# Patent

## Title
Mycobacterium tuberculosis specific peptides for detection of infection or immunization in non-human primates

## Abstract

The present invention relates to novel peptides that may be used in whole or in combination for the detection of Mycobacterium tuberculosis infection. In particular, the present invention relates to compositions and methods involving detection of antibodies contained in the blood of non-human primates that arise from an infection from M. tuberculosis or vaccination using an epitope specific inoculation. More particularly, the present invention provides a means to distinguish early, active, and latent M. tuberculosis infection. More particularly, the present invention describes an immunological diagnostic mechanism for the detection of M. tuberculosis infection.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a national stage of International (PCT) Patent Application Serial No. PCT/US2013/025072, filed Feb. 7, 2013, which claims the benefit of and priority to U.S. Provisional Patent Application No. 61/595,805, filed Feb. 7, 2012, and to U.S. Provisional Patent Application No. 61/723,094, filed Nov. 6, 2012, the contents of each of which are hereby incorporated by reference for all purposes.


FIELD OF THE INVENTION
The present invention relates to novel peptides that may be used in whole or in combination for the detection of Mycobacterium tuberculosis infection. In particular, the present invention relates to compositions and methods involving detection of antibodies contained in the blood of non-human primates that arise from an infection from M. tuberculosis or vaccination using an epitope specific inoculation.
BACKGROUND OF THE INVENTION
The intracellular bacillus pathogen Mycobacterium tuberculosis (M. tb) causes the fatal and rapidly spreading disease tuberculosis (TB) in non-human primates (NHP), similar to active TB in humans. In NHPs, M. tb is typically spread by inhalation of aerosolized infectious particles expelled by infected individuals (humans and animals) [1]. Because of the health threat to captive primates and the zoonotic potential to and from their human caretakers, strict screening protocols have been implemented to prevent outbreaks[2]. Despite the precautions taken to prevent M. tb exposure in captive primate colonies, outbreaks continue to cause a major impact on colony health. Outbreaks result in animal losses, disruption of research, potential exposure to human caretakers, and the immeasurable costs to contain the outbreaks [3-11].
Current methods for TB screening in non-human primates rely on the bi-annual intradermal tuberculin skin test (TST), a test that has been routinely used for decades [2, 12]. Injection of M. tb antigen is typically performed in the eyelid, and relies on immune cell mediated recognition of the antigens generated by previous exposure to M. tb. The antigens currently used in the TST are semi-purified heterogeneous crude protein preparations of either mammalian old tuberculin (MOT) or purified protein derivative (PPD). The cell mediated response resulting in local inflammation and necrotic tissue measured by a TST takes at least 4 weeks after infection to develop and has some severe limitations in terms of diagnostic sensitivity and specificity. Additionally, the TST is labor intensive, and requires increased animal handling over the three days it takes to develop the response of a swelled eyelid or necrotic tissue.
While false positive TST results in loss of individually valuable research animals, the greatest threat to NHP colony and human health are false negative results, which make entire colonies vulnerable to outbreaks [5, 10, 13]. Because NHPs can develop latent TB without obvious clinical symptoms [3, 7, 14-15], false negative results or anergy to TST pose a significant threat to colony health when combined with the low diagnostic sensitivity of the TST. Anergy can also be induced in research primates by immunosuppressive treatment or disease, or concurrent viral infection like measles [4, 9, 16-17]. Additionally, reports of anergy to TST following measles vaccination complicates using the TST as part of importation quarantine procedure[18]. Despite the TST being USDA-approved for diagnostic testing of NHPs for TB, it is widely considered that a negative TST result does not reliably exclude tuberculosis infection (reports between 79 and 90% predictive value)[19]. It is, however, the standard for antemortem diagnostic testing and requires lengthy postmortem confirmation by the “gold standard” of mycobacterial culture and isolation.
Other immune-based screening assays and serological tests, including interferon gamma release assays (IGRA) and commercial antibody detection assays can have a higher sensitivity than the TST for acute infection, but rely on similar sets of M. tb recombinant proteins that often fail to identify latently infected animals. In the case of the commercially available IGRA test PRIMAGAM (Prionics AG, Zurich, Switzerland), the semi-purified PPD antigen set is used to stimulate IFN-γ release by whole blood leukocytes[19]. The PrimaTB STAT-PAK assay is a lateral flow device for measuring presence of TB-specific antibodies in NHP plasma or serum, and uses an antigen cocktail of recombinant antigens including ESAT-6, CFP-10, MPB83, and TBF10 (a fusion protein from Corixa Corp)[20]. Relative to the TST these tests are expensive, technically difficult, and impractical to perform on a colony-wide basis[19]. Moreover, these methods all rely on semi-purified or recombinant antigens for identifying a biological or antibody response, all are subject to the same limitations of sensitivity. At best, reported predictive value in experimentally infected animals is between 83 and 94% for PRIMAGAM and 80 and 94% for PrimaTB STAT-PAK, respectively [19-21]. Unpublished studies have reported significantly lower predictive value (<50%) for naturally occurring infections in NHPs (Table 2). Current recommendations for TB testing include routine TST in conjunction with IGRA or antibody assays for routine screening because no one test is both sensitive and specific enough[22].
What is needed in the art are improved devices and methods for determining if a subject animal has tuberculosis, and especially devices and methods which allow for accurate, specific and sensitive monitoring of primate colonies.
SUMMARY OF THE INVENTION
The present invention relates to novel peptides that may be used in whole or in combination for the detection of Mycobacterium tuberculosis infection. In particular, the present invention relates to compositions and methods involving detection of antibodies contained in the blood of non-human primates that arise from an infection from M. tuberculosis or vaccination using an epitope specific inoculation. More particularly, the present invention provides a means to distinguish early, active, and latent M. tuberculosis infection. More particularly, the present invention describes an immunological diagnostic mechanism for the detection of M. tuberculosis infection.
Accordingly, in some embodiments, the present invention provides an immunoassay device comprising one or more capture reagents comprising a peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the device comprises two or more capture reagents, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the device comprises three or more capture reagents, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the device comprises four or more capture reagents, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the device comprises five or more capture reagents, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the device comprises ten or more capture reagents, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the device comprises one or more capture reagents comprising isolated peptides selected from SEQ ID NOs: 28, 98, 141, 145 and combinations thereof. In some embodiments, the device comprises two or more distinct capture reagents, each comprising a different peptide selected from the group consisting of SEQ ID NOs.141, 145, 147, 98, 139 and 56. In some embodiments, the device comprises three or more distinct capture reagents, each comprising a different peptide selected from the group consisting of SEQ ID NOs.141, 145, 147, 98, 139 and 56. In some embodiments, the device comprises four or more distinct capture reagents, each comprising a different peptide selected from the group consisting of SEQ ID NOs.141, 145, 147, 98, 139 and 56. In some embodiments, the device comprises a first capture agent comprising SEQ ID NO:141, a second capture reagent comprising SEQ ID NO:145, a third capture reagent comprising SEQ ID NO: 147; and a fourth capture reagent comprising SEQ ID NO:98.
In some embodiments, the capture reagent is selected from the group consisting of proteins and protein conjugates. In some embodiments, the one or more capture reagents comprise a polypeptide R1—X—R2, wherein X is a peptide selected from the group consisting of SEQ ID NOs.1-149, R1 is selected from the group consisting of the amino terminus of said polypeptide, an amino acid or a polypeptide chain, and R2 is selected from the group consisting of the amino terminus of said polypeptide, an amino acid or a polypeptide chain. In some embodiments, R1 is a polypeptide chain of from about 2 to about 100 amino acids in length. In some embodiments, R1 is a polypeptide chain of from about 2 to about 20 amino acids in length. In some embodiments, R2 is a polypeptide chain of from about 2 to about 100 amino acids in length. In some embodiments, R2 is a polypeptide chain of from about 2 to about 20 amino acids in length.
In some embodiments, the devices further comprise a surface. In some embodiments, the at least one capture reagent is displayed on said surface. In some embodiments, the devices further comprise at least two of said capture reagents arrayed on said surface.
In some embodiments, the immunoassay device is selected from the group consisting of a chip-based array, an ELISA device, a lateral flow device and beads.
In some embodiments, the present invention provides methods of monitoring, detecting or diagnosing infection by Mycobacterium tuberculosis in a subject or subjects comprising: contacting an immunoassay device as described above with a biological sample from said subject, and detecting the presence of antibodies in said biological sample that bind to said at least one capture reagent. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human primate. In some embodiments, the sample is a blood or serum sample. In some embodiments, the methods further comprise analyzing multiple biological samples from a non-human primate colony. In some embodiments, the methods further comprise contacting said antibodies in said biological sample that bind to said at least one capture reagent that is detectably labeled for direct or indirect detection. In some embodiments, the detection reagent is labeled with a detectable component selected from the group consisting of a fluorescent compound, a luminescent compound, an enzyme, a radiolabel, and a hapten. In some embodiments, the detection reagent is an antigen binding protein.
In some embodiments, the present invention provides methods of monitoring, detecting or diagnosing infection by Mycobacterium tuberculosis in a subject or subjects comprising: detecting the presence of antibodies in a biological sample from said subject or subjects that bind to an antigenic composition comprising a peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the methods comprise detecting the presence of two or more antibodies in said biological sample that bind two or more antigenic compositions, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the methods comprise detecting the presence of three or more antibodies in said biological sample that bind three or more antigenic compositions, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the methods comprise detecting the presence of four or more antibodies in said biological sample that bind four or more antigenic compositions, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the methods comprise detecting the presence of five or more antibodies in said biological sample that bind five or more antigenic compositions, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149. In some embodiments, the methods comprise detecting the presence of ten or more antibodies in said biological sample that bind ten or more antigenic compositions, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149.
In some embodiments, antigenic composition is selected from the group consisting of proteins and protein conjugates. In some embodiments, the one or more antigenic compositions comprise a polypeptide R1—X—R2, wherein X is a peptide selected from the group consisting of SEQ ID NOs.1-149, R1 is selected from the group consisting of the amino terminus of said polypeptide, an amino acid or a polypeptide chain, and R2 is selected from the group consisting of the amino terminus of said polypeptide, an amino acid or a polypeptide chain. In some embodiments, R1 is a polypeptide chain of from about 2 to about 100 amino acids in length. In some embodiments, R1 is a polypeptide chain of from about 2 to about 20 amino acids in length. In some embodiments, R2 is a polypeptide chain of from about 2 to about 100 amino acids in length. In some embodiments, R2 is a polypeptide chain of from about 2 to about 20 amino acids in length. In some embodiments, the methods further comprise detecting the presence of antibodies in said sample that bind to at least two different antigenic compositions each comprising a different peptide selected from the group consisting of SEQ ID NOs:141, 145, 147, 98, 139 and 56. In some embodiments, the methods further comprise detecting the presence of antibodies in said sample that bind to at least three different antigenic compositions each comprising a different peptide selected from the group consisting of SEQ ID NOs: 141, 145, 147, 98, 139 and 56. In some embodiments, the methods further comprise detecting the presence of antibodies in said sample that bind to at least four different antigenic compositions each comprising a different peptide selected from the group consisting of SEQ ID NOs: 141, 145, 147, 98, 139 and 56. In some embodiments, the methods further comprise detecting the presence of antibodies in said sample that bind to a first antigenic composition comprising SEQ ID NO:141, a second antigenic composition comprising SEQ ID NO:145, a third antigenic composition comprising SEQ ID NO: 147; and a fourth antigenic composition comprising SEQ ID NO:98. In some embodiments, the methods further comprise detecting the presence of antibodies in said sample that bind to a fifth antigenic composition comprising SEQ ID NO:139 and a sixth antigenic agent comprising SEQ ID NO:56.
In some embodiments, the at least one antigenic composition is displayed on a device comprising a surface. In some embodiments, at least two of said antigenic compositions are arrayed on said surface. In some embodiments, the surface is a component of a device selected from the group consisting of a chip-based array, an ELISA device, a lateral flow device and beads.
In some embodiments, the method has a specificity of greater than about 80%. In some embodiments, the method has a specificity of greater than about 90%. In some embodiments, the method has a specificity of greater than about 95%. In some embodiments, the method has a sensitivity of greater than about 80%. In some embodiments, the method has a sensitivity of greater than about 90%. In some embodiments, the method has a sensitivity of greater than about 95%.
In some embodiments, the present invention provides a panel of antigenic compositions comprising two or more antigenic compositions, each comprising a different peptide selected from the group consisting of SEQ ID NOs.1-149.
In some embodiments, the present invention provides an immunogenic composition comprising one more peptides selected from the group consisting of peptides identified by SEQ ID NOs:1-149. In some embodiments, the immunogenic compositions further comprise an adjuvant. In some embodiments, the immunogenic compositions comprise a fusion polypeptide comprising two or more peptides identified by SEQ ID NOs:1-149.
In some embodiments, the present invention provides methods of vaccinating a subject comprising administering the immunogenic composition at described above to a subject.
In some embodiments, the present invention provides for the use of the assay devices described above to detect, monitor or diagnose infection or exposure to Mycobacterium tuberculosis in a subject or subjects, particularly a non-human primate or a colony of non-human primates.
In some embodiments, the present invention provides for the use of the immunogenic compositions described above to detect, monitor or diagnose infection or exposure to Mycobacterium tuberculosis in a subject or subjects, particularly a non-human primate or a colony of non-human primates.
In some embodiments, the present invention provides for the use of immunogenic compositions described above to vaccinate a subject or subjects, particularly a non-human primate or a colony of non-human primates.
In some embodiments, the one or more of the peptides or conjugates described above (alone or in combination) are used as an antigen stimulation mixture for cell based assays including, but not limited to, cytokine release assays (particularly interferon gamma release and interleukin 12) as measured by ELISA, Elispot, or bead based methods. In other embodiments, the peptides or conjugates described above (alone or in combination) are used in T-cell capture assays. In still other embodiments, the peptides or conjugates described above (alone or in combination) are used as an antigenic substitute for tuberculin in the tuberculin skin test (TST).



DESCRIPTION OF THE FIGURES
FIG. 1 provides an analysis of positive and negative serum samples from Tulane National Primate Research Center (time course infection study) using a multiplexed Ag microarray with individual and mixed peptide-BSA conjugates. A: Peptide 4; B: Peptide 6; C: Peptide 15; D: Peptide 20; E: Mix A.
FIG. 2 provides an ROC analysis of 141 negative and 35 positive serum samples.
FIG. 3. The Relative Intensity Unit (RIU) is reported for the Mix of peptides (Peptides 6, 15, 17, and 20) and for each peptide individually. Values highlighted in grey show higher signal than the Naïve pooled sample.



DEFINITIONS
The terms “detecting” or “detection” or “determining the level” refer to quantitatively or non-quantitatively determination of the presence of the analyte(s) under investigation (e.g., AMH). “Detecting Formation of a Complex” refers to detecting a complex comprising a detector reagent by any method suitable for observing the particular label associated with the detector reagent; for instance, visual observation of a colored (or otherwise visible) label, measurement or visual detection of a fluorescent, chemiluminescent or radioactive label.
As used herein, the term “sample” is used in its broadest sense. In one sense, it is meant to include a specimen or culture obtained from any source, as well as biological and environmental samples. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues, and gases. Biological samples include urine and blood products, such as plasma, serum and the like. Such examples are not however to be construed as limiting the sample types applicable to the present invention.
As used herein, the terms “protein,” “polypeptide,” and “peptide” refer to a molecule comprising amino acids joined via peptide bonds. In general “peptide” is used to refer to a sequence of 20 or less amino acids and “polypeptide” is used to refer to a sequence of greater than 20 amino acids. The proteins, polypeptides and peptides may be natural, produced by a recombinant process (i.e., expression of exogenous nucleic acid encoding the peptide, polypeptide or protein in an organism, host cell, or cell-free system) or produced by chemical synthesis.
The term “carrier” refers to a molecule that allows conjugation of additional, usually smaller, molecules such as peptides.
The term “specific binding partner (or binding partner)” refers to a member of a pair of molecules that interact by means of specific, noncovalent interactions that depend on the three-dimensional structures of the molecules involved. Typical pairs of specific binding partners include antigen/antibody, hapten/antibody, hormone/receptor, nucleic acid strand/complementary nucleic acid strand, substrate/enzyme, inhibitor/enzyme, carbohydrate/lectin, biotin/(strept)avidin, and virus/cellular receptor.
As used herein, the terms “immunoglobulin” or “antibody” refer to proteins that bind a specific antigen Immunoglobulins include, but are not limited to, polyclonal, monoclonal, chimeric, and humanized antibodies, Fab fragments, F(ab′)2 fragments, and includes immunoglobulins of the following classes: IgG, IgA, IgM, IgD, IbE, and secreted immunoglobulins (sIg) Immunoglobulins generally comprise two identical heavy chains and two light chains. However, the terms “antibody” and “immunoglobulin” also encompass single chain antibodies and two chain antibodies.
The term “label” refers to a molecule or composition bound to an analyte, analyte analog, detector reagent, or binding partner that is detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Examples of labels, including enzymes, colloidal gold particles, colored latex particles, have been disclosed (U.S. Pat. Nos. 4,275,149; 4,313,734; 4,373,932; and 4,954,452, each incorporated by reference herein). Additional examples of useful labels include, without limitation, radioactive isotopes, co-factors, ligands, chemiluminescent or fluorescent agents, protein-adsorbed silver particles, protein-adsorbed iron particles, protein-adsorbed copper particles, protein-adsorbed selenium particles, protein-adsorbed sulfur particles, protein-adsorbed tellurium particles, protein-adsorbed carbon particles, and protein-coupled dye sacs. The attachment of a compound (e.g., a detector reagent) to a label can be through covalent bonds, adsorption processes, hydrophobic and/or electrostatic bonds, as in chelates and the like, or combinations of these bonds and interactions and/or may involve a linking group.
The phrase “label-free detection” refers to the detection of an immunoglobulin or antibody without the addition of a label to the immunoglobulin or a primary or secondary affinity binder that contains a label. Examples of label-free detection may be Surface Plasmon Resonance (SPR), Quartz Crystal Microbalance (QCM), and Optical Interferometry.
The phrase “specifically binds to an analyte” or “specifically immunoreactive with,” when referring to an antibody or polypeptide, refers to a binding reaction which is determinative of the presence of the analyte (which can be an antibody or polypeptide) in the presence of a heterogeneous population of molecules such as proteins and other biologic molecules. Thus, under designated immunoassay conditions, the specified antibodies or polypeptides bind to a particular analyte and do not bind in a significant amount to other analytes present in the sample. A variety of immunoassay formats may be used to select antibodies or polypeptides specifically immunoreactive with a particular analyte. For example, solid-phase ELISA immunoassays are routinely used to select monoclonal antibodies polypeptides specifically immunoreactive with a protein or antibody See Harlow and Lane, Antibodies, A Laboratory Manual, CSHP, New York (1988), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity.
The term “capture agent” refers to an unlabeled specific binding partner that is specific for (i) an analyte, such as an immunoglobulin that has been produced by an animal in response to infection by Mycobacterium tuberculosis, or (ii) a detector reagent or an analyte, as in a competitive assay, or for (iii) an ancillary specific binding partner, which itself is specific for the analyte, as in an indirect assay. As used herein, an “ancillary specific binding partner” is a specific binding partner that binds to the specific binding partner of an analyte. For example, an ancillary specific binding partner may include an antibody specific for another antibody, for example, goat anti-human antibody. A “capture area” is a region of a lateral flow device where the capture reagent is immobilized. A lateral flow device may have more than one capture area, for example, a “primary capture area,” a “secondary capture area,” and so on. Often a different capture reagent will be immobilized in the primary, secondary, or other capture areas. Multiple capture areas may have any orientation with respect to each other on the lateral flow substrate; for example, a primary capture area may be distal or proximal to a secondary (or other) capture area and vice versa. Alternatively, a primary capture area and a secondary (or other) capture area may be oriented perpendicularly to each other such that the two (or more) capture areas form a cross or a plus sign or other symbol.
The term “detector reagent” refers to a specific binding partner that is conjugated to a label. Detector reagents include, for example, labeled analyte-specific binding members or labeled ancillary specific binding members (such as enzyme-conjugate, goat anti-primate antibodies).
The term “lateral flow device” refers to an analytical device in the form of a test strip used in lateral flow chromatography, in which a test sample fluid, suspected of containing an analyte, flows (for example by capillary action) through the strip (which is frequently made of bibulous materials such as paper, nitrocellulose, and cellulose). The test fluid and any suspended analyte can flow along the strip to a detection zone in which the analyte (if present) interacts with a detection agent to indicate a presence, absence and/or quantity of the analyte.
The term “sample application area” refers to an area where a fluid sample is introduced to an immunochromatographic test strip, such as an immunochromatographic test strip present in a lateral flow device. In one example, the sample may be introduced to the sample application area by external application, as with a dropper or other applicator. In another example, the sample application area may be directly immersed in the sample, such as when a test strip is dipped into a container holding a sample. In yet another example, the sample may be poured or expressed onto the sample application area.
The term “solid support” or “substrate” means material which is insoluble, or can be made insoluble by a subsequent reaction. Numerous and varied solid supports are known to those in the art and include, without limitation, nitrocellulose, the walls of wells of a reaction tray, multi-well plates, test tubes, polystyrene beads, magnetic beads, membranes, microparticles (such as latex particles), and sheep (or other animal) red blood cells. Any suitable porous material with sufficient porosity to allow access by detector reagents and a suitable surface affinity to immobilize capture reagents is contemplated by this term. For example, the porous structure of nitrocellulose has excellent absorption and adsorption qualities for a wide variety of reagents, for instance, capture reagents. Nylon possesses similar characteristics and is also suitable. Microporous structures are useful, as are materials with gel structure in the hydrated state.
Further examples of useful solid supports include: natural polymeric carbohydrates and their synthetically modified, cross-linked or substituted derivatives, such as agar, agarose, cross-linked alginic acid, substituted and cross-linked guar gums, cellulose esters, especially with nitric acid and carboxylic acids, mixed cellulose esters, and cellulose ethers; natural polymers containing nitrogen, such as proteins and derivatives, including cross-linked or modified gelatins; natural hydrocarbon polymers, such as latex and rubber; synthetic polymers which may be prepared with suitably porous structures, such as vinyl polymers, including polyethylene, polypropylene, polystyrene, polyvinylchloride, polyvinylacetate and its partially hydrolyzed derivatives, polyacrylamides, polymethacrylates, copolymers and terpolymers of the above polycondensates, such as polyesters, polyamides, and other polymers, such as polyurethanes or polyepoxides; porous inorganic materials such as sulfates or carbonates of alkaline earth metals and magnesium, including barium sulfate, calcium sulfate, calcium carbonate, silicates of alkali and alkaline earth metals, aluminum and magnesium; and aluminum or silicon oxides or hydrates, such as clays, alumina, talc, kaolin, zeolite, silica gel, or glass (these materials may be used as filters with the above polymeric materials); and mixtures or copolymers of the above classes, such as graft copolymers obtained by initializing polymerization of synthetic polymers on a pre-existing natural polymer.
It is contemplated that porous solid supports, such as nitrocellulose, described hereinabove are preferably in the form of sheets or strips. The thickness of such sheets or strips may vary within wide limits, for example, from about 0.01 to 0.5 mm, from about 0.02 to 0.45 mm, from about 0.05 to 0.3 mm, from about 0.075 to 0.25 mm, from about 0.1 to 0.2 mm, or from about 0.11 to 0.15 mm. The pore size of such sheets or strips may similarly vary within wide limits, for example from about 0.025 to 15 microns, or more specifically from about 0.1 to 3 microns; however, pore size is not intended to be a limiting factor in selection of the solid support. The flow rate of a solid support, where applicable, can also vary within wide limits, for example from about 12.5 to 90 sec/cm (i.e., 50 to 300 sec/4 cm), about 22.5 to 62.5 sec/cm (i.e., 90 to 250 sec/4 cm), about 25 to 62.5 sec/cm (i.e., 100 to 250 sec/4 cm), about 37.5 to 62.5 sec/cm (i.e., 150 to 250 sec/4 cm), or about 50 to 62.5 sec/cm (i.e., 200 to 250 sec/4 cm). In specific embodiments of devices described herein, the flow rate is about 62.5 sec/cm (i.e., 250 sec/4 cm). In other specific embodiments of devices described herein, the flow rate is about 37.5 sec/cm (i.e., 150 sec/4 cm).
The surface of a solid support may be activated by chemical processes that cause covalent linkage of an agent (e.g., a capture reagent) to the support. However, any other suitable method may be used for immobilizing an agent (e.g., a capture reagent) to a solid support including, without limitation, ionic interactions, hydrophobic interactions, covalent interactions and the like. The particular forces that result in immobilization of an agent on a solid phase are not important for the methods and devices described herein.
Except as otherwise physically constrained, a solid support may be used in any suitable shapes, such as films, sheets, strips, or plates, or it may be coated onto or bonded or laminated to appropriate inert carriers, such as paper, glass, plastic films, or fabrics.
A “lateral flow substrate” is any solid support or substrate that is useful in a lateral flow device.
The term “Western blot” refers to the analysis of protein(s) (or polypeptides) immobilized onto a support such as nitrocellulose or a membrane. The proteins are run on acrylamide gels to separate the proteins, followed by transfer of the protein from the gel to a solid support, such as nitrocellulose or a nylon membrane. The immobilized proteins are then exposed to antibodies with reactivity against an antigen of interest. The binding of the antibodies may be detected by various methods, including the use of radiolabeled antibodies.
As used herein, the terms “protein microarray” and “protein chip” refer to protein-detecting molecules immobilized at high density on a substrate, and probed for various biochemical activities. (See, for example: Zhu H and Snyder M, “Protein chip technology”, Current Opinion in Chemical Biology 7: 55-63, 2003; Cutler P, “Protein arrays: The current state of the art”, Proteomics 3; 3-18, 2003; and MacBeath G, “Protein microarrays and proteomics”, Nature Genetics Supplement 32: 526-532, 2002, each of which is incorporated herein by reference in its entirety).
As used herein, the term “sensitivity” when used in reference to an assay refers to the proportion of actual positives which are correctly identified as such (e.g., the percentage of infected, latent or symptomatic subjects who are correctly identified as having the condition). Sensitivity may be calculated as the number of true positives divided by the sum of the number of true positives and the number of false negatives.
As used herein the term “specificity” when used in relation to an assay refers to proportion of negatives which are correctly identified (e.g., the percentage of healthy subjects who are correctly identified as not having the condition). Specificity may be calculated as the number of true negatives divided by the sum of the number of true negatives and the number of false positives.
“Blocking agent” means a molecular arrangement that will absorb to the surface of the substrate. The absorption can result because of non-covalent bonding attractive forces or because the blocking agent contains a reactive group. For example, a polyethylene glycol group can act as a blocking agent when it is covalently bonded to the surface or the protein bovine serum albumin can act as a blocking agent when it is non-covalently attached to the surface.
“Fusion protein” means a protein that contains additional molecular arrangements including, but not limited to, naturally or non-naturally amino acids usually the result of producing the protein by manipulating biological processes.
“Linker” means a molecular arrangement with a reactive group that binds a biological entity by exposure to the reactive group resulting in a biological entity linked to the molecular arrangement. The linker includes the molecular arrangements before and after the reactive group binds to the biological entity.
DETAILED DESCRIPTION OF THE INVENTION
The present invention relates to novel peptides that may be used in whole or in combination for the detection of Mycobacterium tuberculosis and related infections, including Mycobacterium bovis. In particular, the present invention relates to compositions and methods involving detection of antibodies contained in the blood of human or non-human primates that arise from an infection from M. tuberculosis or vaccination using an epitope specific inoculation. More particularly, the present invention provides a means to distinguish early, active, and latent M. tuberculosis infection. More particularly, the present invention describes an immunological diagnostic mechanism for the detection of M. tuberculosis infection.
Historically, antigens used for TB immunoassays in non-human primates have focused on secreted antigens that have been shown to have diagnostic potential in humans. Work by Brusasca et al. first used 14 proteins identified as immunodominant in human TB to identify the antibody response to these proteins in experimentally infected NHPs[23]. Of these 14, only 3 proteins (ESAT-6, α-crystallin, and CFP-10) identified antibodies in more than 85% of infected animals with an antibody reaction. Importantly, the most seroreactive human antigen at the time of that study (38 kDa, Rv0934) was only reactive with 14% of infected animals, highlighting the need for NHP specific antigen discovery. More recent studies have shown that individual recombinant proteins previous used in commercial immunochromatographic kits for both human and NHPs have at best 75% diagnostic sensitivity, and several TST positive animals were seronegative to the panel of 10 recombinant proteins [24]. Our preliminary studies showed that neither purified recombinant proteins (ESAT-6 and 16 kDa α-crystallin) nor the heterogeneous TST antigen MOT were able to accurately distinguish between positive and negative samples in our microarray based assay for antibody detection. Overall, current TB tests are limited by the poorly defined antigens for NHP testing and cannot use those antigens successfully in humans.
Accordingly, the present invention provides individual peptides, polypeptides, and proteins as well as panels of peptides, polypeptides, and proteins which are useful detecting, monitoring or diagnosing infection by Mycobacterium tuberculosis and for making vaccines to protect against infection by Mycobacterium tuberculosis. In some embodiments, the peptides, proteins, or polypeptides are encoded by or comprise SEQ ID Nos.: 1-149 or are at least 80%, 90%, 95% or 99% identical to SEQ ID NOs.:1-149 and have the property of binding to an antibody that recognizes the corresponding unaltered sequence.












Sequence




ID
Peptide Sequence

















1
AAATHSPRNVQFYCI



 


2
AAIPLLTAPVIGMAM



 


3
AAQVWSQCHSYGFDA



 


4
ADEEQQQALSSQMGF



 


5
AFEWYYQSGLSIVMP



 


6
AIGLGGGAGGDGGQG



 


7
AKLIIWYPHYAWLLL



 


8
AMEDLVRAYHAMSST



 


9
ANNWYQPARRGFSTG



 


10
APAPIASPIPVGAPG



 


11
AREVVELDRDEAMRL



 


12
ASQSTTNPIFGMPSP



 


13
ASVSIDGAQQASVAL



 


14
DAERFGARLVASPQH



 


15
DALAGKGASAIVLRG



 


16
DGITLFNPAAVPIRR



 


17
DGTHQTLQGADLTVI
Peptide 2


 


18
DQDTAELHRRATHFR



 


19
DVSVAQGVTNLHTAI



 


20
DYAIVGGAPGSAPRE



 


21
EARRADLGCDIVDAT



 


22
EFPDLEGQVQDLAAQ



 


23
EGLWAGVVIPESGRA



 


24
ESPAPHVPSHGPHQP



 


25
FDETIDKSTDKTLHS



 


26
FDWRYPPSPPPQPTQ



 


27
FLIIDGWPGFVGEFP



 


28
FPQYRELGVYLVRGI
Peptide 4


 


29
FQIHDPTTKDRQGND



 


30
FSIVRRSSRPEPSPR



 


31
GAGGSLTRTPLMSQL



 


32
GAGSGFANFGSLGSG



 


33
GCGTCNIAEALKMSL



 


34
GDFYAGEKSMTLDRA



 


35
GFDFTAQGVWAFARP



 


36
GGAPQTGKSTLLQTM



 


37
GGARFAVEQGHGVAL



 


38
GGREGPTAQISAGFC



 


39
GIAFGLFIVTNAAKL



 


40
GLDPVNYQNFAVTND



 


41
GLYNTGGLPPGTPAV



 


42
GNAGLFGDGGAGGDG



 


43
GPSIQARLRAEEASG



 


44
GRGAPEDAPLIMRGK



 


45
GTTQFGDTTANKDAW



 


46
HLAKGELRSIHNRTD



 


47
HLREKGVKLEAQRPH



 


48
HRHPSANQQMLWTLV



 


49
HVKPTGSAVVGLSMA



 


50
HYLHVRPADQFDAMI



 


51
IELTKRTLWSGLDAA



 


52
ILLECTMAGMATCTL



 


53
IPIGLRETDLTPAHC



 


54
ITYQAWQAQWNQAME



 


55
IVGAAGGMPPMAPLA



 


56
KGRSSEMIICGGVNI
Peptide 9


 


57
KVKPQKPKATKPPKV



 


58
KYVEADLRVLDEIAP



 


59
LAAPVDPSTPAPSTT



 


60
LAIPGTNWIGQAAEA



 


61
LDWERNFLRQLQSHR



 


62
LGGGVAANLGRAASV



 


63
LGNSVYTSNAQLVVY
Peptide 10


 


64
LGQPRSYLAPPTRPA



 


65
LLSQGKFPYKSSWIE



 


66
LNTARLMAGAGPAPM



 


67
LPGTAVANPVDPARI



 


68
LQVIERTWRYLKVPC



 


69
LRCGDFALGGPQGRG



 


70
LRILKTDIYAPTGAV
Peptide 11


 


71
LTYWTAGDTRNRGRE



 


72
MAGDTTITIVGNLTA



 


73
MASGSGLCKTTSNFI



 


74
MELLDAFGIAMAGAP



 


75
MGTTLTAILFAGNRL



 


76
MIDGVYKVCKGLEKI



 


77
MKLTTMIKTAVAVVA
Peptide 12


 


78
MNSAIIKIAKWAQSQ



 


79
MQLVDRVRGAVTGMS



 


80
MRLSLTALSAGVGAV



 


81
MSAPAVAAGPTAAGA



 


82
NAEIAATIANGGITM



 


83
NARTADGINYRVLWQ



 


84
NDPDRASMLFEGSTI



 


85
NKPVISWAGDNGIYF



 


86
NVDGAQREIDILEND



 


87
NVDGAQREIDILEND



 


88
PANRPGRAVSMEKHH



 


89
PLDDGDVIDSMFMSK



 


90
PLQALQTVQQNVLTV



 


91
PPAATQTLGQLGEMS



 


92
PPGDERHMLWFELMK



 


93
PPIRAPGGDAADTRL



 


94
PPTPPMPIAGPEPAP



 


95
PSGGPVAASAAPSIP



 


96
PSGTAVGAGARSSVG



 


97
QAQLISSQAQQGGQQ



 


98
QEAGNFERISGDLKT
Peptide 20


 


99
QMQDAFETGVMFSLH



 


100
QSGPAHADESAASVT



 


101
RGIPPGHVGVAWRGT



 


102
RNIIDMHLPRHRLDS



 


103
RQRRTKGAGGSFTSR



 


104
RRHLQDVWGVDVSGA
Peptide 14


 


105
RSEPDKVNRVVAEMQ



 


106
RTYSQIDDGAAGVFA



 


107
SAASVTPAAASGVPG



 


108
SADDGTPVSMIPVSA



 


109
SAKMLSVVPLMAGGG



 


110
SDVFTTITPATAQGI



 


111
SKAATDMLAYQYHKS



 


112
SKIPRGEEAGKLWDA



 


113
SKLMTRIAGAGAMGS



 


114
SLFPEFSELFAAFPS



 


115
SMEKHHLMIGVPRFD



 


116
SPGQQPGGGVPAQAM



 


117
SQRGWRHWVHALTRI



 


118
SSTHEANTMAMMARD



 


119
STVSGVVVVASVSID



 


120
TASDFWGGAGSAACQ



 


121
TDAKLLSSILTYHVI



 


122
TGQGNSLKVGNADVV



 


123
TLLQTMVMSAAATHS



 


124
TMLVVPVGAGPGLRE



 


125
TNAAKLTVAVARIAL



 


126
TPKTKIETALDRQKI



 


127
TQAVLTATNFFGINT



 


128
TRDKFLSAATSSTPR



 


129
TRLMRLEDEMKEGRY



 


130
TRQLHQLGLESSERE



 


131
TTGPKPLVQDEYAKH



 


132
TYSQIDDGAAGVFAE



 


133
VHLARDLRLHRDVAV



 


134
VLDESPEFDRTALNR



 


135
VLESKTVGDSCVVLE



 


136
VTSLFSQVGGTGGGN



 


137
VVVGGSIDAAIDTAK



 


138
APHESFDTQYTRHVE
Peptide 1


 


139
EAEHQAIISDVLTAS
Peptide 3


 


140
HARDVLADRRLFVLT
Peptide 5


 


141
IHSLLDEGKQSLTKL
Peptide 6



AAAWGGSGSEAY



 


142
KELHLRLGTATADLS
Peptide 7


 


143
KFRQLGDIVLELAAA
Peptide 8


 


144
NSLVTATHGANVSLV
Peptide 13


 


145
TKLAAAWGGSGSEAY
Peptide 15



QGVQQKWDATAT



 


146
VWRRDLRAIVRLLAW
Peptide 16


 


147
APRADLATREEQIAV
Peptide 17


 


148
HDIQVTLSAGQSVTL
Peptide 18


 


149
IRTNQVSTILASDGS
Peptide 19









SEQ ID NOs.: 1-149 encode peptide sequences that serve as antigens when a subject is infected by Mycobacterium tuberculosis or related organisms. The present invention encompasses these peptides in isolation as well as proteins, polypeptides, fusion proteins and protein conjugates that comprise the identified peptide sequences. In preferred embodiments, the proteins, polypeptides, fusion proteins and protein conjugates that comprise one or more of SEQ ID NOs:1-149 have the property of binding to antibodies that specifically recognize peptides encoded by SEQ ID NOs:1-149. In some embodiments, polypeptides comprising a peptide (or peptides) encoded by SEQ ID NOs: 1-149 comprise the base peptide and from 1, 2, 5, 10, 20, 30, 40, or 50 to about 100 or 200 amino acids on either or both of the amino- or carboxy-terminus of the base peptide. In some embodiments, polypeptides comprising a peptide (or peptides) encoded by SEQ ID NOs: 1-149 comprise the base peptide and 1, 2, 5, at least 5, at least 10, at least 20, at least 30, at least 40, or at least 50 amino acids on either or both of the amino- or carboxy-terminus of the base peptide.
In some embodiments, the present invention provides devices, kits and methods for determining whether a subject has been exposed to Mycobacterium tuberculosis or related organisms, infected by Mycobacterium tuberculosis or related organisms or has tuberculosis or other disease. In some embodiments, the subject is a human or non-human primate. In some embodiments, the methods, kits and devices are used to assay the presence or amount of antibodies in the serum, blood or tissue of a subject to specified Mycobacterium tuberculosis peptides. A number of methods and devices can be used to assay samples from subjects for the presence of antibodies to Mycobacterium tuberculosis (Mtb), including, but not limited to, protein detection chips, bead-based assays, lateral flow devices, and enzyme-linked immunosorbent assays (ELISAs). The assays may be singleplex assays or multiplex assays.
In singleplex assays, an antigenic composition or capture reagent comprising one of the peptides encoded by SEQ ID NOs:1-149 is utilized in the assay. In some embodiments, the capture reagent comprises an isolated peptide encoded by one of by SEQ ID NOs:1-149. For example, the capture reagent may comprise the isolated peptide in addition to a conjugate or linker molecule. In some embodiments, the isolated base peptide may be flanked by from 1, 2, 5, 10, 20, 30, 40, or 50 to about 100 or 200 amino acids on either or both of the amino- or carboxy-terminus of the base peptide. In multiplex assays, a panel of antigenic compositions or capture reagents are utilized in the assay. In some embodiments, the panel comprises at least 2, 3, 5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 60, 70, 80, 90 or 100 or more of SEQ ID NOs: 1-149. In some embodiments, the panel comprises 2, 3, 5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 60, 70, 80, 90 or 100 of SEQ ID NOs: 1-149. In some embodiments, the specific capture reagents utilized in the multiplex assay comprise an isolated peptide encoded by one of by SEQ ID NOs:1-149. For example, the capture reagent may comprise the isolated peptide in addition to a conjugate or linker molecule. In some embodiments, the isolated base peptide may be flanked by from 1, 2, 5, 10, 20, 30, 40, or 50 to about 100 or 200 amino acids on either or both of the amino- or carboxy-terminus of the base peptide. In some embodiments, the assays have a specificity of at least 80%, 90%, 95% or 99%. In some embodiments, the assays have a sensitivity of at least 80%, 90%, 95% or 99%. In some embodiments, the present invention provides an antigenic composition or capture reagent comprising one of the peptides encoded by SEQ ID NOs:1-149 that is conjugated to a carrier molecule.
In some embodiments, the Mtb capture reagent of antigenic composition is brought in contact with, and allowed to bind to, a solid support or carrier, such as nitrocellulose or polystyrene or any other solid support known in the art (see below), allowing the antigens to adsorb and become immobilized to the solid support. This immobilized antigen is then allowed to interact with the biological fluid sample which is being tested for the presence of anti-Mtb antibodies, such that any antibodies in the sample will bind to the immobilized antigen. The support to which the antibody is now bound may then be washed with suitable buffers after which a detectably labeled binding partner for the antibody is introduced. The binding partner binds to the immobilized antibody. Detection of the label is a measure of the immobilized antibody. In some embodiments, the immunoassay of this invention may be a “two-site” or “sandwich” assay. The fluid containing the antibody being assayed is allowed to contact a solid support. After addition of the Mtb antigen(s), a quantity of detectably labeled soluble antibody is added to permit detection and/or quantitation of the ternary complex formed between solid-phase antibody, antigen, and labeled antibody. Sandwich assays are described by Wide, Radioimmune Assay Method, Kirkham et al, Eds., E. & S. Livingstone, Edinburgh, 1970, pp 199-206.
A preferred binding partner for these assays is an anti-immunoglobulin antibody (“second antibody”) produced in a different species. Thus to detect a nonhuman primate antibody, a detectably labeled goat anti-simian immunoglobulin “second” antibody may be used. The solid phase support may then be washed with the buffer a second time to remove unbound antibody. The amount of bound label on the solid support may then be detected by conventional means appropriate to the type of label used (see below).
Such a “second antibody” may be specific for epitopes characteristic of a particular human immunoglobulin isotype, for example IgM, IgG1, IgG2a, IgA and the like, thus permitting identification of the isotype or isotypes of antibodies in the sample which are specific for the Mtb antigen. Alternatively, the second antibody may be specific for an idiotype of the anti-Mtb antibody of the sample.
As alternative binding partners for detection of the sample antibody, other known binding partners for human immunoglobulins may be used. Examples are the staphylococcal immunoglobulin binding proteins, the best know of which is protein A. Also intended is staphylococcal protein G, or a recombinant fusion protein between protein A and protein G. Protein G of group G and group C streptococci binds to the Fc portion of Ig molecules as well as to IgG Fab fragment at the VH3 domain. Protein C of Peptococcus magnus binds to the Fab region of the immunoglobulin molecule. Any other microbial immunoglobulin binding proteins, for example from Streptococci, are also intended (for example, Langone, J. J., Adv. Immunol 32:157 (1982)).
In another embodiment of this invention, a biological fluid suspected of containing antibodies specific for Mtb antigens may be brought into contact with a solid support or carrier which is capable of immobilizing soluble proteins. The support may then be washed with suitable buffers followed by treatment with Mtb antigens reagent, which may be detectably labeled. Bound antigen is then measured by measuring the immobilized detectable label. If the Mtb antigen reagent is not directly detectably labeled, a second reagent comprising a detectably labeled binding partner for the Mtb antigen, generally a second anti-Mtb antibody such as a murine mAb, is allowed to bind to any immobilized antigen. The solid phase support may then be washed with buffer a second time to remove unbound antibody. The amount of bound label on said solid support may then be detected by conventional means.
By “solid phase support” or carrier is intended any support capable of binding a proteinaceous antigen or antibody molecules or other binding partners according to the present invention. Well-known supports, or carriers, include glass, polystyrene, polypropylene, polyethylene, polyvinylidene difluoride, dextran, nylon, magnetic beads, amylases, natural and modified celluloses, polyacrylamides, agaroses, and magnetite. The nature of the carrier can be either soluble to some extent or insoluble for the purposes of the present invention. The support material may have virtually any possible structural configuration so long as it is capable of binding to an antigen or antibody. Thus, the support configuration may be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod. Alternatively, the surface may be flat such as a sheet, test strip, etc. Preferred supports include polystyrene beads, 96-well polystyrene microplates and test strips, all well-known in the art. Those skilled in the art will know many other suitable carriers for binding antibody or antigen, or will be able to ascertain the same by use of routine experimentation.
Using any of the assays described herein, those skilled in the art will be able to determine operative and optimal assay conditions for each determination by employing routine experimentation. Furthermore, other steps as washing, stirring, shaking, filtering and the like may be added to the assays as is customary or necessary for the particular situation.
In some embodiments, the present invention provides protein chip assays comprising one or more capture reagents or antigenic compositions comprising at least one of SEQ ID NOs:1-149. In such an assay, the capture reagents or antigenic compositions are immobilized on a solid support such as a chip. In some embodiments, the protein chip assay utilizes a solid support coated with ultrathin or clear nitrocellulose. See, e.g., US PAT PUBL. 20090253586 and 20090075828, both of which are incorporated herein by reference in their entirety. In preferred embodiments, the capture reagents or antigenic compositions are arrayed on the solid support. In multiplexed assays, a panel of capture reagents or antigenic compositions as described above is arrayed on the solid support. See, e.g., US PAT PUBL. 20090253586 and 20090075828, both of which are incorporated herein by reference in their entirety. A sample from a subject is passed over the solid support. Bound antibodies from the sample are then detected using any suitable method. Other suitable protein chip assays are described, for example, in U.S. Pat. No. 6,197,599; U.S. Pat. No. 6,294,790 and US Patent Application US20010014461A1, each of which is herein incorporated by reference in its entirety).
In some embodiments, a cytometric bead array assay is used (Quantum Plex kit, Bangs Laboratories; Cytometric Bead Array kit, BD Biosciences). These systems allow for multiple analyte detection with small volume samples. In other embodiments, a LUMINEX bead assay is used. See, e.g., U.S. Pat. Nos. 6,916,661; 6,939,720; 7,141,431; 7,445,844; 7,465,540; 8,038,734; and 8,088,629, all of which are incorporated herein by reference in their entirety.
In some embodiments, the immunoassay used to detect an antibody specific for an Mtb antigen according to the present invention is an enzyme-linked immunosorbent assay (ELISA) or more generically termed an enzyme immunoassay (EIA). In such assays, a detectable label bound to either an antibody-binding or antigen-binding reagent is an enzyme. When exposed to its substrate, this enzyme will react in such a manner as to produce a chemical moiety which can be detected, for example, by spectrophotometric, fluorometric or visual means. Enzymes which can be used to detectably label the reagents useful in the present invention include, but are not limited to, horseradish peroxidase, alkaline phosphatase, glucose oxidase, β-galactosidase, ribonuclease, urease, catalase, malate dehydrogenase, staphylococcal nuclease, asparaginase, delta-5-steroid isomerase, yeast alcohol dehydrogenase, α-glycerophosphate dehydrogenase, triose phosphate isomerase, glucose-6-phosphate dehydrogenase, glucoamylase and acetylcholinesterase. For descriptions of EIA procedures, see reference cited above or, additionally, Voller, A. et al., J. Clin. Pathol. 31:507-520 (1978); Butler, J. E., Meth. Enzymol. 73:482-523 (1981); Maggio, E. (ed.), Enzyme Immunoassay, CRC Press, Boca Raton, 1980.
In some embodiments, the immunoassay devices of the present invention permit the performance of relatively inexpensive, disposable, membrane-based assays for the visual identification of the presence (or absence) of an analyte in a liquid sample. Such devices are usually formatted as freestanding dipsticks (e.g., test strips) or as devices having some sort of housing. Typically, an immunoassay device of the present invention can be used with as little as about 200 μl of liquid sample, and detection of an analyte in the sample can (but need not) be complete within 2-5 minutes. In preferred embodiments, no ancillary instrumentation is required to perform such tests, and such devices easily can be used in clinics, laboratories, field locations, and the home even by inexperienced persons.
In some embodiments, the ELISA is an immunochromatographic “sandwich” assay. In general, sandwich immunochromatographic procedures call for mixing the sample that may contain the analyte to be assayed, for example, Mtb antibodies, with an antigenic composition or capture reagent as described above. A detector reagent is utilized which is mobile and typically is linked to a label or another signaling reagent, such as dyed latex, a colloidal metal sol, or a radioisotope. This mixture is then applied to a chromatographic medium containing a band or zone of immobilized antigenic compositions that serve as antigens for Mtb antibodies (i.e., the capture reagent). The chromatographic medium often is in the form of a strip that resembles a dipstick. When the complex of Mtb antibody and the detector reagent reaches the zone of the immobilized capture antibody on the chromatographic medium, binding occurs and the detector reagent complex is localized at the zone. This indicates the presence of the molecule to be assayed. This technique can be used to obtain quantitative or semi-quantitative results. Examples of sandwich immunoassays performed on test strips are described in U.S. Pat. Nos. 4,168,146 and 4,366,241, each of which is incorporated herein by reference.
In other embodiments, the ELISA is a solid phase immunoassay device that provides sensitive detection of analytes in biological fluid samples. Solid phase immunoassay devices incorporate a solid support to which one member of a ligand-receptor pair, usually an antibody, antigen, or hapten, is bound. Common early forms of solid supports were plates, tubes, or beads of polystyrene, which were known from the fields of radioimmunoassay and enzyme immunoassay. More recently, a number of porous materials such as nylon, nitrocellulose, cellulose acetate, glass fibers, and other porous polymers have been employed as solid supports. In other common forms of membrane-based immunoassays, as typified by some home pregnancy and ovulation detection kits, a test strip (or dipstick) is “dipped” into a sample suspected of containing the subject analyte. Enzyme-labeled detector reagent is then added, either simultaneously or after an incubation period. The device next is washed and then inserted into a second solution containing a substrate for the enzyme. The enzyme label, if present, interacts with the substrate, causing the formation of colored products, which either deposit as a precipitate onto the solid phase or produce a visible color change in the substrate solution. EP-A 0 125 118 describes such a sandwich type dipstick immunoassay. EP-A 0 282 192 describes a dipstick device for use in competition type assays.
In other embodiments, the assay device of the present invention is a flow through immunoassay device. Flow-through immunoassay devices involve a capture reagent (such as an immunogenic composition comprising at least of SEQ ID NOs:1-149) bound to a porous membrane or filter to which a liquid sample is added. As the liquid flows through the membrane, target analyte (such as an Mtb antibody) binds to the capture reagent. The addition of sample is followed by (or made concurrent with) addition of detector reagent (e.g., labeled second antibody). Alternatively, the detector reagent may be placed on the membrane in a manner that permits the detector to mix with the sample and thereby label the analyte. The visual detection of detector reagent provides an indication of the presence of target analyte in the sample. Representative flow-through immunoassay devices are described in U.S. Pat. Nos. 4,246,339; 4,277,560; 4,632,901; 4,812,293; 4,920,046; and 5,279,935; and U.S. Patent Application Publication Nos. 20030049857 and 20040241876, all of which are incorporated by reference in their entirety. In some embodiments, the assay device is a migration assay device. Such devices usually incorporate within them reagents that have been attached to colored labels, thereby permitting visible detection of the assay results without addition of further substances. See, for example, U.S. Pat. No. 4,770,853; PCT Publication No. WO 88/08534 and European Patent No. EP-A 0 299 428, all of which are incorporated by reference in their entirety.
In some embodiments, the assay device is lateral flow assay device. There are a number of commercially available lateral flow type tests and patents disclosing methods for the detection of analytes. See, e.g., U.S. Pat. Nos. 5,229,073; 5,591,645; 4,168,146; 4,366,241; 4,855,240; 4,861,711; 4,703,017; 5,451,504; 5,451,507; 5,798,273; 6,001,658; and 5,120,643; European Patent No. 0296724; WO 97/06439; and WO 98/36278, all of which are incorporated herein by reference.
The lateral flow assay devices of the present invention include a strip of absorbent or porous material (such as a microporous membrane), which, in some instances, can be made of different substances each joined to the other in zones, which may be abutted and/or overlapped. In some examples, the absorbent strip can be fixed on a supporting non-interactive material (such as nonwoven polyester), for example, to provide increased rigidity to the strip. Zones within each strip may differentially contain the specific binding partner(s) and/or other reagents required for the detection and/or quantification of the particular analyte being tested for, for example, Mtb antibodies. Thus these zones can be viewed as functional sectors or functional regions within the test device.
In some embodiments, a fluid sample (or a sample suspended in a fluid) is introduced to the strip at the proximal end of the strip, for instance by dipping or spotting. A sample is collected or obtained using methods well known to those skilled in the art. The sample containing the Mtb antibodies to be detected may be obtained from any biological source. Examples of biological sources include blood serum, blood plasma, urine, spinal fluid, saliva, fermentation fluid, lymph fluid, tissue culture fluid and ascites fluid of a human or animal. The sample may be diluted, purified, concentrated, filtered, dissolved, suspended or otherwise manipulated prior to immunoassay to optimize the immunoassay results. The fluid migrates distally through all the functional regions of the strip. The final distribution of the fluid in the individual functional regions depends on the adsorptive capacity and the dimensions of the materials used.
In some embodiments, porous solid supports, such as nitrocellulose, described hereinabove are preferably in the form of sheets or strips. The thickness of such sheets or strips may vary within wide limits, for example, from about 0.01 to 0.5 mm, from about 0.02 to 0.45 mm, from about 0.05 to 0.3 mm, from about 0.075 to 0.25 mm, from about 0.1 to 0.2 mm, or from about 0.11 to 0.15 mm. The pore size of such sheets or strips may similarly vary within wide limits, for example from about 0.025 to 15 microns, or more specifically from about 0.1 to 3 microns; however, pore size is not intended to be a limiting factor in selection of the solid support. The flow rate of a solid support, where applicable, can also vary within wide limits, for example from about 12.5 to 90 sec/cm (i.e., 50 to 300 sec/4 cm), about 22.5 to 62.5 sec/cm (i.e., 90 to 250 sec/4 cm), about 25 to 62.5 sec/cm (i.e., 100 to 250 sec/4 cm), about 37.5 to 62.5 sec/cm (i.e., 150 to 250 sec/4 cm), or about 50 to 62.5 sec/cm (i.e., 200 to 250 sec/4 cm). In specific embodiments of devices described herein, the flow rate is about 62.5 sec/cm (i.e., 250 sec/4 cm). In other specific embodiments of devices described herein, the flow rate is about 37.5 sec/cm (i.e., 150 sec/4 cm).
In some embodiments, the assay devices include a detector reagent. The detector reagent provides a means to detect the formation of a complex between an analyte (such as an Mtb antibody or antibodies) and a capture reagent (such as an antigenic composition as described above). A detector may be integrated into an immunoassay device (for example included in a conjugate pad, as described below), or may be applied to the device from an external source.
A detector may be a single reagent or a series of reagents that collectively serve the detection purpose. In some instances, a detector reagent is a labeled binding partner specific for the analyte. In other instances, a detector reagent collectively includes an unlabeled first binding partner specific for the analyte and a labeled second binding partner specific for the first binding partner and so forth. In each instance, a detector reagent specifically detects bound analyte of an analyte-capture reagent complex and, therefore, a detector reagent preferably does not substantially bind to or react with the capture reagent or other components localized in the analyte capture area. Such non-specific binding or reaction of a detector may provide a false positive result. Optionally, a detector reagent can specifically recognize a positive control molecule (such as a non-specific human IgG for a labeled Protein A detector, or a labeled Protein G detector, or a labeled anti-human Ab(Fc)) that is present in a secondary capture area.
The flow-through devices of the present invention comprise a capture reagent (e.g., antigenic composition as described above) immobilized on a solid support such as a microtiter plate or a membrane (such as, nitrocellulose, nylon, or PVDF). Characteristics of useful membrane have been previously described; however, it is useful to note that in a flow-through assay capillary rise is not a particularly important feature of a membrane as the sample moves vertically through the membrane rather than across it as in a lateral flow assay. In a simple representative format, the membrane of a flow-through device is placed in functional or physical contact with an absorbent layer (see, e.g., description of “absorbent pad” below), which acts as a reservoir to draw a fluid sample through the membrane. Optionally, following immobilization of a capture reagent, any remaining protein-binding sites on the membrane can be blocked (either before or concurrent with sample administration) to minimize nonspecific interactions.
In operation of a flow-through device, a fluid sample (such as a bodily fluid sample) is placed in contact with the membrane. Typically, a flow-through device also includes a sample application area (or reservoir) to receive and temporarily retain a fluid sample of a desired volume. The sample passes through the membrane matrix. In this process, an analyte in the sample (e.g., Mtb antibody or antibodies) can specifically bind to the immobilized capture reagent. Where detection of an analyte-capture reagent complex is desired, a detector reagent (e.g., labeled Protein A, labeled second antibody) can be added with the sample or a solution containing a detector reagent can be added subsequent to application of the sample.
If an analyte is specifically bound by capture reagent, a visual representative attributable to the particular detector reagent can be observed on the surface of the membrane. Optional wash steps can be added at any time in the process, for instance, following application of the sample, and/or following application of a detector reagent. A lateral flow device is an analytical device comprising a test strip, through which flows a test sample fluid that is suspected of containing an analyte of interest. The test fluid and any suspended analyte can flow along the strip to a detection zone in which the analyte (if present) interacts with a capture agent and a detection agent to indicate a presence, absence and/or quantity of the analyte. Many lateral flow devices are one-step lateral flow assays in which a biological fluid is placed in a sample area on a bibulous strip (though, non-bibulous materials can be used, and rendered bibulous, e.g., by applying a surfactant to the material), and allowed to migrate along the strip until the liquid comes into contact with a specific binding partner that interacts with an analyte in the liquid. Once the analyte interacts with the binding partner, a signal (such as a fluorescent or otherwise visible dye) indicates that the interaction has occurred. Multiple discrete binding partners can be placed on the strip (for example in parallel lines) to detect multiple analytes in the liquid. The test strips can also incorporate control indicators, which provide a signal that the test has adequately been performed, even if a positive signal indicating the presence (or absence) of an analyte is not seen on the strip.
The construction and design of lateral flow devices is described, for example, in Millipore Corporation, A Short Guide Developing Immunochromatographic Test Strips, 2nd Edition, pp. 1-40, 1999, available by request at (800) 645-5476; and Schleicher & Schuell, Easy to Work with BioScience, Products and Protocols 2003, pp. 73-98, 2003, available by request at Schleicher & Schuell BioScience, Inc., 10 Optical Avenue, Keene, N.H. 03431, (603) 352-3810; both of which are incorporated herein by reference. Lateral flow devices have a wide variety of physical formats. Any physical format that supports and/or houses the basic components of a lateral flow device in the proper function relationship is contemplated by this disclosure.
In some embodiments, lateral flow devices of the present invention comprise an elongated housing containing a bibulous lateral flow strip that extends substantially the entire length of housing. In some embodiments, the lateral flow strip is divided into a proximal sample application pad positioned below a sample introduction port, an intermediate test result membrane, and a distal absorbent pad. The flow strip is interrupted by a conjugate pad that contains labeled conjugate (such labeled second antibody). A flow path along the strip passes from the proximal pad, through conjugate pad, into a test result membrane, for eventual collection in absorbent pad. Selective binding agents (such as the antigenic compositions described above) are positioned on a proximal test line in the test result membrane. A control line is provided in the test result membrane slightly distal to the test line. A fluid sample containing an analyte of interest, such as Mtb antibody or antibodies, is applied to the sample pad through the sample introduction port. In some embodiments, the sample may be applied to the sample introduction port dropwise or by dipping the end of the device containing the sample introduction port into the sample. From the sample pad, the sample passes, for instance by capillary action, to the conjugate pad. In the conjugate pad, the analyte of interest may bind (or be bound by) a mobilized or mobilizable detector reagent. For example, an Mtb antibody may bind to a labeled (e.g., gold-conjugated) detector reagent (such as a second antibody contained in the conjugate pad. The analyte complexed with the detector reagent may subsequently flow to the test result membrane where the complex may further interact with a capture reagent, such as an antigenic composition as described above, which is immobilized at the proximal test line. The formation of the immunocomplex between Mtb antibody, labeled (e.g., gold-conjugated) detector reagent, and immobilized antigenic composition can be detected by the appearance of a visible line at the proximal test line, which results from the accumulation of the label (e.g., gold) in the localized region of the proximal test line. The control line may contain an immobilized, detector-reagent-specific binding partner, which can bind the detector reagent in the presence or absence of the analyte. Such binding at the control line indicates proper performance of the test, even in the absence of the analyte of interest.
The particular materials used in a particular lateral flow device will depend on a number of variables, including, for example, the analyte to be detected, the sample volume, the desired flow rate and others. In some embodiments, the sample pad receives the sample, and may serve to remove particulates from the sample. In some embodiments, the sample pad is cellulose. Sample pads may be treated with one or more release agents, such as buffers, salts, proteins, detergents, and surfactants. Such release agents may be useful, for example, to promote resolubilization of conjugate-pad constituents, and to block non-specific binding sites in other components of a lateral flow device, such as a nitrocellulose membrane. Representative release agents include, for example, trehalose or glucose (1%-5%), PVP or PVA (0.5%-2%), Tween 20 or Triton X-100 (0.1%-1%), casein (1%-2%), SDS (0.02%-5%), and PEG (0.02%-5%).
The conjugate pad holds a detector reagent. In some embodiments, a detector reagent may be applied externally, for example, from a developer bottle, in which case a lateral flow device need not contain a conjugate pad (see, for example, U.S. Pat. No. 4,740,468). Detector reagent(s) contained in a conjugate pad is typically released into solution upon application of the test sample. A conjugate pad may be treated with various substances to influence release of the detector reagent into solution. For example, the conjugate pad may be treated with PVA or PVP (0.5% to 2%) and/or Triton X-100 (0.5%). Other release agents include, without limitation, hydroxypropylmethyl cellulose, SDS, Brij and β-lactose.
The absorbent pad acts to increase the total volume of sample that enters the device. This increased volume can be useful, for example, to wash away unbound analyte from the membrane. Any of a variety of materials is useful to prepare an absorbent pad. In some device embodiments, an absorbent pad can be paper (i.e., cellulosic fibers). One of skill in the art may select a paper absorbent pad on the basis of, for example, its thickness, compressibility, manufacturability, and uniformity of bed volume. The volume uptake of an absorbent made may be adjusted by changing the dimensions (usually the length) of an absorbent pad.
A wide variety of detectable labels are useful with the assays described above in addition to the described enzymatic labels.
In another embodiment, the detectable label may be a gold or silver nanoparticle that can be enhanced with non-enzymatic silver deposition (SilverQuantTM). Methods for detection with silver or gold nanoparticles are described in detail in U.S. Pat. No. 7,321,829, incorporated by reference herein its entirety, as well as in US PUBL. 20090253586, also incorporated herein by reference in its entirety.
In another embodiment, the detectable label may be a Proximity Ligation Assay (PLA) reagent[25]. Proximity ligation assay (PLA) is an approach for protein quantitation that can use two different binder molecules (proximity probes) to bind to a specific detection target (See for example Fredriksson, S. et al., Nat. Biotechnol. 2002; 20(5): 473-77, Gullberg, M., et. al., Proc Natl Acad Sci USA. 2004; 101(22): 8420-24, Gullberg, M., et. al., Curr Opin Biotechnol. 2003; 14: 1-5, Pai, S., Ellington, A. D. and Levy, M., Nuc Acids Res. Oct. 19 2005; 33(18): e162, Landegren, U. and Fredriksson, S., US Patent Application 20020064779, May 30, 2002, Fredriksson, S., US Patent Application 20050003361, all pof which are incorporated by reference herein in their entirety. Typical binders include polyclonal or monoclonal antibody pairs. Each binder molecule can be conjugated to a specific oligonucleotide. One binder's oligonucleotide can form the “left” side of a real-time PCR amplicon, while the other binder can form the “right” side. When the two binders find and attach to the same target, the left and right oligomers are brought into close proximity. With the addition of a connector oligonucleotide (splint) and ligase enzyme, the left and right oligomers can become ligated and thereby allow for the formation of a complete target for a real-time PCR. Further addition of Taqman reaction components followed by thermocycling generates real-time sequence detection data output.
In another embodiment, the detectable label may be a radiolabel, and the assay termed a radioimmunoassay (RIA), as is well known in the art. The radioisotope can be detected by a gamma counter, a scintillation counter or by autoradiography. Isotopes which are particularly useful for the purpose of the present invention are 125I, 131I, 35S, 3H and 14C.
It is also possible to label the antigen or antibody reagents with a fluorophore. When the fluorescently labeled antibody is exposed to light of the proper wave length, its presence can then be detected due to fluorescence of the fluorophore. Among the most commonly used fluorophores are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde, fluorescamine or fluorescence-emitting metals such as 152Eu or other lanthanides. These metals are attached to antibodies using metal chelators.
The antigen or antibody reagents useful in the present invention also can be detectably labeled by coupling to a chemiluminescent compound. The presence of a chemiluminescent-tagged antibody or antigen is then determined by detecting the luminescence that arises during the course of a chemical reaction. Examples of useful chemiluminescent labeling compounds are luminol, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester. Likewise, a bioluminescent compound such as a bioluminescent protein may be used to label the antigen or antibody reagent useful in the present invention. Binding is measured by detecting the luminescence. Useful bioluminescent compounds include luciferin, luciferase and aequorin.
Detection of the detectably labeled reagent according to the present invention may be accomplished by a scintillation counter, for example, if the detectable label is a radioactive gamma emitter, or by a fluorometer, for example, if the label is a fluorophore. In the case of an enzyme label, the detection is accomplished by colorimetry to measure the colored product produced by conversion of a chromogenic substrate by the enzyme. Detection may also be accomplished by visual comparison of the colored product of the enzymatic reaction in comparison with appropriate standards or controls.
In some embodiments, the one or more of the peptides or conjugates described above (alone or in combination) are used as an antigen stimulation mixture for cell based assays including, but not limited to, cytokine release assays (particularly interferon gamma release and interleukin 12) as measured by ELISA, Elispot, or bead based methods. In other embodiments, the peptides or conjugates described above (alone or in combination) are used in T-cell capture assays. In still other embodiments, the peptides or conjugates described above (alone or in combination) are used as an antigenic substitute for tuberculin in the tuberculin skin test (TST).
In some embodiments, the present invention provides kits for use in detecting Mtb antibodies in a sample (such as, a biological sample). Such kits can be used, for example, to determine whether an animal has been exposed to Mtb or has an Mtb infection. Certain embodiments of the disclosed kits are generally portable and provide a simple, rapid, and/or cost-effective way to determine Mtb infection without the need for specialized laboratory facilities, such as in a point-of-care facility.
In some embodiments, the kits of the present invention include one or more immunoassay devices (and/or antigen-coated microtiter plates) as disclosed herein and a carrier means, such as a box, a bag, a satchel, plastic carton (such as molded plastic or other clear packaging), wrapper (such as, a sealed or sealable plastic, paper, or metallic wrapper), or other container. In some examples, kit components will be enclosed in a single packaging unit, such as a box or other container, which packaging unit may have compartments into which one or more components of the kit can be placed. In other examples, a kit includes one or more containers, for instance vials, tubes, and the like that can retain, for example, one or more biological samples to be tested, positive and/or negative control samples or solutions (such as, a positive control serum containing Mtb antibodies), diluents (such as, phosphate buffers, or saline buffers), detector reagents (e.g., for external application to a kit device), substrate reagents for visualization of detector reagent enzymes (such as, 5-bromo-4-chloro-3-indolyl phosphate, nitroblue tetrazolium in dimethyl formamide), and/or wash solutions (such as, Tris buffers, saline buffer, or distilled water).
Other kit embodiments include syringes, finger-prick devices, alcohol swabs, gauze squares, cotton balls, bandages, latex gloves, incubation trays with variable numbers of troughs, adhesive plate sealers, data reporting sheets, which may be useful for handling, collecting and/or processing a biological sample. Kits may also optionally contain implements useful for introducing samples into a sample chamber of an immunoassay device, including, for example, droppers, Dispo-pipettes, capillary tubes, rubber bulbs (e.g., for capillary tubes), and the like. Still other kit embodiments may include disposal means for discarding a used immunoassay device and/or other items used with the device (such as patient samples, etc.). Such disposal means can include, without limitation, containers that are capable of containing leakage from discarded materials, such as plastic, metal or other impermeable bags, boxes or containers.
In some embodiments, a kit of the present invention will include instructions for the use of an immunoassay device or antigen-coated plate. The instructions may provide direction on how to apply sample to the test device or plate, the amount of time necessary or advisable to wait for results to develop, and details on how to read and interpret the results of the test. Such instructions may also include standards, such as standard tables, graphs, or pictures for comparison of the results of a test. These standards may optionally include the information necessary to quantify analyte using the test device, such as a standard curve relating intensity of signal or number of signal lines to an amount of analyte therefore present in the sample.
In some embodiments, the present invention provides a vaccine comprising one or more of the peptides described above (i.e. SEQ ID NOs.:1-149). As used herein, the term “vaccine” refers to any combination of peptides or a single peptide formulation. There are various reasons why one might wish to administer a vaccine of a combination of the peptides of the present invention rather than a single peptide. Depending on the particular peptide that one uses, a vaccine might have superior characteristics as far as clinical efficacy, solubility, absorption, stability, toxicity and patient acceptability are concerned. It should be readily apparent to one of ordinary skill in the art how one can formulate a vaccine of any of a number of combinations of peptides of the present invention. There are many strategies for doing so, any one of which may be implemented by routine experimentation.
The peptides of the present invention may be administered as a single agent therapy or in addition to an established therapy, such as inoculation with live, attenuated, or killed virus, or any other therapy known in the art to treat the target disease or epitope-sensitive condition.
The appropriate dosage of the peptides of the invention may depend on a variety of factors. Such factors may include, but are in no way limited to, a patient's physical characteristics (e.g., age, weight, sex), whether the compound is being used as single agent or adjuvant therapy, the type of MHC restriction of the patient, the progression (i.e., pathological state) of the infection or other epitope-sensitive condition, and other factors that may be recognized by one skilled in the art. In general, an epitope or combination of epitopes may be administered to a patient in an amount of from about 50 micrograms to about 5 mg; dosage in an amount of from about 50 micrograms to about 500 micrograms is especially preferred.
In some embodiments, the peptides are expressed on bacteria, such as lactococcus and lactobacillus, or expressed on virus or virus-like particles for use as vaccines. In some embodiments, the peptides are incorporated into other carriers as are known in the art. For example, in some embodiments, the polypeptides comprising one or more epitopes are conjugated or otherwise attached to a carrier protein. Suitable carrier proteins include, but are not limited to keyhole limpet hemocyanin, bovine serum albumin, ovalbumin, and thyroglobulin. In yet other embodiments the polypeptide may be fused to an Fc region of an immunoglobulin for delivery to a mucosal site bearing corresponding receptors.
One may administer a vaccine of the present invention by any suitable method, which may include, but is not limited to, systemic injections (e.g., subcutaneous injection, intradermal injection, intramuscular injection, intravenous infusion) mucosal administrations (e.g., nasal, ocular, oral, vaginal and anal formulations), topical administration (e.g., patch delivery), or by any other pharmacologically appropriate technique. Vaccination protocols using a spray, drop, aerosol, gel or sweet formulation are particularly attractive and may be also used. The vaccine may be administered for delivery at a particular time interval, or may be suitable for a single administration.
Vaccines of the invention may be prepared by combining at least one peptide with a pharmaceutically acceptable liquid carrier, a finely divided solid carrier, or both. As used herein, “pharmaceutically acceptable carrier” refers to a carrier that is compatible with the other ingredients of the formulation and is not toxic to the subjects to whom it is administered. Suitable such carriers may include, for example, water, alcohols, natural or hardened oils and waxes, calcium and sodium carbonates, calcium phosphate, kaolin, talc, lactose, combinations thereof and any other suitable carrier as will be recognized by one of skill in the art. In a most preferred embodiment, the carrier is present in an amount of from about 10 uL (micro-Liter) to about 100 uL.
In some embodiments, the vaccine composition includes an adjuvant. Examples of adjuvants include, but are not limited to, mineral salts (e.g., aluminum hydroxide and aluminum or calcium phosphate gels); oil emulsions and surfactant based formulations (e.g., MF59 (microfluidized detergent stabilized oil-in-water emulsion), QS21 (purified saponin), Ribi Adjuvant Systems, AS02 [SBAS2] (oil-in-water emulsion+MPL+QS-21), Montanide ISA-51 and ISA-720 (stabilized water-in-oil emulsion); particulate adjuvants (e.g., virosomes (unilamellar liposomal vehicles incorporating influenza haemagglutinin), AS04 ([SBAS4] A1 salt with MPL), ISCOMS (structured complex of saponins and lipids), polylactide co-glycolide (PLG); microbial derivatives (natural and synthetic), e.g., monophosphoryl lipid A (MPL), Detox (MPL+M. Phlei cell wall skeleton), AGP [RC-529] (synthetic acylated monosaccharide), DC_Chol (lipoidal immunostimulators able to self organize into liposomes), OM-174 (lipid A derivative), CpG motifs (synthetic oligonucleotides containing immunostimulatory CpG motifs), modified LT and CT (genetically modified bacterial toxins to provide non-toxic adjuvant effects); endogenous human immunomodulators (e.g., hGM-CSF or hIL-12 (cytokines that can be administered either as protein or plasmid encoded), Immudaptin (C3d tandem array); and inert vehicles, such as gold particles. In various embodiments, vaccines according to the invention may be combined with one or more additional components that are typical of pharmaceutical formulations such as vaccines, and can be identified and incorporated into the compositions of the present invention by routine experimentation. Such additional components may include, but are in no way limited to, excipients such as the following: preservatives, such as ethyl-p-hydroxybenzoate; suspending agents such as methyl cellulose, tragacanth, and sodium alginate; wetting agents such as lecithin, polyoxyethylene stearate, and polyoxyethylene sorbitan mono-oleate; granulating and disintegrating agents such as starch and alginic acid; binding agents such as starch, gelatin, and acacia; lubricating agents such as magnesium stearate, stearic acid, and talc; flavoring and coloring agents; and any other excipient conventionally added to pharmaceutical formulations.
Further, in various embodiments, vaccines according to the invention may be combined with one or more of the group consisting of a vehicle, an additive, a pharmaceutical adjunct, a therapeutic compound or agent useful in the treatment of the desired disease, and combinations thereof.
EXAMPLES
Example 1
Material and Methods
Peptides
A partial proteome mapping peptide array of 6912 peptides 15 amino acids in length with a 12 amino acid overlap (product RT-HD-TUB) for the reference strain Mycobacterium tuberculosis H37Rv (JPT Peptide Technologies, GmbH, Berlin, Germany) was used to perform preliminary studies. A refined set of 1075 peptides were designed for proteins of interest from these experiments, covering 246 proteins, with 15 amino acid length with a 3 amino acid overlap.
Array Preparation
Arrays were manufactured with peptides synthesized in the manner described in Nahtman et al[27]. Briefly, 1 mM solution of each peptide was printed on epoxy functionalized glass slides (Corning Epoxy #440042) using a contact array printer (JPT Peptide). Arrays were printed such that each peptide was printed in triplicate. For the refined set of 1075 peptides, arrays were printed with 4 subarrays per slide, with triplicate spots. Human IgG was printed as internal controls for the assay, and orientation for the data analysis.
Serum Samples
Preliminary experiments were performed with samples generously donated by the Pathogen Detection Laboratory at the California National Primate Center (University of California-Davis, Davis, Calif.). Six serum samples were used for the preliminary studies, including 4 time points during a course of an intentional experimental infection, and serum from 2 known test positive macaques.
Samples for assays performed on the refined arrays were generously donated by the Oregon National Primate Research Center (Oregon Health and Science University, Beaverton, Oreg.). Sera from twelve animals quarantined and necropsied following an outbreak of M. tb in the colony were compared with sera from previous blood collections, 1-2 years prior to the outbreak. In addition to pre-infection sera, 4 test negative samples from the same colony were also run on the refined arrays to establish an average “non-infected” immune profile. Additionally, 56 test negative samples from the Wisconsin National Primate Center (gift of Dr. Jonah Sacha) and the Caribbean National Primate Center (gift of Dr. Carlos Sariol) were also included in the negative serum set. Table 1 shows the individual serum samples, their source, and previous test results for tuberculin skin test (TST) and other confirmatory testing. Sera were stored at −80° C. until use.











TABLE 1





Sample

Sample 
Disease



ID
Source
Type
State 
TST Test







17846
WNPRC
Normal
Naïve
Negative


17847
WNPRC 
Normal
Naïve
Negative


17848
WNPRC
Normal
Naïve
Negative


17849
WNPRC 
Normal
Naïve
Negative


17850
WNPRC 
Normal
Naïve
Negative


17851
WNPRC 
Normal
Naïve
Negative


17852
WNPRC 
Normal
Naïve
Negative


17853
WNPRC 
Normal
Naïve
Negative


17854
WNPRC 
Normal
Naïve
Negative


17855
WNPRC 
Normal
Naïve
Negative


17856
WNPRC 
Normal
Naïve
Negative


17857
WNPRC 
Normal
Naïve
Negative


17858
WNPRC 
Normal
Naïve
Negative


17859
WNPRC 
Normal
Naïve
Negative


17860
WNPRC 
Normal
Naïve
Negative


17861
WNPRC 
Normal
Naïve
Negative


17862
WNPRC 
Normal
Naïve
Negative


17863
WNPRC 
Normal
Naïve
Negative


17864
WNPRC 
Normal
Naïve
Negative


17865
WNPRC 
Normal
Naïve
Negative


17866
WNPRC 
Normal
Naïve
Negative


17867
WNPRC 
Normal
Naïve
Negative


17868
WNPRC 
Normal
Naïve
Negative


17869
WNPRC 
Normal
Naïve
Negative


20758
ONPRC 
Disease
Post
Positive


20284
ONPRC 
Disease
Post
Positive


22319
ONPRC 
Disease
Post
Positive


28642
ONPRC 
Disease
Post
Positive


28643
ONPRC 
Disease
Post
Positive


28655
ONPRC 
Disease
Post
Positive


28667
ONPRC 
Disease
Post
Positive


28674
ONPRC 
Disease
Post
Positive


28676
ONPRC 
Disease
Post
Positive


28677
ONPRC 
Disease
Post
Positive


29417
ONPRC 
Disease
Post
Positive


20758
ONPRC 
Normal 
Pre
Negative


20284
ONPRC 
Normal 
Pre
Negative


22319
ONPRC 
Normal 
Pre
Negative


28642
ONPRC 
Normal 
Pre
Negative


28643
ONPRC 
Normal 
Pre
Negative


28655
ONPRC 
Normal 
Pre
Negative


28667
ONPRC 
Normal 
Pre
Negative


28674
ONPRC 
Normal 
Pre
Negative


28676
ONPRC 
Normal 
Pre
Negative


28677
ONPRC 
Normal 
Pre
Negative


29417
ONPRC 
Normal 
Pre
Negative


27790
ONPRC 
Normal 
Naïve
Negative


26023
ONPRC 
Normal 
Naïve 
Negative


22819
ONPRC 
Normal 
Naïve
Negative


23351
ONPRC 
Normal 
Naïve 
Negative


18171
CaNPRC
Normal
Naïve 
Negative


18172
CaNPRC
Normal
Naïve 
Negative


18173
CaNPRC
Normal
Naïve
Negative


18174
CaNPRC
Normal
Naïve
Negative


18175
CaNPRC
Normal
Naïve 
Negative


18176
CaNPRC
Normal
Naïve 
Negative


18177
CaNPRC
Normal
Naïve 
Negative


18178
CaNPRC
Normal
Naïve 
Negative


18179
CaNPRC
Normal
Naïve 
Negative


18180
CaNPRC
Normal
Naïve 
Negative


18181
CaNPRC
Normal
Naïve 
Negative


18182
CaNPRC
Normal
Naïve 
Negative


18183
CaNPRC
Normal
Naïve 
Negative


18184
CaNPRC
Normal
Naïve 
Negative


18185
CaNPRC
Normal
Naïve 
Negative


18186
CaNPRC
Normal
Naïve 
Negative


18187
CaNPRC
Normal
Naïve 
Negative


18188
CaNPRC
Normal
Naïve
Negative


18189
CaNPRC
Normal
Naïve
Negative


18190
CaNPRC
Normal
Naïve
Negative


18191
CaNPRC
Normal
Naïve
Negative


18192
CaNPRC
Normal
Naïve
Negative


18193
CaNPRC
Normal
Naïve
Negative


18194
CaNPRC
Normal
Naïve
Negative


18195
CaNPRC
Normal
Naïve
Negative


18196
CaNPRC
Normal
Naïve
Negative


18197
CaNPRC
Normal
Naïve
Negative


18198
CaNPRC
Normal
Naïve
Negative


18199
CaNPRC
Normal
Naïve
Negative


18200
CaNPRC
Normal
Naïve
Negative


18201
CaNPRC
Normal
Naïve
Negative


18202
CaNPRC
Normal
Naïve
Negative










Key








Naïve
Normal, uninfected animal


Pre
Normal sample from animal that later was diagnosed with TB


Post
Disease sample from animal diagnosed with TB


ONPRC
Oregon National Primate Center


WNPRC
Wisconsin National Primate Center


CaNRPC
Caribbean National Primate Center






Sample Processing

A reusable frame and gasket system (Intuitive Biosciences, Madison, Wis.) for incubation was applied to the peptide microarrays. Serum was diluted 1:100 in Dilution Buffer (Intuitive Biosciences), and incubated in one well of the array. Detection of bound IgG from the serum samples was performed using the CSA: Simian Detection kit (Intuitive Biosciences). Briefly, diluted serum was incubated for 1 hr at room temperature. Each well was washed 5 times, followed by addition of a biotinylated anti-simian IgG antibody diluted 1:10,000, and incubated for 1 hour at room temperature. After 5 repeat washes, 1 mL of gold conjugated anti-biotin was incubated for 45 minutes at room temperature. After 5 wash steps, slides were rinsed with 1 mL of water and immune complexes visualized by addition of SilverQuant® reagents (Intuitive Biosciences). After 3 minutes incubation in dark, slides were quickly washed with water and dried.
Data Acquisition
The peptide microarray slides were scanned with the AthenaQuant System from Intuitive Biosciences. Saved images were analyzed with AthenaQuant® software from Intuitive Biosciences, and background subtracted data exported in Excel files. Relative Intensity Units (RIU) were calculated by AthenaQuant and reported for each peptide feature on the microarray.
Statistical Analysis
Preliminary studies used RIU data from the mean of triplicate spots for each sample to calculate a fold over normal value.
The majority of the data management and analysis steps were accomplished with the Golden Helix SNP & Variation Suite (SVS) software version 7.5 (Golden Helix, Boseman, Mont.). Data was normalized by two methods: quantile normalization and Principal Components Analysis. Comparisons of infected and normal samples were conducted using two statistical tests: a Two-Sample T-Test and a Mann-Whitney (MW) Rank Sum Test. Two t-tests and two MW tests were performed. Each test was performed for the comparison of the matched pair (pre infection vs post infection) data and the comparison of the 12 TB-positive samples to the 60 naive samples. The matched-pair tests were performed only in quantile-normalized data, while the 12 positive vs 60 naive tests were performed in the PCA-corrected data. The resulting p-values for each comparison were reported in Excel, and a sum of the p-values for the four tests were calculated and used to sort the peptides in order of significance.
Results
Samples from the Oregon National Primate Center (ONPRC) were acquired following a series of positive TST during routine screening. One animal presented a positive TST, resulting in the immediate quarantine of that animal and the other housed in the same room, a total of twelve animals. Several tests were performed in parallel with repeated TST on the quarantined animals. Of the 12 animals, 7 tested positive by TST performed at the ONPRC. A PrimaTB STAT-Pak, referred to as Lateral Flow in Table 2, was performed according to the manufacturer's instructions by the ONPRC. Whole blood samples were collected from these animals and sent to the Pathogen Detection Laboratory at UC-Davis (PDL), where the Primagam assay for measuring IFN-γ release was performed alongside an ESAT-6 ELISA for detection of ESAT-6 specific antibodies. At least 7 animals tested positive by these methods, and the animals were euthanized and post-mortem testing performed. Mycobacterium culture was performed from lung samples by the National Veterinary Services Laboratories (Ames, Iowa) and found 8 samples culture positive. Additionally, PCR testing for detection of Mycobacteria from the samples was performed by the Washington Animal Disease Diagnostic Lab (WADDL) but only found a few positive samples. Lastly, gross pathology of lungs was performed during necropsy of the animals and lesions were found in ten of the twelve animals. Serum samples collected from these twelve animals during quarantine were received along with serum samples from blood draws at least 2 years prior to the outbreak, when the animals had negative TST. These pre-infection and post-infection samples were used in addition to the other naïve samples listed in Table 1 to perform antibody detection assays using the refined TB peptide microarrays. Statistical analysis of the 12 positive sera compared to the 60 naïve sera was performed, and a set of 5 peptides were chosen as epitopes to distinguish between naïve and positive samples. Using these 5 peptides as classifiers, the results for the “post” or infected samples for the 12 animals was divided by the “pre” or non-infected sample. The log 2 ratio of the fold over naïve was calculated for the 12 animals, and the sum of these 5 ratios calculated. The sum of the log 2 ratios is shown in Table 2. Importantly, animal 28647 that was negative by every method of testing showed no difference in the “pre” and “post” measurements, while the remaining 11 samples scored greater than 6 (at least a 2-fold increase in the “pre” to “post” measurement for several of the 5 classifier peptides).







TABLE 2







TB analysis summary for NHPs from ONPRC. Twelve NHPs were assessed


for TB disease using TST, PRIMAGRAM, Lateral Flow (PrimaTB SAT-Pak), ESAT-6


ELISA, tubercule lesions, M. tb culture, and PCR analysis for M. tb gene sequences.


Results from this work are shown as Intuitive Bio. Analysis was determined by the sum of


the fold-change (FC) of specific peptides compared to negative controls (see text).


Analysis results: Red: positive (+), Yellow: weak positive (+/−), Green: negative (−), and


No color: not analyzed (N/A).























Example 2
This example demonstrates the use of peptide microarrays to discover novel peptide biomarkers. Briefly, JPT microarrays were incubated with diluted serum from M. tb infected and normal NHPs and absorbed Ab detected with biotinylated anti-simian IgG. Anti-biotin IgG-gold conjugate and SilverQuant® silver deposition technology detected the biotin on the microarray slides. Slides with silver spots were imaged using the AthenaQuant® System, scanned, and analyzed to quantify the silver spots. Relative spot intensities from infected animals were compared to normal samples to identify peptides that best differentiated infected from normal. These peptides were synthesized, conjugated to BSA, and the discrimination verified in an Ag microarray using additional serum samples and the same detection technology.
Methods
Screening Peptide Microarrays—The initial Ab screen employed a selected segment of the M. tb proteome, determined from the sequenced genome of the reference strain M. tb H37Rv. The peptide microarray consisted of 6,912 15-aa peptides, each with a 12-aa overlap. Based on the results, JPT constructed a custom peptide micro-array with 1,075 15-aa peptides, each with a 3-aa overlap, that encompass 246 different M. tb proteins (secondary screen). The initial screen contained 1 array/slide (i.e., for 1 sample); the custom array had 4 sub-arrays per slide.
Verification Peptide Microarray—Based on the initial and secondary screening results, 20 peptides were synthesized with a carboxyl terminal cysteine and conjugated to BSA through a NHS-maleimide linker (Pierce Bio-technologies) and arrayed, both individually and mixed, at optimal concentrations and printing formulations onto Protein Microarray Slides (IBI) in a 24 sub-array format. From these experiments, 4 peptide-BSA conjugates were mixed, each at 25 μg/ml in Array Print Buffer (IBI) and arrayed onto Protein Microarray Slides along with other viral Ag from the CSA: Simian Basic (IBI).
Serum samples—The initial Ab screen was performed in 2 separate experiments using serum samples from rhesus macaques donated by the Pathogen Detection Laboratory at the California NPRC (CNPRC; University of California-Davis). A total of 4 positive serum samples were analyzed; 3 samples from an experimental infection time-course experiment [2, 4, and 20 weeks post-infection (WPI)] and 1 sample from a macaque that tested positive by the TST, PCR, and culture (natural infection). The pre-infection sample was used as the negative control serum.
The secondary screen using the custom array was performed using samples donated by the Pathogen Detection Laboratory at CNPRC, the Oregon NPRC(ONPRC; Oregon Health and Science University, Beaverton, Oreg.), and Tulane NRPC (TNPRC; Tulane University). Positive serum samples from the ONPRC were derived from 12 animals that were initially quarantined, then euthanized and necropsied following an M. tb outbreak (natural infection) in a colony. The negative control sera from the same animals were from stored collections. Positive and negative (pre-infection) samples from TNPRC were drawn from an experimental infection time-course experiment with 5-6 points from 6 animals. In addition, 56 negative samples from the Wisconsin NPRC and the Caribbean NPRC were also analyzed in the secondary screen.
Screening Microarray Assay Method—For the initial screen, the peptide microarray slides were assayed using the CSA: Simian Detection kit (Prod. No. 12-1006, Intuitive Biosciences) protocol. Briefly, Abs in diluted serum were permitted to bind to peptide Ags and were detected with a combination of biotinylated anti-simian IgG Ab and anti-biotin IgG-gold conjugate. Ab-gold complexes were visualized by adding SilverQuant® Reagents, the slides quickly washed with water and dried. The slides were imaged with the AthenaQuant System by Intuitive Biosciences, and scanned. Silver spots in the images were identified, quantified, and the background subtracted using AthenaQuant® software (Intuitive Biosciences). Quantified spot intensities were reported as relative intensity units (RIU) in Excel and matched to the appropriate peptide spot using a GAL (GenePix Array List) file from JPT (except for the verification assays).
Results
For the primary screening assay, we calculated the average RIU of triplicate spots for each peptide for each sample then divided this average by the average of the negative control sample for the same peptide. For each peptide, we calculated the sum of the fold change over the negative control ratio by adding the individual ratios of 2, 4, and 20 WPI with the natural infection sample to a Sum Fold Change (data not shown). We selected the top 756 peptides for further evaluation and inclusion on the secondary screening arrays.
The entire collection of available serum samples was assayed using the secondary screen peptide microarray. Heilman Consulting (Madison, Wis.) used quantile normalization and principal components analysis (PCA) to analyze 88 positive and 68 negative samples from ONPRC, CNPRC, and TNPRC. Infected and normal samples were compared using a Two-Sample T-Test and a Mann-Whitney (MW) Rank Sum Test. The 20 peptides with the highest rank are summarized in Table 3. Some peptides originate from well-known antigenic proteins, such as ESAT-6, while others are derived from proteins with unknown function and previously not known for immunogenicity in NHPs.







TABLE 3







Top 20 peptides. Using Two-Sample T-Test and a Mann-Whitney


Rank Sum Test, peptides were assessed for discrimination of 


M. tb positive serum samples compared to negative samples.









Peptide
Gene name
Protein Name












1
Rv0104
conserved hypothetical protein


2
Rv2873
cell surface lipoprotein MPT83


3
Rv1037c,
putative ESAT-6 like protein



Rv1198,




Rv3619c



4
Rv2497c
putative alpha-keto acid dehydrogenase


5
Rv0918
conserved hypothetical protein


6
Rv3875
ESAT-6


7
Rv3286c
sigF, sigma factor F


8
Rv1509
conserved hypothetical protein


9
Rv0099
possible fatty-acid-CoA synthetase


10
Rv0040c
28 kDa antigen


11
Rv0019
conserved hypothetical protein


12
Rv1926c
MPT63


13
Rv3879c
espK


14
Rv3871
ESX conserved, unknown function


15
Rv3875
ESAT-6


16
Rv0085
putative hydrogenase


17
Rv1009
putative resuscitation promoting factor


18
Rv2006
putative trehalose-6-phosphate phosphatase


19
Rv0050
putative ponA1, penicillin binding protein


20
Rv3874
CFP-10









The samples acquired from the ONPRC had positive TST results during routine screening at the facility [personal communication, K. Andrews]. After one animal presented a positive TST, it was immediately quarantined along with the NHPs that were housed in the same enclosure—a total of 12 animals. Additional tests were performed in parallel on the quarantined animals. Of the 12 animals, 7 tested positive by TST (performed at the ONPRC). All 12 were then tested with a PrimaTB STAT-Pak lateral flow device (Chembio Diagnostic Systems), an IFGA (PRIMAGAM), and an ESAT-6 ELISA. Each animal was euthanized and a necropsy performed. M. tb culture was performed at National Veterinary Services Laboratories (Ames, Iowa) and PCR analysis at Washington Animal Disease Diagnostic Lab (WADDL). Finally, gross pathology of lungs was performed during necropsy to identify lesions indicative of tuberculosis. Table 2 above shows the results of the analyses and demonstrates the inability of current assays to conclusively identify a true tuberculosis infection as indicated by the necropsy results.
Serum samples from the same 12 NHPs were assayed using the secondary screen peptide microarray. The fold change (FC) increase in signal intensity for each peptide was calculated by dividing the RIU for the TB-infected sample by the mean of the 40 negative samples (pre-infection plus TST negatives). The sum of the FC for 20 individual peptides was calculated for each animal and shown in Table 2 as negative (<30), weak positive (30-45), and positive (>45). Using these qualifications, our assay results showed 11 of 12 animals had Abs specific to these 20 peptides.
Samples from experimentally TB-infected animals at TNPRC were run on IBI's verification peptide microarrays to determine each peptide's utility at identifying positive samples. Using 141 negatives and 35 positives (experimental and natural infections), a receiver operating characteristic (ROC) analysis was performed for each peptide (data not shown). Peptides 4, 6, 15, and 20 provided the best sensitivity and specificity, but no single peptide had >90% sensitivity. To improve this sensitivity, we pooled equal volumes of the 4 peptides (Mix A) to create an Ag mix that detected all positive samples (FIG. 1). For example, Sample CA75 was detected by Peptide 20 alone and Sample HI36 was detected by Peptide 15 alone. Notably, only 4 out of 20 peptides could discriminate between positive and negative serum samples. The Mix A formulation was optimized to reduce background signal (data not shown), arrayed, and used to screen 141 negative and 35 positive serum samples. An ROC analysis was performed and using a cutoff value of 7364 RIU, the calculated sensitivity was 97.1% and specificity was 87.2% (FIG. 2).
Example 3
This example demonstrates that not all ESAT-6 spanning peptides are useful to identify TB-positive animals. As can be seen in the following table, the first two peptides from the N-C terminus of ESAT-6 are not useful in distinguishing between TB positive and negative groups. This was taken from the second round of screening data. Peptides were selected that had a high p-value AND Mann-Whitney rank. The peptides not highlighted were not used any further in the development process because they were not statistically relevant (no change between TB and negative groups) and had a low fold change rank. FC rank measured the magnitude of the response.

















P-value
P-Value
MW
FC


Order
Probe ID
(T-test)
rank
Rank
rank




















1
MTEQQWNF
0.019702746
239
304
44



AGIEAAA






 


2
AAASAIQG
0.029676213
275
104
263



NVTSIHS






 


3
IHSLLDEG
5.92E−06
4
36
47



KQSLTKL






 


4
TKLAAAWG
5.04E−06
3
1
3



SGSEAY






 


5
EAYQGVQQ
1.04E−07
2
4
1



KWDATAT






 


6
ELNNALQN
3.64E−05
9
677
20



LARTISE






 


8
QAMASTEG
0.079415726
409
687
320



NVTGMFA









Example 4
Using a mix of peptides 6, 15, 17, and 20 on the CSA: Simian array platform, 6 of 12 positive samples were correctly identified. See FIG. 3. Looking at signal for individual peptides, early and active infection may be better identified by examining the RTU for Peptides 3 and 9, in addition to 6, 15, and 20. For latently infected animals, Peptides 2, 3, 15, 19, and 20 are seroreactive and may better identify latently infected animals.
REFERENCES


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## Claims

1. An immunoassay device comprising a first capture agent comprising a base peptide comprising SEQ ID NO:141 and up to 5 amino acids on either or both of the amino- or carboxy-terminus of the base peptide, a second capture reagent comprising a base peptide comprising SEQ ID NO:145 and up to 5 amino acids on either or both of the amino- or carboxy-terminus of the base peptide, a third capture reagent comprising a peptide encoding SEQ ID NO:147; and a fourth capture reagent comprising a peptide encoding SEQ ID NO:98.

2. The immunoassay device of claim 1, further comprising a surface having at least one capture agent displayed thereon.