NO: 5); a second immunogenic portion comprising at least residues 2110-2343 of K39 (SEQ ID NO: 6); and a third immunogenic portion comprising at least residues 1-399 of K9 (SEQ ID NO: 7). In yet more particular embodiments, the fusion polypeptide comprises an amino acid sequence as set forth in amino acid residues 10-262 of SEQ ID NO: 8. In yet more particular related embodiments, the fusion polypeptide further comprises an N-terminal amino acid sequence of MHHHHHHTS (SEQ ID NO: 21).
In related embodiments, methods of identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis employ a fusion polypeptide bound to a solid support, wherein the solid support may comprise, for example, nitrocellulose, latex or a plastic material. In certain related embodiments, the methods further comprise i) removing unbound sample from each solid support; ii) adding a detection reagent to each solid support; and iii) comparing the level of detection reagent bound to each solid support, relative to a predetermined cutoff value, therefrom identifying a patient afflicted with asymptomatic or sub-clinical leishmaniasis that is likely to develop acute visceral leishmaniasis.
In particular embodiments, the detection reagent comprises a reporter group conjugated to a binding agent. In related embodiments the binding agent is selected from the group consisting of anti-immunoglobulin, Protein G, Protein A and lectins. In further related embodiments, the reporter group is selected from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, colloidal gold, biotin and dye particles.
In various other embodiments, the present invention provides diagnostic kits for detecting asymptomatic or sub-clinical visceral leishmaniasis in a biological sample. In particular embodiments, kits for detecting asymptomatic or sub-clinical visceral leishmaniasis in a biological sample, wherein the sample is selected from the group consisting of sera, blood, and saliva, comprise a fusion polypeptide comprising two or more Leishmania antigens selected from the group consisting of K26, K39, and K9, or immunogenic portions thereof; and a detection reagent.
In certain embodiments, a diagnostic kit for identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis, contains a first polypeptide that is a fusion polypeptide comprising two or more Leishmania antigens selected from the group consisting of K26, K39, and K9, or immunogenic portions thereof; and a second polypeptide comprising an amino acid sequence as set forth in SEQ ID NOs: 10 or 11; and a detection reagent.
Kits of the present invention may further comprise, a detection reagent comprising a reporter group conjugated to a binding agent and/or a binding agent is selected from the group consisting of anti-immunoglobulin, Protein G, Protein A and lectins and/or a reporter group is selected from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, colloidal gold, biotin and dye particles.



BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
FIG. 1 shows a schematic diagram of the K28 fusion gene construct, which comprises an N-terminal 9 amino acid motif comprising a 6×HIS tag (i.e., 6 histidine residues), polynucleotides 142-267 of an LdK26 gene sequence (SEQ ID NO: 1), polynucleotides 2110-2343 of an LdK39 gene sequence (SEQ ID NO: 2), and polynucleotides 1-399 of an LdK9 gene sequence (SEQ ID NO: 3).
FIG. 2 shows a comparison of the ability of K28, K39, and K9 antigens to detect VL in the serum of human patients from Venezuela.
FIG. 3 shows a comparison of the ability of K9, K26, K28, and K39 antigens to detect VL in the serum of canines from Venezuela.



BRIEF DESCRIPTION OF THE SEQUENCE IDENTIFIERS
SEQ ID NO: 1 represents polynucleotides 142-267 of a L. donovani K26 gene sequence, which encode an immunogenic portion of the K26 antigen.
SEQ ID NO: 2 represents polynucleotides 2110-2343 of a L. donovani K39 gene sequence, which encode an immunogenic portion of the K39 antigen.
SEQ ID NO: 3 represents polynucleotides 1-399 of a L. donovani K9 gene sequence, which encodes an immunogenic portion and the full-length K9 antigen.
SEQ ID NO: 4 represents the polynucleotide sequence of a synthetic gene, K28, which comprises an N-terminal 9 amino acid motif comprising a 6×HIS tag, the polynucleotide sequence of SEQ ID NO: 1, fused to the polynucleotide sequence of SEQ ID NO:2, which is fused to the polynucleotide sequence of SEQ ID NO3. The ORF begins at nucleotide 4.
SEQ ID NO: 5 represents the amino acid sequence of an immunogenic polypeptide encoded by polynucleotides 142-267 of a L. donovani K26 antigen.
SEQ ID NO: 6 represents the amino acid sequence of an immunogenic polypeptide encoded by polynucleotides 2110-2343 of a L. donovani K39 antigen.
SEQ ID NO: 7 represents the amino acid sequence of the immunogenic full-length polypeptide encoded by polynucleotides 1-399 of a L. donovani K9 antigen.
SEQ ID NO: 8 represents the amino acid sequence of the K28 polypeptide encoded by SEQ ID NO: 4.
SEQ ID NO: 9 represents the amino acid sequence of a single repeat unit of a L. donovani K26 antigen.
SEQ ID NO: 10 represents the amino acid sequence of a single repeat unit of a L. donovani K39 antigen.
SEQ ID NO: 11 represents the amino acid sequence of a single repeat unit of a L. donovani K39 antigen.
SEQ ID NO: 12 represents a polynucleotide sequence encoding a single repeat unit of a L. donovani K26 antigen according to SEQ ID NO: 9.
SEQ ID NO: 13 represents a polynucleotide sequence encoding a single repeat unit of a L. donovani K26 antigen according to SEQ ID NO: 9.
SEQ ID NO: 14 represents a polynucleotide sequence encoding the single repeat unit of a L. donovani K39 antigen according to SEQ ID NO: 10.
SEQ ID NO: 15 represents a polynucleotide sequence encoding the single repeat unit of a L. donovani K39 antigen according to SEQ ID NO: 11.
SEQ ID NO: 16 represents the full-length polynucleotide sequence of a L. donovani K26 gene.
SEQ ID NO: 17 represents the full-length polynucleotide sequence of a L. donovani K39 gene.
SEQ ID NO: 18 represents the full-length polynucleotide sequence of a L. donovani K9 gene.
SEQ ID NO: 19 represents the amino acid sequence encoded by SEQ ID NO: 16.
SEQ ID NO: 20 represents the amino acid sequence encoded by SEQ ID NO: 17.
SEQ ID NO: 21 represents an illustrative N-terminal histidine tag used in the recombinant production of polypeptides of the present invention.
DETAILED DESCRIPTION
Leishmania Antigens and Fusions Thereof
The present invention relates generally to compositions and methods of using Leishmania antigens. The compositions of the present invention generally comprise at least two heterologous antigens or immunogenic portion thereof of a Leishmania species. Leishmania antigen sequences can be obtained, for example, from the National Center for Biotechnology Information (NCBI) database for a variety of Leishmania species, including L. donovani, L. chagasi, L. infantum, L. major, L. amazonensis, L. venezuelensis, L. braziliensis, L. panamensis, L. mexicana, L. tropica, and L. guyanensis. 
In one aspect, the present invention provides isolated Leishmania polypeptides, as described herein, including fusion polypeptides, and compositions containing the same. Generally, a polypeptide of the present invention will be an isolated polypeptide and may comprise a polypeptide fragment (e.g., an antigenic/immunogenic portion), multiple polypeptide fragments (e.g., a fusion polypeptide), or a full-length polypeptide of an amino acid sequence from two or more of the Leishmania genes, including, but not limited to K26, K39, and/or K9. One of ordinary skill in the art would appreciate that antigenic polypeptide fragments could also be obtained from those already available in the art. Polypeptides of the invention, antigenic/immunogenic fragments thereof, and other variants may be prepared using conventional recombinant and/or synthetic techniques.
In certain embodiments, the polypeptides of the present invention are fusion polypeptides. In particular embodiments, the fusion polypeptides comprise K26, K39, and/or K9 antigens or immunogenic portions thereof, which are antigenic/immunogenic, i.e., they react detectably within an immunoassay (such as an ELISA or T cell stimulation assay) with antisera and/or T cells from an infected subject. Screening for immunogenic activity can be performed using techniques well known to the skilled artisan. For example, such screens can be performed using methods such as those described in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1988. In one illustrative example, a polypeptide of the present invention (e.g., a fusion polypeptide) may be immobilized on a solid support and contacted with patient sera to allow binding of antibodies within the sera to the immobilized polypeptide. Unbound sera may then be removed and bound antibodies detected using, for example, 125I-labeled Protein A.
As would be recognized by the skilled artisan, the fusion polypeptides of the present invention may comprise antigenic or immunogenic portions or fragments of the Leishmania K26, K39, and/or K9 polypeptides disclosed herein. An “immunogenic portion,” as used herein, is a fragment of an immunogenic polypeptide of the invention that itself is immunologically reactive (i.e., specifically binds) with the B-cells and/or T cell surface antigen receptors that recognize the polypeptide. Immunogenic portions may generally be identified using well known techniques, such as those summarized in Paul, Fundamental Immunology, 5th ed., Lippincott Williams & Wilkins, 2003 and references cited therein. Such techniques include screening polypeptides for the ability to react with antigen-specific antibodies, antisera and/or T cell lines or clones. As used herein, antisera and antibodies are “antigen-specific” if they specifically bind to an antigen (i.e., they react with the protein in an immunoassay, and do not react detectably with unrelated proteins). Such antisera and antibodies may be prepared as described herein and using well-known techniques.
In a particular embodiment, an antigenic/immunogenic portion or polypeptide fragment of a fusion polypeptide of the present invention is a portion that reacts with antisera and/or T cells at a level that is not substantially less than the reactivity of the full-length fusion polypeptide (e.g., in an ELISA and/or T cell reactivity assay). Preferably, the level of immunogenic activity of the antigenic/immunogenic portion within a fusion polypeptide is at least about 50%, preferably at least about 70% and most preferably greater than about 90% of the immunogenicity for the full-length fusion polypeptide. In some instances, preferred immunogenic portions will be identified that have a level of immunogenic activity greater than that of the corresponding full-length fusion polypeptide, e.g., having greater than about 100% or 150% or more immunogenic activity. In particular embodiments, the immunogenicity of the full-length fusion polypeptide will have additive immunogenicity contributed by of each of the antigenic/immunogenic portions contained therein.
A fusion polypeptide of the invention may also comprise one or more polypeptides that are immunologically reactive with T cells and/or antibodies generated against a polypeptide of the invention, particularly a polypeptide having an amino acid sequence disclosed herein, or to an immunogenic fragment or variant thereof. In particular embodiments, the polypeptide is a fusion polypeptide as described herein.
In another embodiment of the invention, fusion polypeptides are provided that comprise two or more polypeptides that are capable of eliciting T cells and/or antibodies that are immunologically reactive with two or more polypeptides described herein, or two or more polypeptides encoded by contiguous polynucleotide sequences contained in the polynucleotide sequences disclosed herein, or immunogenic fragments or variants thereof, or to two or more polynucleotide sequences which hybridize to two or more of these sequences under conditions of moderate to high stringency.
The present invention also provides fusion polypeptides comprising fragments, of K26, K29, and/or K9 polypeptides, including antigenic/immunogenic fragments comprising at least about 5, 10, 15, 20, 25, 50, 75, 100, 150, 200, 250, 300, or 350 contiguous amino acids, or more, including all intermediate lengths, of a Leishmania K26, K39, and/or K9 antigen, such as those set forth herein, or those encoded by a polynucleotide sequence set forth herein.
In another aspect, fusion polypeptides of the present invention contain multiple copies of polypeptide fragments, repeats of polypeptide fragments, or multimeric polypeptide fragments, including antigenic/immunogenic fragments such as Leishmania K26, K39, and/or K9 polypeptides, comprising at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more contiguous fragments, in any order, and including all lengths of a polypeptide composition set forth herein, or those encoded by a polynucleotide sequence set forth herein. In another aspect, fusion polypeptides of the present invention may comprise two or more Leishmania antigen fragments as recited in SEQ ID NOs: 5-7, and 9-11. In a related aspect, the fusion polypeptide comprises the amino acid sequence set forth in SEQ ID NO: 8 or amino acids 10-262 of SEQ ID NO: 8.
In yet another aspect, the present invention provides fusion polypeptides comprising two or more variants of the Leishmania K26, K29, and/or K9 polypeptides described herein. Polypeptide variants generally encompassed by the present invention will typically exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identity (determined as described below), along its length, to a polypeptide sequence set forth herein. Preferably, such variants will have the same, similar or improved immunological activity relative to a native K26, K29, and/or K9 sequence.
A polypeptide “variant,” as the term is used herein, is a polypeptide that typically differs from a polypeptide specifically disclosed herein (e.g., Leishmania K26, K29, and/or K9 polypeptides) in one or more substitutions, deletions, additions and/or insertions. Such variants may be naturally occurring or may be synthetically generated, for example, by modifying one or more of the above polypeptide sequences of the invention and evaluating their immunogenic activity as described herein using any of a number of techniques well known in the art.
In many instances, a variant will contain conservative substitutions. A “conservative substitution” is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged. As described above, modifications may be made in the structure of the polynucleotides and polypeptides of the present invention and still obtain a functional molecule that encodes a variant or derivative polypeptide with desirable characteristics, e.g., with immunogenic characteristics. When it is desired to alter the amino acid sequence of a polypeptide to create an equivalent, or even an improved, immunogenic variant or portion of a polypeptide of the invention, one skilled in the art will typically change one or more of the codons of the encoding DNA sequence according to Table 1.
For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid sequence substitutions can be made in a protein sequence, and, of course, its underlying DNA coding sequence, and nevertheless obtain a protein with like properties. It is thus contemplated that various changes may be made in the peptide sequences of the disclosed compositions, or corresponding DNA sequences which encode said peptides without appreciable loss of their biological utility or activity.








TABLE 1





Amino Acids
Codons























Alanine
Ala
A
GCA
GCC
GCG
GCU




Cysteine
Cys
C
UGC
UGU


Aspartic acid
Asp
D
GAC
GAU


Glutamic acid
Glu
E
GAA
GAG


Phenylalanine
Phe
F
UUC
UUU


Glycine
Gly
G
GGA
GGC
GGG
GGU


Histidine
His
H
CAC
CAU


Isoleucine
Ile
I
AUA
AUC
AUU


Lysine
Lys
K
AAA
AAG


Leucine
Leu
L
UUA
UUG
CUA
CUC
CUG
CUU


Methionine
Met
M
AUG


Asparagine
Asn
N
AAC
AAU


Proline
Pro
P
CCA
CCC
CCG
CCU


Glutamine
Gln
Q
CAA
CAG


Arginine
Arg
R
AGA
AGG
CGA
CGC
CGG
CGU


Serine
Ser
S
AGC
AGU
UCA
UCC
UCG
UCU


Threonine
Thr
T
ACA
ACC
ACG
ACU


Valine
Val
V
GUA
GUC
GUG
GUU


Tryptophan
Trp
W
UGG


Tyrosine
Tyr
Y
UAC
UAU









In making such changes, the hydropathic index of amino acids may be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982, incorporated herein by reference). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics (Kyte and Doolittle, 1982). These values are: isoleucine (+4.5); valine (+4:2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9); and arginine (−4.5).
It is known in the art that certain amino acids may be substituted by other amino acids having a similar hydropathic index or score and still result in a protein with similar biological activity, i.e. still obtain a biological functionally equivalent protein. In making such changes, the substitution of amino acids whose hydropathic indices are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred. It is also understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity.
As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4). It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent protein. In such changes, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.
As outlined above, amino acid substitutions are generally therefore based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions that take various of the foregoing characteristics into consideration are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.
In addition, any polynucleotide may be further modified to increase stability in vivo. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends; the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl- methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.
Amino acid substitutions may further be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine. Other groups of amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gln, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. A variant may also, or alternatively, contain nonconservative changes. In a preferred embodiment, variant polypeptides differ from a native sequence by substitution, deletion or addition of five amino acids or fewer. Variants may also (or alternatively) be modified by, for example, the deletion or addition of amino acids that have minimal influence on the immunogenicity, secondary structure and hydropathic nature of the polypeptide.
As noted above, polypeptides may comprise a signal (or leader) sequence at the N-terminal end of the protein, which co-translationally or post-translationally directs transfer of the protein. The polypeptide may also be conjugated to a linker or other sequence for ease of synthesis, purification or identification of the polypeptide (e.g., poly-Histidine tag (6×His), GST, MBP, TAP/TAG, FLAG epitope, MYC epitope, V5 epitope, VSV-G epitope, etc.), or to enhance binding of the polypeptide to a solid support. For example, a polypeptide may be conjugated to an immunoglobulin Fc region.
When comparing polypeptide sequences, two sequences are said to be “identical” if the sequence of amino acids in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity. A “comparison window” as used herein, refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters. This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins—Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington DC Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.; Higgins, D. G. and Sharp, P. M. (1989) CAB/OS 5:151-153; Myers, E. W. and Muller W. (1988) CABIOS 4:11-17; Robinson, E. D. (1971) Comb. Theor 11:105; Santou, N. Nes, M. (1987) Mol. Biol. Evol. 4:406-425; Sneath, P. H. A. and Sokal, R. R. (1973) Numerical Taxonomy—the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.; Wilbur, W. J. and Lipman, D. J. (1983) Proc. Nat'l Acad., Sci. USA 80:726-730.
Alternatively, optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Nat'l Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
One preferred example of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. For amino acid sequences, a scoring matrix can be used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
In one preferred approach, the “percentage of sequence identity” is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.
In certain preferred embodiments of the invention, there are provided Leishmania fusion polypeptides, and polynucleotides encoding fusion polypeptides, wherein the fusion polypeptides comprise two or more of K26, K39, and/or K9 polypeptide sequences or immunogenic portions thereof. Fusion polypeptide and fusion proteins refer to a polypeptide having at least two heterologous Leishmania sp. polypeptides, such as Leishmania donovani polypeptides, covalently linked, either directly or via an amino acid linker. The K26, K39, and/or K9 antigenic sequences may, but need not, be derived from the same Leishmania species. The polypeptides forming the fusion protein are typically linked C-terminus to N-terminus, although they can also be linked C-terminus to C-terminus, N-terminus to N-terminus, or N-terminus to C-terminus. The polypeptides of the fusion protein can be in any order and may contain multiple copies of, repeats of, or multimers of each or any of the polypeptides comprising the fusion protein. Fusion polypeptides or fusion proteins can also include conservatively modified variants, polymorphic variants, alleles, mutants, subsequences, interspecies homologs, and immunogenic fragments of the antigens that make up the fusion protein. In particular embodiments, fusion polypeptides of the present invention may comprise one or more Leishmania antigen fragments as recited in SEQ ID NOs: 5-7, and 9-11. In a related embodiment, the fusion polypeptide comprises the amino acid sequence set forth in SEQ ID NO: 8 or amino acids 10-262 of SEQ ID NO: 8.
Antigens from other Leishmania species that correspond to Leishmania donovani antigens may also be used and can be identified, e.g., using sequence comparison algorithms, as described herein, or other methods known to those of skill in the art, e.g., hybridization assays and antibody binding assays.
The fusion polypeptides of the invention generally comprise at least two antigenic/immunogenic portions or fragments from K26, K39, and/or K9 polypeptides as described herein, and may further comprise other unrelated sequences, such as a sequence that assists in providing T helper epitopes (an immunological fusion partner), preferably T helper epitopes recognized by humans, or that assists in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein. Certain preferred fusion partners are both immunological and expression enhancing fusion partners. Other fusion partners may be selected so as to increase the solubility of the protein or to enable the protein to be targeted to desired intracellular compartments. Still further fusion partners may include affinity tags such as V5, 6×HIS, MYC, FLAG, and GST, which facilitate purification of the protein. It would be understood by one having ordinary skill in the art that those unrelated sequences may, but need not, be present in a fusion polypeptide used in accordance with the present invention.
Fusion proteins may generally be prepared using standard techniques. Preferably, a fusion protein is expressed as a recombinant protein. For example, DNA sequences encoding the polypeptide components of a desired fusion may be assembled separately, and ligated into an appropriate expression vector. The 3′ end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5′ end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion protein that retains the biological activity of both component polypeptides.
A peptide linker sequence may be employed to separate the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures, if desired. Such a peptide linker sequence is incorporated into the fusion protein using standard techniques well known in the art. Certain peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. Preferred peptide linker sequences contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39 46 (1985); Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258 8262 (1986); U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5′ to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3′ to the DNA sequence encoding the second polypeptide.
Within preferred embodiments, an immunological fusion partner for use in a fusion polypeptide of the invention is derived from protein D, a surface protein of the gram-negative bacterium Haemophilus influenza B (WO 91/18926). Preferably, a protein D derivative comprises approximately the first third of the protein (e.g., the first N-terminal 100 110 amino acids), and a protein D derivative may be lipidated. Within certain preferred embodiments, the first 109 residues of a lipoprotein D fusion partner is included on the N-terminus to provide the fusion polypeptide with additional exogenous T cell epitopes and to increase the expression level in E. coli (thus functioning as an expression enhancer). The lipid tail ensures optimal presentation of the antigen to antigen presenting cells. Other fusion partners include the non-structural protein from influenzae virus, NS1 (hemaglutinin). Typically, the N-terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used. In another embodiment, an immunological fusion partner comprises an amino acid sequence derived from the protein known as LYTA, or a portion thereof (preferably a C-terminal portion). LYTA is derived from Streptococcus pneumoniae, which synthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytA gene; Gene 43:265-292 (1986)). LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone. The C-terminal domain of the LYTA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE. This property has been exploited for the development of E. coli C-LYTA expressing plasmids useful for expression of fusion proteins. Purification of hybrid proteins containing the C-LYTA fragment at the amino terminus has been described (see Biotechnology 10:795-798 (1992)). Within a preferred embodiment, a repeat portion of LYTA may be incorporated into fusion polypeptides of the present invention, as described herein. A repeat portion is found in the C-terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.
In general, polypeptides and fusion polypeptides (as well as their encoding polynucleotides) are isolated. An “isolated” polypeptide or polynucleotide is one that is removed from its original environment. For example, a naturally-occurring protein is isolated if it is separated from some or all of the coexisting materials in the natural system. Preferably, such polypeptides are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure. A polynucleotide is considered to be isolated if, for example, it is cloned into a vector that is not a part of the natural environment.
In certain embodiments, the fusion polypeptides of the invention will comprise at least one epitope from each of K26, K39 and K9. Epitopes may generally be determined by generating polypeptides containing portions or fragments of the sequence and evaluating the reactivity of the polypeptides with sera from Leishmania-infected individuals using, for example, an enzyme linked immunosorbent assay (ELISA). Suitable assays for evaluating reactivity of a polypeptide with Leishmania-infected sera are described in more detail below. Within such representative assays, portions of the sequence that generate a signal that differentiates between positive and negative sera in a manner substantially similar to that of the full length are considered to contain an epitope. In other words, a portion of the antigen that contains an epitope will generate a signal indicating Leishmania infection in substantially all (i.e., at least about 80%, and preferably at least about 90%) of the biological samples for which such infection would be indicated using the full length antigen and will generate a signal indicating the absence of Leishmania infection in substantially all of those samples that would be negative with the full length polypeptide.
In a related aspect, fusion polypeptides comprising epitopes of multiple Leishmania polypeptides are disclosed. In certain particular embodiments, epitopes of different Leishmania polypeptides, repeats, or variants thereof, are joined though a peptide linkage into a single amino acid chain. The epitopes may be joined directly (i.e., with no intervening amino acids) or may be joined by way of a linker sequence (e.g., Gly-Cys-Gly) that does not significantly alter the antigenic properties of the epitopes. In particular embodiments the fusion polypeptide is derived from two or more antigenic/immunogenic portions or fragments. In another aspect, fusion polypeptides of the present invention may comprise two or more Leishmania antigen fragments as recited in SEQ ID NOs: 5-7 and 9-11. In a related aspect, the fusion polypeptide comprises the amino acid sequence set forth in SEQ ID NO: 8 or amino acid residues 10-262 of SEQ ID NO: 8.
The fusion polypeptides of this invention may be generated using techniques well known to those of ordinary skill in the art. Polypeptides of the present invention having fewer than about 100 amino acids, and generally fewer than about 50 amino acids, can be synthesized using, for example, the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain (Merrifield, J. Am. Chem. Soc. 85:2149-2146, 1963). Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Applied Biosystems, Inc., Foster City, Calif. Thus, for example, Leishmania K26, K39 and K9 antigens, or portions thereof, may be synthesized by this method.
Alternatively, the polypeptides of this invention may be prepared by expression of recombinant DNA encoding the polypeptide in cultured host cells. Preferably, the host cells are E. coli, yeast, an insect cell line (such as Spodoptera or Trichoplusia) or a mammalian cell line, including (but not limited to) CHO, COS, HEK-293T and NS-1. The DNA sequences expressed in this manner may encode naturally occurring proteins, and fusion proteins comprising Leishmania antigens such as K26, K9 and/or K39, portions thereof, and repeats or other variants of such proteins. Expressed fusion polypeptides of this invention are generally isolated in substantially pure form. Preferably, the fusion polypeptides are isolated to a purity of at least 80% by weight, more preferably, to a purity of at least 95% by weight, and most preferably to a purity of at least 99% by weight. In general, such purification may be achieved using, for example, the standard techniques of ammonium sulfate fractionation, SDS-PAGE electrophoresis, and affinity chromatography.
Polynucleotide Compositions
The present invention also provides isolated polynucleotides, particularly those encoding the fusion polypeptides of the invention, as well as compositions comprising such polynucleotides. As used herein, the terms “DNA” and “polynucleotide” and “nucleic acid” refer to a DNA molecule that has been isolated free of total genomic DNA of a particular species. Therefore, a DNA segment encoding a polypeptide refers to a DNA segment that contains one or more coding sequences yet is substantially isolated away from, or purified free from, total genomic DNA of the species from which the DNA segment is obtained. Included within the terms “DNA segment” and “polynucleotide” are DNA segments and smaller fragments of such segments, and also recombinant vectors, including, for example, plasmids, cosmids, phagemids, phage, viruses, and the like.
As will be understood by those skilled in the art, the polynucleotide sequences of this invention can include genomic sequences, extra-genomic and plasmid-encoded sequences and smaller engineered gene segments that express, or may be adapted to express, proteins, fusion polypeptides, peptides and the like. Such segments may be naturally isolated, recombinant, or modified synthetically by the hand of man.
As will be recognized by the skilled artisan, polynucleotides may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the present invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.
Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a Leishmania antigen or a portion thereof) or may comprise a variant, or a biological or antigenic functional equivalent of such a sequence. In particular embodiments polynucleotides may encode for two or more antigenic/immunogenic portions, fragments, or variants derived from the Leishmania K26, K39, and/or K9 antigens. In certain embodiment, polynucleotides encoding fusion polypeptides of the present invention may encode two or more Leishmania antigen fragments as recited in SEQ ID NOs: 5-7, and 9-11. In a related aspect, the fusion polypeptide is encoded by polynucleotides encoding the amino acid sequence set forth in SEQ ID NO: 8 or amino acids 10-262 of SEQ ID NO: 8.
Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions, as further described below, preferably such that the immunogenicity of the encoded polypeptide is not diminished, relative to the native protein. The effect on the immunogenicity of the encoded polypeptide may generally be assessed as described herein. The term “variants” also encompasses homologous genes of xenogenic origin.
In additional embodiments, isolated fusion polynucleotides will comprise various lengths of contiguous stretches of sequence identical to or complementary to two or more K26, K39, and or K9, such as those sequences disclosed herein, portions or variants thereof. For example, polynucleotides are provided by this invention that comprise at least about 15, 20, 30, 40, 50, 75, 100, 150, 200, 300, 400, 500 or 1000 or more contiguous nucleotides of two or more of the sequences disclosed herein as well as all intermediate lengths there between. It will be readily understood that “intermediate lengths”, in this context, means any length between the quoted values, such as 16, 17, 18, 19, etc.; 21, 22, 23, etc.; 30, 31, 32, etc.; 50, 51, 52, 53, etc.; 100, 101, 102, 103, etc.; 150, 151, 152, 153, etc.; including all integers through 200-500; 500-1,000, and the like.
The fusion polynucleotides of the present invention, or fragments thereof, regardless of the length of the coding sequence itself, may be combined with other DNA sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably. It is therefore contemplated that a polynucleotide fragment of almost any length may be employed; with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol.
Moreover, it will be appreciated by those of ordinary skill in the art that, as a result of the degeneracy of the genetic code, there are many nucleotide sequences that encode a polypeptide as described herein. Some of these polynucleotides bear minimal homology to the nucleotide sequence of any native gene. Nonetheless, polynucleotides that vary due to differences in codon usage are specifically contemplated by the present invention, for example polynucleotides that are optimized for human and/or primate codon selection. Further, alleles of the genes comprising the polynucleotide sequences provided herein are within the scope of the present invention. Alleles are endogenous genes that are altered as a result of one or more mutations, such as deletions, additions and/or substitutions of nucleotides. The resulting mRNA and protein may, but need not, have an altered structure or function. Alleles may be identified using standard techniques (such as hybridization, amplification and/or database sequence comparison).
Leishmania polynucleotides and fusions thereof may be prepared, manipulated and/or expressed using any of a variety of well established techniques known and available in the art. For example, polynucleotide sequences or fragments thereof which encode polypeptides of the invention, or fusion proteins or functional equivalents thereof, may be used in recombinant DNA molecules to direct expression of a polypeptide in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences that encode substantially the same or a functionally equivalent amino acid sequence may be produced and these sequences may be used to clone and express a given polypeptide of the present invention.
As will be understood by those of skill in the art, it may be advantageous in some instances to produce fusion polypeptide-encoding nucleotide sequences possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce a recombinant RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.
Moreover, the polynucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter fusion polypeptide encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, expression and/or immunogenicity of the gene product.
In order to express a desired fusion polypeptide comprising two or more antigenic/immunogenic fragments or portions of K26, K39, and/or K9 polypeptides, a nucleotide sequence encoding the fusion polypeptide, or a functional equivalent, may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding a polypeptide of interest and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described in Sambrook et al., Molecular Cloning, A Laboratory Manual (2001), and Ausubel et al., Current Protocols in Molecular Biology (January 2008, updated edition).
A variety of expression vector/host systems are known and may be utilized to contain and express polynucleotide sequences. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems.
The “control elements” or “regulatory sequences” present in an expression vector are those non-translated regions of the vector—enhancers, promoters, 5′ and 3′ untranslated regions—which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the PBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are generally preferred. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.
In bacterial systems, a number of expression vectors may be selected depending upon the use intended for the expressed polypeptide. For example, when large quantities are needed, vectors which direct high level expression of fusion proteins that are readily purified may be used. Such vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as PBLUESCRIPT (Stratagene), in which the sequence encoding the polypeptide of interest may be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of β-galactosidase so that a hybrid protein is produced; pIN vectors (Van Heeke & Schuster, J. Biol. Chem. 264:5503-5509 (1989)); and the like. pGEX Vectors (Promega, Madison, Wis.) may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. Proteins made in such systems may be designed to include heparin, thrombin, or factor XA protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.
In the yeast, Saccharomyces cerevisiae, a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH may be used. For reviews, see Ausubel et al. (supra) and Grant et al., Methods Enzymol. 153:516-544 (1987).
In cases where plant expression vectors are used, the expression of sequences encoding polypeptides may be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV may be used alone or in combination with the omega leader sequence from TMV (Takamatsu, EMBO J. 6:307-311 (1987)). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used (Coruzzi et al., EMBO J. 3:1671-1680 (1984); Broglie et al., Science 224:838-843 (1984); and Winter et al., Results Probl. Cell Differ. 17:85-105 (1991)). These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. Such techniques are described in a number of generally available reviews (see, e.g., Hobbs in McGraw Hill, Yearbook of Science and Technology, pp. 191-196 (1992)).
An insect system may also be used to express a polypeptide of interest. For example, in one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. The sequences encoding the polypeptide may be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of the polypeptide-encoding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses may then be used to infect, for example, S. frugiperda cells or Trichoplusia larvae in which the polypeptide of interest may be expressed (Engelhard et al., Proc. Natl. Acad. Sci. U.S.A. 91:3224-3227 (1994)).
In mammalian host cells, a number of viral-based expression systems are generally available. For example, in cases where an adenovirus is used as an expression vector, sequences encoding a polypeptide of the present invention may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing the polypeptide in infected host cells (Logan & Shenk, Proc. Natl. Acad. Sci. U.S.A. 81:3655-3659 (1984)). In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.
Specific initiation signals may also be used to achieve more efficient translation of sequences encoding a fusion polypeptide of interest. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding the polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used, such as those described in the literature (Scharf. et al., Results Probl. Cell Differ. 20:125-162 (1994)).
In addition, a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed fusion protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a “prepro” form of the protein may also be used to facilitate correct insertion, folding and/or function. Different host cells such as CHO, HeLa, MDCK, HEK293, and W138, which have specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.
For long-term, high-yield production of recombinant proteins, stable expression is generally preferred. For example, cell lines which stably express a fusion polynucleotide of the present invention may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for 1-2 days in an enriched media before they are switched to selective media. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.
Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler et al., Cell 11:223-232 (1977)) and adenine phosphoribosyltransferase (Lowy et al., Cell 22:817-823 (1990)) genes which can be employed in tk- or aprt- cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler et al., Proc. Natl. Acad. Sci. U.S.A. 77:3567-70 (1980)); npt, which confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin et al., J. Mol. Biol. 150:1-14 (1981)); and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murry, supra). Additional selectable genes have been described, for example, trpB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman & Mulligan, Proc. Natl. Acad. Sci. U.S.A. 85:8047-51 (1988)). The use of visible markers has gained popularity with such markers as anthocyanins, β-glucuronidase and its substrate GUS, and luciferase and its substrate luciferin, being widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes et al., Methods Mol. Biol. 55:121-131 (1995)).
A variety of protocols for detecting and measuring the expression of polynucleotide-encoded products, using either polyclonal or monoclonal antibodies specific for the product are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS). These and other assays are described, among other places, in Hampton et al., Serological Methods, a Laboratory Manual (1990) and Maddox et al., J. Exp. Med. 158:1211-1216 (1983).
A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide. Alternatively, the sequences, or any portions thereof may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures may be conducted using a variety of commercially available kits. Suitable reporter molecules or labels, which may be used, include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
Host cells transformed with a polynucleotide sequence of interest may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides of the invention may be designed to contain signal sequences which direct secretion of the encoded polypeptide through a prokaryotic or eukaryotic cell membrane. Other recombinant constructions may be used to join sequences encoding a polypeptide of interest to nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins.
In addition to recombinant production methods, fusion polypeptides of the invention, and fragments thereof, may be produced by direct peptide synthesis using solid-phase techniques (Merrifield, J. Am. Chem. Soc. 85:2149-2154 (1963)). Protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be achieved, for example, using Applied Biosystems 431A Peptide Synthesizer (Perkin Elmer). Alternatively, various fragments, for example, two or more antigenic/immunogenic fragments from Leishmania K26, K39, and/or K9 antigens, may be chemically synthesized separately and combined using chemical methods to produce the full length molecule.
Diagnostic Methods and Kits
In another aspect, this invention provides compounds and methods for detecting leishmaniasis in individuals and in blood supplies. In a particular embodiment, the individual is a mammal. In a more particular embodiment the mammal is a human or canine.
In one aspect, there are provided methods for detecting asymptomatic or sub-clinical visceral leishmaniasis in a biological sample, comprising: (a) contacting a biological sample with a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the Leishmania antigens are selected from K39, K26, and/or K9 or a variant thereof that differs only in conservative substitutions and/or modifications; and (b) detecting in the biological sample the presence of antibodies that bind to the fusion polypeptide, thereby detecting asymptomatic or sub-clinical visceral Leishmania infection in the biological sample.
In a particular aspect, the present invention provides methods for detecting asymptomatic or sub-clinical visceral leishmaniasis in a biological sample, comprising: (a) contacting a biological sample with a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the Leishmania antigens are selected from K39, K26, and/or K9 polypeptide sequences according any of SEQ ID NOs: 5-7, and 9-11, in any combination, or a variant thereof that differs only in conservative substitutions and/or modifications; and (b) detecting in the biological sample the presence of antibodies that bind to the polypeptide, thereby detecting asymptomatic or sub-clinical visceral Leishmania infection in the biological sample. In related embodiments, at least one of the Leishmania antigens K26, K39, and K9 is from the Leishmania donovani species.
In certain aspects, the present invention provides methods for detecting visceral Leishmania infection in a biological sample, comprising: (a) contacting a biological sample with a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the fusion protein comprises the amino acid sequence set forth in SEQ ID NO: 8 or amino acids 10-262 of SEQ ID NO: 8, or variants thereof that differ only in conservative substitutions and/or modifications; and (b) detecting in the biological sample the presence of antibodies that bind to the polypeptide, thereby detecting visceral Leishmania infection in the biological sample.
In yet another related aspect, methods are provided for identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis. In one embodiment, the method comprises: (a) contacting a biological sample obtained from a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis with a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the Leishmania antigens are selected from K39, K26, and/or K9 or a variant thereof that differs only in conservative substitutions and/or modifications; (b) detecting in the biological sample obtained from a patient the presence of antibodies that bind to the fusion polypeptide in step (a), thereby identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis (VL).
Within related aspects, diagnostic kits for diagnosing leishmaniasis are provided. In one embodiment, for example, there are provided kits for detecting visceral leishmaniasis in a biological sample, comprising: (a) a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the Leishmania antigens are selected from K39, K26, and/or K9 or a variant thereof that differs only in conservative substitutions and/or modifications; and (b) detecting in the biological sample the presence of antibodies that bind to the polypeptide, thereby detecting visceral leishmaniasis in the biological sample.
In yet another related aspect, methods are provided for identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis. In one embodiment, the method comprises: (a) contacting a biological sample obtained from a patient afflicted with asymptomatic or sub-clinical leishmaniasis with a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the Leishmania antigens are selected from K39, K26, and/or K9 polypeptide sequences according any of SEQ ID NOs: 5-7 and 9-11, in any combination, or a variant thereof that differs only in conservative substitutions and/or modifications; and (b) detecting in the biological sample obtained from a patient the presence of antibodies that bind to the fusion polypeptide in step (a), thereby identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis (VL).
Within related aspects, diagnostic kits for diagnosing leishmaniasis are provided. In one embodiment, there are provided kits for detecting visceral leishmaniasis in a biological sample, comprising: (a) a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the Leishmania antigens are selected from K39, K26, and/or K9 polypeptide sequences according any of SEQ ID NOs: 5-7 and 9-11, in any combination, or a variant thereof that differs only in conservative substitutions and/or modifications; or a variant thereof that differs only in conservative substitutions and/or modifications; and (b) detecting in the biological sample the presence of antibodies that bind to the polypeptide, thereby detecting visceral leishmaniasis in the biological sample.
In yet another related aspect, methods are provided for identifying a patient afflicted with asymptomatic or sub-clinical visceral leishmaniasis that is likely to develop acute visceral leishmaniasis. In one embodiment, the method comprises: (a) contacting a biological sample obtained from a patient afflicted with asymptomatic or sub-clinical leishmaniasis with a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the fusion protein comprises the amino acid sequence set forth in SEQ ID NO: 8 or amino acids 10-262 of SEQ ID NO: 8, or variants thereof that differ only in conservative substitutions and/or modifications; and (b) detecting in the biological sample the presence of antibodies that bind to the polypeptide, thereby detecting visceral leishmaniasis in the biological sample.
Within related aspects, diagnostic kits for diagnosing leishmaniasis are provided. In one embodiment, there are provided kits for detecting visceral leishmaniasis in a biological sample, comprising: (a) a fusion polypeptide as described herein, e.g., comprising at least two heterologous Leishmania antigens, wherein the fusion protein comprises the amino acid sequence set forth in SEQ ID NO: 8 or amino acids 10-262 of SEQ ID NO: 8, or variants thereof that differ only in conservative substitutions and/or modifications; and (b) detecting in the biological sample the presence of antibodies that bind to the polypeptide, thereby detecting visceral leishmaniasis in the biological sample.
In another aspect of this invention, methods are disclosed for detecting and monitoring Leishmania infection, as well as for distinguishing among types of Leishmania infections, in individuals and blood supplies. In general, Leishmania infection may be detected in any biological sample that contains antibodies. Preferably, the sample is blood, serum, plasma, saliva, cerebrospinal fluid, stool, or urine. More preferably, the sample is a blood or serum sample obtained from a patient or a blood supply.
In another aspect, Leishmania infection may be detected using a fusion polypeptide comprising two or more polypeptides containing one or more of the epitopes discussed above, repeats, or variants thereof. If multiple epitopes are employed, these epitopes may be present on one or more Leishmania antigens. For example, in one aspect, a fusion polypeptide of the present invention comprises two or more K26, K29, and/or K9 antigenic polypeptides. The fusion polypeptide is then used to determine the presence or absence of antibodies to the same antigenic polypeptides in the sample, relative to a predetermined cut-off value.
There are a variety of assay formats known to those of ordinary skill in the art for using a fusion polypeptide to detect antibodies in a sample. See, e.g., Harlow and Lane, Antibodies. A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1988, which is incorporated herein by reference. In a preferred embodiment, the assay involves the use of fusion polypeptide immobilized on a solid support to bind to and remove the antibody from the sample. The bound antibody may then be detected using a detection reagent that binds to the antibody/peptide complex and contains a detectable reporter group. Suitable detection reagents include antibodies that bind to the antibody/polypeptide complex and free polypeptide labeled with a reporter group (e.g., in a semi-competitive assay). Suitable reporter groups include fluorescent labels, enzyme labels, radioisotopes, chemiluminescent labels, electrochemiluminescent labels, bioluminescent labels, polymers, polymer particles, metal particles, haptens, and dyes. Alternatively, a competitive assay may be utilized, in which an antibody that binds to a fusion polypeptide of the present invention labeled with a reporter group and allowed to bind to the immobilized fusion polypeptide after incubation of the fusion polypeptide with the sample. The extent to which components of the sample inhibit the binding of the labeled antibody to the fusion polypeptide is indicative of the reactivity of the sample with the immobilized fusion polypeptide.
The solid support may be any material known to those of ordinary skill in the art to which the fusion polypeptide may be attached. For example, the support may be a test well in a microtiter plate or a nitrocellulose or other suitable membrane. Alternatively, the support may be a bead or disc, such as glass, fiberglass, latex or a plastic material such as polystyrene or polyvinylchloride. The support may also be a magnetic particle or a fiber optic sensor, such as those disclosed, for example, in U.S. Pat. No. 5,359,681.
The fusion polypeptide may be bound to the solid support using a variety of techniques known to those in the art, which are amply described in the patent and scientific literature. In the context of the present invention, the term “bound” refers to both non-covalent association, such as adsorption, and covalent attachment (which may be a direct linkage between the antigen and functional groups on the support or may be a linkage by way of a cross-linking agent). Binding by adsorption to a well in a microtiter plate or to a membrane is preferred. In such cases, adsorption may be achieved by contacting the polypeptide, in a suitable buffer, with the solid support for a suitable amount of time. The contact time varies with temperature, but is typically between about 1 hour and 1 day. In general, contacting a well of a plastic microtiter plate (such as polystyrene or polyvinylchloride) with an amount of fusion polypeptide ranging from about 10 ng to about 1 μg, and preferably about 100 ng, is sufficient to bind an adequate amount of antigen. Nitrocellulose will bind approximately 100 μg of protein per cm3.
Covalent attachment of fusion polypeptide to a solid support may generally be achieved by first reacting the support with a bifunctional reagent that will react with both the support and a functional group, such as a hydroxyl or amino group, on the fusion polypeptide. For example, the fusion polypeptide may be bound to a support having an appropriate polymer coating using benzoquinone or by condensation of an aldehyde group on the support with an amine and an active hydrogen on the polypeptide (see, e.g., Pierce Immunotechnology Catalog and Handbook (1991) at A12-A13).
In certain embodiments, the assay is an enzyme linked immunosorbent assay (ELISA). This assay may be performed by first contacting a fusion polypeptide of the present invention that has been immobilized on a solid support, commonly the well of a microtiter plate, with the sample, such that antibodies to the Leishmania antigens of the fusion polypeptide within the sample are allowed to bind to the immobilized fusion polypeptide. Unbound sample is then removed from the immobilized fusion polypeptide and a detection reagent capable of binding to the immobilized antibody-polypeptide complex is added. The amount of detection reagent that remains bound to the solid support is then determined using a method appropriate for the specific detection reagent.
Once the fusion polypeptide is immobilized on the support, the remaining protein binding sites on the support are typically blocked. Any suitable blocking agent known to those of ordinary skill in the art, such as bovine serum albumin (BSA) or Tween 20TM (Sigma. Chemical Co., St. Louis, Mo.) may be employed. The immobilized polypeptide is then incubated with the sample, and antibody (if present in the sample) is allowed to bind to the antigen. The sample may be diluted with a suitable diluent, such as phosphate-buffered saline (PBS) prior to incubation. In general, an appropriate contact time (i.e., incubation time) is that period of time that is sufficient to permit detection of the presence of antibody within a Leishmania-infected sample. Preferably, the contact time is sufficient to achieve a level of binding that is at least 95% of that achieved at equilibrium between bound and unbound antibody. Those of ordinary skill in the art will recognize that the time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.
Unbound sample may then be removed by washing the solid support with an appropriate buffer, such as PBS containing 0.1% Tween 20TM. Detection reagent may then be added to the solid support. An appropriate detection reagent is any compound that binds to the immobilized antibody-polypeptide complex and that can be detected by any of a variety of means known to those in the art. Preferably, the detection reagent contains a binding agent (such as, for example, Protein A, Protein G, immunoglobulin, lectin or free antigen) conjugated to a reporter group. Preferred reporter groups include enzymes (such as horseradish peroxidase), substrates, cofactors, inhibitors, dyes, radionuclides, luminescent groups, fluorescent groups and biotin. The conjugation of binding agent to reporter group may be achieved using standard methods known to those of ordinary skill in the art. Common binding agents may also be purchased conjugated to a variety of reporter groups from many sources (e.g., Zymed Laboratories, San Francisco, Calif. and Pierce, Rockford, Ill.).
The detection reagent is then incubated with the immobilized antibody polypeptide complex for an amount of time sufficient to detect the bound antibody. An appropriate amount of time may generally be determined from the manufacturer's instructions or by assaying the level of binding that occurs over a period of time. Unbound detection reagent is then removed and bound detection reagent is detected using the reporter group. The method employed for detecting the reporter group depends upon the nature of the reporter group. For radioactive groups, scintillation counting or autoradiographic methods are generally appropriate. Pectroscopic methods may be used to detect dyes, luminescent groups and fluorescent groups. Biotin may be detected using avidin, coupled to a different reporter group (commonly a radioactive or fluorescent group or an enzyme). Enzyme reporter groups may generally be detected by the addition of substrate (generally for a specific period of time), followed by spectroscopic or other analysis of the reaction products.
To determine the presence or absence of anti-Leishmania antibodies in the sample, the signal detected from the reporter group that remains bound to the solid support is generally compared to a signal that corresponds to a predetermined cut-off value. In one preferred embodiment, the cut-off value is preferably the average mean signal obtained when the immobilized polypeptide is incubated with samples from an uninfected patient. In general, a sample generating a signal that is three standard deviations above the predetermined cut-off value is considered positive (i.e., reactive with the polypeptide). In an alternate preferred embodiment, the cut-off value is determined using a Receiver Operator Curve, according to the method of Sackett et al., Clinical Epidemiology: A Basic Science for Clinical Medicine, p. 106-7 (Little Brown and Co., 1985). Briefly, in this embodiment, the cut-off value may be determined from a plot of pairs of true positive rates (i.e., sensitivity) and false positive rates (100%-specificity) that correspond to each possible cut-off value for the diagnostic test result. The cut-off value on the plot that is the closest to the upper lefthand corner (i.e., the value that encloses the largest area) is the most accurate cut-off value, and a sample generating a signal that is higher than the cut-off value determined by this method may be considered positive. Alternatively, the cut-off value may be shifted to the left along the plot, to minimize the false positive rate, or to the right, to minimize the false negative rate.
In a related embodiment, the assay is performed in a flow-through or strip test format, wherein the antigen is immobilized on a membrane such as nitrocellulose. In the flow-through test, antibodies within the sample bind to the immobilized polypeptide as the sample passes through the membrane. A detection reagent (e.g., protein A-colloidal gold) then binds to the antibody-polypeptide complex as the solution containing the detection reagent flows through the membrane. The detection of bound detection reagent may then be performed as described above. In the strip test format, one end of the membrane to which polypeptide is bound is immersed in a solution containing the sample. The sample migrates along the membrane through a region containing detection reagent and to the area of immobilized fusion polypeptide. Concentration of detection reagent at the fusion polypeptide indicates the presence of Leishmania antibodies in the sample. Typically, the concentration of detection reagent at that site generates a pattern, such as a line, that can be read visually. The absence of such a pattern indicates a negative result. In general, the amount of fusion polypeptide immobilized on the membrane is selected to generate a visually discernible pattern when the biological sample contains a level of antibodies that would be sufficient to generate a positive signal in an ELISA, as discussed above. Preferably, the amount of fusion polypeptide immobilized on the membrane ranges from about 25 ng to about 1 μg, and more preferably from about 50 ng to about 500 ng. Such tests can typically be performed with a very small amount (e.g., one drop) of patient serum or blood.
Of course, numerous other assay protocols exist that are suitable for use with the fusion polypeptides of the present invention. The above descriptions are intended to be exemplary only.
In one aspect of the invention, the assays discussed above may be used to specifically detect visceral leishmaniasis. In this aspect, antibodies in the sample may be detected using a fusion polypeptide comprising the amino acid sequence of two or more antigenic/immunogenic fragments or epitopes of a Leishmania K26, K39, and/or K9 antigen. In another aspect, antibodies in the sample may be detected using a fusion polypeptide comprising the amino acid sequence of two or more immunogenic fragments or epitopes as set forth in any of SEQ ID NOs: 5-7 and 9-11. In another aspect, antibodies in, the sample may be detected using a fusion polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 8 or amino acids 10-262 of SEQ ID NO: 8. Preferably, the Leishmania antigens are immobilized by adsorption to a solid support such as a well of a microtiter plate or a membrane, as described above, in roughly similar amounts such that the total amount of fusion polypeptide in contact with the support ranges from about 10 ng to about 100 μg. The remainder of the steps in the assay may generally be performed as described above. It will be readily apparent to those of ordinary skill in the art that, by combining polypeptides described herein with other polypeptides that can detect cutaneous and mucosal leishmaniasis, the polypeptides disclosed herein may be used in methods that detect all types of leishmaniasis.
In another aspect of the invention, patients with asymptomatic or sub-clinical VL whose disease is likely to progress to acute visceral leishmaniasis may be distinguished from infected patients whose disease is not likely to progress. Such progression may occur within a year (and typically within 5-12 months) for sub-clinical disease, or within many years in the case of asymptomatic patients. This determination may be made using any of several approaches. In one embodiment, the assay is performed using a polypeptide as described herein, e.g., that comprises at least one repeat unit of the K39 antigen, as set forth in SEQ ID NOs: 6, 10 or 11, for example. In a related embodiment, the polypeptide comprises a K39 repeat unit antigen encoded by the polynucleotide sequence recited in SEQ ID NOs: 2, 14 or 15. While a K39 repeat unit antigen generates a positive result (relative to the predetermined cut-off value) when reacted with sera from more than 97% of patients with acute visceral leishmaniasis, patients with asymptomatic leishmaniasis react very weakly, if at all, with this antigen. Those sera that react weakly are likely to indicate infections that are in the process of progression, or are likely to progress, to acute visceral leishmaniasis (or infections that are in remission or responding to treatment, which may be distinguished based on patient history).
In another embodiment, the assay is separately performed with a fusion polypeptide of the invention, e.g., comprising the amino acid sequence of two or more antigenic/immunogenic fragments or epitopes of a Leishmania K26, K39, and/or K9 antigen, such as K28 for example, and with a polypeptide that comprises at least one repeat unit of the K39 antigen. In this embodiment, the optical density (OD) obtained in the assay using the K28 fusion polypeptide is compared to the value obtained using the K39 polypeptide. A significantly higher OD in the assay using the K28 fusion polypeptide, when compared to the OD in the assay using the K39 polypeptide indicates a more robust, reliable detection of an asymptomatic or sub-clinical VL infection. Those asymptomatic or sub-clinical patients for whom both values are relatively high are likely to be in the process of developing acute visceral leishmaniasis (or in the process of recovering from infection). In another aspect, the assay is separately performed with a fusion polypeptide comprising the amino acid sequence of two or more immunogenic fragments or epitopes as set forth in any of SEQ ID NOs: 5-7 and 9-11 and with a polypeptide that comprises at least one repeat unit of a K39 antigen. In another aspect, the assay is separately performed with a fusion polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 8 or amino acids 10-262 of SEQ ID NO: 8, and with a polypeptide that comprises at least one repeat unit of a K39 antigen.
In another embodiment, asymptomatic or sub-clinical patients that are likely to develop acute visceral leishmaniasis may be identified using separate fusion polypeptide (e.g., K28) and K39 polypeptide assays (as described above) that are performed over a period of time. For example, the assays may be performed every 1, 2, 3, 4, 5, or 6 months for a period of months or years. Asymptomatic or sub-clinical patients that are likely to remain asymptomatic or sub-clinical will generally have sera that show a high reactivity with K28 and a low reactivity with the. K39 polypeptide, as discussed above, at each time point. However, patients that are progressing toward acute visceral leishmaniasis will show an increase in the reactivity of both K28 and K39 polypeptides over the time period of the assays. By monitoring an individual patient in this manner, the development of acute visceral leishmaniasis may be identified before other symptoms become apparent. This early identification allows selective treatment of only those asymptomatic patients that are predisposed to develop a more serious form of the disease.
In another aspect of this invention, immobilized fusion polypeptides may be used to purify antibodies that bind thereto. Such antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art. See, e.g., Harlow and Land, Antibodies. A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1988. In one such technique, an immunogen comprising a fusion polypeptide of the present invention is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep and goats). In this step, the polypeptide may serve as the immunogen without modification. Alternatively, particularly for relatively short polypeptides, a superior immune response may be elicited if the polypeptide is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin. The immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically. Polyclonal antibodies specific for the polypeptide may then be purified from such antisera by, for example, affinity chromatography using the polypeptide coupled to a suitable solid support.
Monoclonal antibodies specific for the antigenic fusion polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed. For example, the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells. A preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and tested for binding activity against the polypeptide. Hybridomas having high reactivity and specificity are preferred.
Monoclonal antibodies may be isolated from the supernatants of growing hybridoma colonies. In this process, various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as a mouse. Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation, and extraction. One or more polypeptides may be used in the purification process in, for example, an affinity chromatography step.
Monospecific antibodies that bind to a fusion polypeptide comprising two or more immunogenic portions of Leishmania K26, K39, and/or K9 antigens may be used, for example, to detect Leishmania infection in a biological sample using one of a variety of immunoassays, which may be direct or competitive. Briefly, in one direct assay format, a monospecific antibody may be immobilized on a solid support (as described above) and contacted with the sample to be tested. After removal of the unbound sample, a second monospecific antibody, which has been labeled with a reporter group, may be added and used to detect bound antigen. In an exemplary competitive assay, the sample may be combined with the monoclonal or polyclonal antibody, which has been labeled with a suitable reporter group. The mixture of sample and antibody may then be combined with polypeptide antigen immobilized on a suitable solid support. Antibody that has not bound to an antigen in the sample is allowed to bind to the immobilized antigen and the remainder of the sample and antibody is removed. The level of antibody bound to the solid support is inversely related to the level of antigen in the sample. Thus, a lower level of antibody bound to the solid support indicates the presence of Leishmania in the sample. Other formats for using monospecific antibodies to detect Leishmania in a sample will be apparent to those of ordinary skill in the art, and the above formats are provided solely for exemplary purposes.
Pharmaceutical and Vaccine Compositions
In another aspect, the present invention concerns formulations of one or more of the polynucleotide, fusion polypeptide or other compositions disclosed herein in pharmaceutically-acceptable or physiologically-acceptable solutions for administration to a cell or an animal, either alone, or in combination with one or more other modalities of therapy. Such pharmaceutical compositions are particularly preferred for use as vaccines when formulated with a suitable immunostimulant/adjuvant system. The compositions are also suitable for use in a diagnostic context.
It will also be understood that, if desired, the compositions of the invention may be administered in combination with other agents as well, such as, e.g., other proteins or polypeptides or various pharmaceutically-active agents. There is virtually no limit to other components that may also be included, provided that the additional agents do not cause a significant adverse effect upon the objectives according to the invention.
In certain embodiments, the compositions of the invention are used as vaccines and are formulated in combination with one or more immunostimulants. An immunostimulant may be any substance that enhances or potentiates an immune response (antibody and/or cell-mediated) to an exogenous antigen. Examples of immunostimulants include adjuvants, biodegradable microspheres (e.g., polylactic galactide) and liposomes (into which the compound is incorporated; see, e.g., Fullerton, U.S. Pat. No. 4,235,877). Vaccine preparation is generally described in, for example, Powell & Newman, eds., Vaccine Design (the subunit and adjuvant approach) (1995).
Any of a variety of immunostimulants may be employed in the vaccines of this invention. For example, an adjuvant may be included. Many adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A (natural or synthetic), Bortadella pertussis or Mycobacterium species or Mycobacterium derived proteins. Suitable adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2 and derivatives thereof (SmithKline Beecham, Philadelphia, Pa.); CWS, TDM, Leif, aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF or interleukin-2, -7, or -12, may also be used as adjuvants.
Other illustrative adjuvants useful in the context of the invention include Toll-like receptor agonists, such as TLR7 agonists, TLR7/8 agonists, and the like. Still other illustrative adjuvants include imiquimod, gardiquimod, resiquimod, and related compounds.
Certain vaccines employ adjuvant systems designed to induce an immune response predominantly of the Th1 type. High levels of Th1-type cytokines (e.g., IFN-γ, TNF-α, IL-2 and IL-12) tend to favor the induction of cell mediated immune responses to an administered antigen. In contrast, high levels of Th2-type cytokines (e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoral immune responses. Following application of a vaccine as provided herein, a patient will support an immune response that includes Th1- and Th2-type responses. Within one embodiment, in which a response is predominantly Th1-type, the level of Th1-type cytokines will increase to a greater extent than the level of Th2-type cytokines. The levels of these cytokines may be readily assessed using standard assays. For a review of the families of cytokines, see Mossman & Coffman, Ann. Rev. Immunol. 7:145-173 (1989).
Certain adjuvants for use in eliciting a predominantly Th1-type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A (3D-MPLTM), together with an aluminum salt (U.S. Pat. Nos. 4,436,727; 4,877,611; 4,866,034; and 4,912,094). CpG-containing oligonucleotides (in which the CpG dinucleotide is unmethylated) also induce a predominantly Th1 response. Such oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Pat. Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352 (1996). Another illustrative adjuvant comprises a saponin, such as Quil A, or derivatives thereof, including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, Mass.); Escin; Digitonin; or Gypsophila or Chenopodium quinoa saponins. Other illustrative formulations include more than one saponin in the adjuvant combinations of the present invention, for example combinations of at least two of the following group comprising QS21, QS7, Quil A, escin, or digitonin.
In a particular embodiment, the adjuvant system includes the combination of a monophosphoryl lipid A and a saponin derivative, such as the combination of QS21 and 3D-MPLTM. adjuvant, as described in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol, as described in WO 96/33739. Other formulations comprise an oil-in-water emulsion and tocopherol. Another adjuvant formulation employing QS21, 3D-MPLTM adjuvant and tocopherol in an oil-in-water emulsion is described in WO 95/17210.
Another enhanced adjuvant system involves the combination of a CpG-containing oligonucleotide and a saponin derivative as disclosed in WO 00/09159.
Other illustrative adjuvants include Montanide ISA 720 (Seppic, France), SAF (Chiron, Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2, AS2′, AS2,′′ SBAS-4, or SBAS6, available from SmithKline Beecham, Rixensart, Belgium), Detox, RC-529 (Corixa, Hamilton, Mont.) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. patent application Ser. Nos. 08/853,826 and 09/074,720, the disclosures of which are incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants such as those described in WO 99/52549A1.
Compositions of the invention may also, or alternatively, comprise T cells specific for a Leishmania fusion polypeptide as described herein throughout. Such cells may generally be prepared in vitro or ex vivo, using standard procedures. For example, T cells may be isolated from bone marrow, peripheral blood, or a fraction of bone marrow or peripheral blood of a patient. Alternatively, T cells may be derived from related or unrelated humans, non-human mammals, cell lines or cultures.
T cells may be stimulated with a fusion polypeptide comprising, two or more immunogenic portions of Leishmania K26, K39, and/or K9 antigens, polynucleotide encoding such a fusion polypeptide, and/or an antigen presenting cell (APC) that expresses such a fusion polypeptide. Such stimulation is performed under conditions and for a time sufficient to permit the generation of T cells that are specific for the fusion polypeptide. Preferably, the fusion polypeptide or polynucleotide is present within a delivery vehicle, such as a microsphere, to facilitate the generation of specific T cells.
T cells are considered to be specific for a fusion polypeptide of the invention if the T cells specifically proliferate, secrete cytokines or kill target cells coated with the polypeptide or expressing a gene encoding the polypeptide. T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1070 (1994)). Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques. For example, T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA). Contact with a polypeptide of the invention (100 ng/ml-100 μg/ml, preferably 200 ng/ml-25 μg/ml) for 3-7 days should result in at least a two fold increase in proliferation of the T cells. Contact as described above for 2-3 hours should result in activation of the T cells, as measured using standard cytokine assays in which a two fold increase in the level of cytokine release (e.g., TNFα or IFN-γ) is indicative of T cell activation (see Coligan et al., Current Protocols in Immunology, vol. 1 (1998)). T cells that have been activated in response to a fusion polypeptide, polynucleotide or fusion polypeptide-expressing APC may be CD4+ and/or CD8+. Protein-specific T cells may be expanded using standard techniques. Within preferred embodiments, the T cells are derived from a patient, a related donor or an unrelated donor, and are administered to the patient following stimulation and expansion.
In the pharmaceutical compositions of the invention, formulation of pharmaceutically-acceptable excipients and carrier solutions is well-known to those of skill in the art, as is the development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens, including e.g., oral, parenteral, intravenous, intranasal, and intramuscular administration and formulation.
In certain applications, the pharmaceutical compositions disclosed herein may be delivered via oral administration to a subject. As such, these compositions may be formulated with an inert diluent or with an assimilable edible carrier, or they may be enclosed in hard- or soft-shell gelatin capsule, or they may be compressed into tablets, or they may be incorporated directly with the food of the diet.
In certain circumstances it will be desirable to deliver the pharmaceutical compositions disclosed herein parenterally, intravenously, intramuscularly, or even intraperitoneally as described, for example, in U.S. Pat. Nos. 5,543,158; 5,641,515 and 5,399,363 (each specifically incorporated herein by reference in its entirety). Solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.
The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (U.S. Pat. No. 5,466,468, specifically incorporated herein by reference in its entirety). In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be facilitated by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, a sterile aqueous medium that can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion (see, e.g., Remington's Pharmaceutical Sciences, 15th Edition, pp. 1035-1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. Moreover, for human administration, preparations should meet sterility, pyrogenicity, and the general safety and purity standards as required by FDA Office of Biologics standards.
Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with the various other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
The compositions disclosed herein may be formulated in a neutral or salt form. Pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms such as injectable solutions, drug-release capsules, and the like.
As used herein, “carrier” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
The phrase “pharmaceutically-acceptable” refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human. The preparation of an aqueous composition that contains a protein as an active ingredient is well understood in the art. Typically, such compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared. The preparation can also be emulsified.
In certain embodiments, the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles. Methods for delivering genes, polynucleotides, and peptide compositions directly to the lungs via nasal aerosol sprays has been described e.g., in U.S. Pat. Nos. 5,756,353 and 5,804,212 (each specifically incorporated herein by reference in its entirety). Likewise, the delivery of drugs using intranasal microparticle resins (Takenaga et al., 1998) and lysophosphatidyl-glycerol compounds (U.S. Pat. No. 5,725,871, specifically incorporated herein by reference in its entirety) are also well-known in the pharmaceutical arts. Likewise, transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is described in U.S. Pat. No. 5,780,045 (specifically incorporated herein by reference in its entirety).
In certain embodiments, the delivery may occur by use of liposomes, nanocapsules, microparticles, microspheres, lipid particles, vesicles, and the like, for the introduction of the compositions of the present invention into suitable host cells. In particular, the compositions of the present invention may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, a nanoparticle or the like. The formulation and use of such delivery vehicles can be carried out using known and conventional techniques.
In another aspect of this invention, vaccines and pharmaceutical compositions are provided for the prevention of Leishmania infection, and complications thereof, in a mammal, preferably a human or dog. Pharmaceutical compositions generally comprise one or more fusion polypeptides as described herein, and a physiologically acceptable carrier. The vaccines comprise one or more of the above fusion polypeptides and an adjuvant, for enhancement of the immune response.
Routes and frequency of administration and fusion polypeptide doses will vary from individual to individual and may parallel those currently being used in immunization against other protozoan infections. In general, the pharmaceutical compositions and vaccines may be administered by injection (e.g., intramuscular, intravenous or subcutaneous), intranasally (e.g., by aspiration) or orally. Between 1 and 4 doses may be administered for a 2-6 week period. Preferably, two doses are administered, with the second dose 2-4 weeks later than the first. A suitable dose is an amount of fusion polypeptide that is effective to raise antibodies in a treated mammal that are sufficient to protect the mammal from Leishmania infection for a period of time. In general, the amount of fusion polypeptide present in a dose ranges from about 1 pg to about 100 mg per kg of host, typically from about 10 pg to about 1 mg, and preferably from about 100 pg to about 1 μg. Suitable dose sizes will vary with the size of the animal, but will typically range from about 0.01 mL to about 5 mL for 10-60 kg animal.
While any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of this invention, the type of carrier will vary depending on the mode of administration. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactic galactide) may also be employed as carriers for the pharmaceutical compositions of this invention.
Any of a variety of adjuvants may be employed in the vaccines of this invention to nonspecifically enhance the immune response. Most adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a nonspecific stimulator of immune response, such as lipid A, Bordella pertussis or Mycobacterium tuberculosis. Such adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.) and Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.).
The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheet, are incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, applications and publications to provide yet further embodiments.
EXAMPLES
Example 1
Cloning and Expression of Leishmania Fusion Polypeptide
The present invention relates to a synthetic gene construct, referred to as K28, comprising sequences derived from 3 Leishmania donovani genes. The synthetic gene comprises partial DNA sequences of the K26 and K39 genes and the complete DNA sequences of the K9 gene. Additionally, the synthetic gene comprises a nine amino acid N-terminal motif, which includes 6 histidines (e.g., a 6×HIS epitope tag). The synthetic DNA construct was cloned into the NdeI/XhoI site of plasmid pCRX2.1 in order to express the fusion protein of this gene. The synthetic gene contains three 14 amino acid repeats of K26 encoded by SEQ ID NO: 1, two 39 amino acid repeats of K39 encoded by SEQ ID NO: 2, and the complete open reading frame for the K9 gene encoded by SEQ ID NO: 3. This fusion construct was designed to improve the diagnostic potential of each of these single proteins into one molecule and offers a broader coverage, increased sensitivity and reduced costs in terms of manufacturing a single protein instead of all three.
Example 2
Detection of Asymptomatic and Sub-Clinical Visceral Leishmania Infections in Humans Using a K28 Polypeptide
This Example illustrates the increased detection sensitivity of Leishmania infection in humans using a fusion polypeptide of the invention, prepared as described in Example 1, in an ELISA format.
The ELISA assays were performed as follows. Three series of Polysorp 96 well plates (Nunc, Rochester, N.Y.) were each coated with 2 μg/ml of a different recombinant antigen in bicarbonate buffer overnight at 4° C. and blocked for 2 hours at room temperature with PBST with 1% (w/v) BSA on a plate shaker. Sera were diluted appropriately to 1/200 in PBST with 0.1% BSA, added to each well and plates were incubated at room temperature for 2 hours with shaking.
Plates were washed with PBST with 0.1% BSA and then HRP conjugated IgG immunoglobulin (Sigma, St. Louis, Mo.), diluted 1:10000 in PBST and 0.1% BSA, was added to each well and incubated at room temperature for 60 minutes with shaking. After washing, plates were developed with peroxidase color substrate (KPL, Baltimore Md.) with reaction quenched by addition of 1N H2SO4 after 10 minutes. The corrected optical density of each well at 450-570 nm was read using a VERSAmax® microplate reader (Molecular Devices, Sunnyvale, Calif.). The cut-off value was determined for each test by calculating the mean of the Enzyme Conjugate negative controls plus three standard deviations (EC).
Venezuelan individuals with visceral leishmaniasis (VL) were identified based on serology (e.g., IFAT or IHA immunofluorescence or hemaglutination), clinical symptoms (e.g., malaise, diarrhea, splenomegaly and hepatomegaly) and whole lysate ELISA. Of 52 serum samples from patients with VL, 94% tested positive using the above assay. However, the K28 antigen test displayed significantly higher ODs in 33% of the weak or marginally detected samples using the K39 antigen alone. In addition, 3 samples that were initially characterized as negative using the K39 assay were reliably detected using the K28 antigen test.
These results are depicted in FIG. 2, which show the distribution of absorbance values at 450-570 nm for the 52 VL serum samples assayed with K26, K28, and K39. These results indicate that using K28 provides increased sensitivity over using K39 alone to detect asymptomatic or sub-clinical visceral leishmaniasis.
Example 3
Detection of Asymptomatic and Sub-Clinical Visceral Leishmania Infections in Canines Using a K28 Polypeptide
This Example illustrates the increased detection sensitivity of Leishmania infection in canines using a fusion polypeptide of the invention, prepared as described in Example 1, in an ELISA format.
The ELISA assays were performed as described in Example 2, except that 4 different recombinant antigens were used. Four series of Polysorp 96 well plates were each coated with 2 μg/ml of either K9, K26, K28, or K39 recombinant antigens. Venezuelan canines with visceral leishmaniasis (VL) were identified based on serology (e.g., IFAT or IHA immunofluorescence or hemaglutination), clinical symptoms (e.g., malaise, diarrhea, splenomegaly and hepatomegaly) and whole lysate ELISA.
The results depicted in FIG. 3 show that K28 identified a significantly greater number of cases than either of the other three antigens used alone. This indicates that using K28 provides increased sensitivity in canines to detect asymptomatic or sub-clinical leishmaniasis, and moreover, K28 provides increased sensitivity of detection over using K9, K26, and K39 antigens alone.
Example 4 
Detection of Visceral Leishmania Infections in Humans Using a K28 Polypeptide or a K39 Polypeptide in a Dual Path Rapid Test Format Compared to Direct Agllutination Assay
This Example illustrates the increased detection sensitivity of Leishmania infection in humans using a fusion polypeptide of the invention (K28), prepared as described in Example 1, versus a single antigen (K39) in a dual path rapid test format, as compared to a direct agglutination assay (DAT) using sera from Sudan.
The dual path rapid test was performed essentially as described in U.S. Pat. No. 7,189,522, which is herein incorporated by reference in its entirety. Briefly, K28 or K39 was coated onto a strip of nitrocellulose. A drop of appropriately diluted human serum was added to the sample well in a test cartridge containing the antigen-impregnated nitrocellulose. Two drops of sample buffer were then added to the sample well and the sample was allowed to migrate by capillary action until the lines in the detection window of the test cartridge disappeared. Two drops of buffer were then added to the detection reagent well in the test cartridge to reconstitute immobilized detection reagent (colloidal gold-conjugated Staphylococcal protein A).
The detection reagent migrates by capillary flow to the detection window. If the sample contains antibodies to the test antigen, they bind to the immobilized antigen in the detection window where they will be visualized as two pink lines by binding of the detection reagent. A single pink line indicates that there is no antibody in the sample and that the detection reagent is bound to immobilized, control immunoglobulin (Ig) in the detection window. The absence of any pink lines is indicative of a defective test.
The DAT test was performed essentially as described by Sundar and Rai in Clin Diag Lab Immunol 9: 951-958, 2002.
The results of this analysis demonstated that K28 identified a significantly greater number of cases of human VL than did K39 alone. More specifically, K28 provided increased sensitivity in humans (66/69 samples, 95.6%) to detect visceral leishmaniasis versus K39 alone (61/69 samples, 88.4%) when employed in a dual path rapid test format. In addition, 4 patient samples with very low DAT titers (<3200) were correctly identified by the K28 rapid test, while only 2 of the 4 were correctly identified by the K39 rapid test.
These and other changes can be made to the embodiments in light of the above-detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. Accordingly, the claims are not limited by the disclosure.
The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheetare incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, applications and publications to provide yet further embodiments.

## Claims

1. A method for detecting asymptomatic or sub-clinical Leishmania infection in a biological sample comprising:
(a) contacting a biological sample with a fusion polypeptide comprising Leishmania antigens K26, K39, and K9, wherein the Leishmania antigen K26 comprises a sequence having at least 95% identity to SEQ ID NO:5, the Leishmania antigen K39 comprises a sequence having at least 95% identity to SEQ ID NO:6, and the Leishmania antigen K9 comprises a sequence having at least 95% identity to SEQ ID NO:7 ; and
(b) detecting in the biological sample the presence of antibodies that bind to the fusion polypeptide, thereby detecting asymptomatic or sub-clinical Leishmania infection in the biological sample.

2. The method of claim 1, wherein the fusion polypeptide comprises an amino acid sequence as set forth in 10-262 of SEQ ID NO: 8, or a sequence haying at least 95% identity thereto along its entire length.

3. The method of claim 2, wherein the fusion polypeptide further comprises an N-terminal amino acid sequence of MHHHHHHTS (SEQ ID NO: 21).

4. The method of claim 1, wherein the fusion polypeptide is bound to a solid support.

5. The method of claim 4, wherein the solid support comprises nitrocellulose, latex or a plastic material.

6. The method of claim 1, wherein the step of detecting comprises:
(a) removing unbound sample from the solid support;
(b) adding a detection reagent to the solid support; and
(c) determining the level of detection reagent bound to the solid support, relative to a predetermined cutoff value.

7. The method of claim 6, wherein the detection reagent comprises a reporter group conjugated to a binding agent.

8. The method of claim 7 wherein the binding agent is selected from the group consisting of anti-immunoglobulin, Protein G, Protein A and lectins.

9. The method of claim 7 wherein the reporter group is selected from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin and dye particles.

10. The method of claim 1 wherein the biological sample is selected from the group consisting of sera, blood, and saliva.