OF INVASIVE FUNGAL INFECTIONS

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.

61/916,542, filed December 16, 2013, and U.S. Provisional Application No.

62/062,523, filed October 10, 2014, which are incorporated herein by reference in their entirety.

BACKGROUND

Histoplasma capsulatum is a fungus that has a distribution in temperate climates, especially in endemic areas of North, South, and Central America (Scheel et al, 2009; Daher et al, 2007; Huber et al, 2008; Baddley et al, 201 1; Chu et al, 2006). Histoplasmosis is the most common endemic mycosis in the U.S. Infection occurs after inhalation exposure to microconidia from mold that grows in soil. After acquisition into the lungs, conidia are ingested by resident and recruited phagocytes, which migrate to resident lymphatic tissue and organs of the reticuloendothelial system (RES). The intracellular yeast form of the organism can remain viable inside macrophages, but robust interferon-gamma (INFy) Thl immunity assists to keep disease in check, with development of granulomatous inflammation. Hence, infection is usually asymptomatic or subclinical in subjects who have intact cellular immunity. However, in subjects in whom immunity is impaired, such as subjects with transplanted organs or TNFa inhibition, infection can occur after acquisition and with reactivation of latent infection. Such an infection can be severe or fatal.

Studies performed in the 1960s measured skin-test hypersensitivity to assess exposure (Furcolow, 1963), with results suggesting high rates of latent infection in healthy subjects, with rates some areas exceeding 80%. Establishing the diagnosis of infection and disease, however, remains difficult today. No commercial tests are available to detect skin hypersensitivity responses. Even with active, disseminated disease, diagnosis is difficult, and clinicians are often misled both by the variety of clinical manifestations and the low sensitivity of diagnostic assays. Sensitivity of organism culture and cytopathology is very low; hence, immunodiagnostics have become important. Reference laboratories currently provide tests to measure circulating antibodies (Ab) and/or antigens (Ag), but the performance of these tests is limited, with low sensitivity of Ab detection, and Ag cross-reactivity with other fungi. With diagnostic limitations, outcomes can be poor. Also, the inability to reliably detect latent infection has limited development of strategies to prevent progression of disease in settings of impending immune suppression, as is done with other latent infections, such as tuberculosis (TB).

The pathogenesis of histoplasmosis and TB are similar. Both infections develop after inhaled exposure of an organism that remains latent in host phagocytes and kept dormant with T-cell dependent host response. Clinical syndromes are almost exactly alike. For years, skin tests to measure delayed type sensitivity to

Mycobacterial antigens (Purified Protein Derivative; PPD) were the backbone for identifying prior infection. More recently, T-cell diagnostic assays have

revolutionized TB diagnostics, with two commercially available interferon-gamma release assays (IGRAs) now proving to have improved sensitivity and specificity compared to skin testing. Also, these tests allow interpretation of more quantitative Type-1 responses, potentially providing prognostic implications. Being able to uncover latent infection better has enabled therapeutic strategies to prevent TB in subjects with impending immune suppression, such as with organ transplant and TNF- a inhibition. Because of the difficulties of identifying latent infection with pathogenic fungi, therapeutic strategies to prevent active pathogenic fungi infection are not available.

Although infection is typically self-limited in subjects who can mount effective Type-1 responses, severe disease occurs when immune suppressed subjects become acutely infected, and when the host response fails to keep the organism in check, such as with aging, progressive HIV infection, after treatment with biological inhibitors of TNF-a and after transplant (Wood et al, 2003). These are situations in which it would be beneficial to reliably predict latent infection to devise prevention strategies. Instead, now, infection is usually fairly widespread when it is recognized in the subject. A recent retrospective cohort study of documented histoplasmosis in U.S. organ transplant patients noted that most disease was diagnosed after dissemination and associated with a mortality rate of 10% (Assi et al). SUMMARY

In one aspect, the presently disclosed subject matter provides a method for diagnosing an invasive fungal infection in a subject, the method comprising: (a) obtaining a biological sample comprising at least one peripheral blood mononuclear cell (PBMC) from a subject; (b) adding at least one antigen from an invasive fungus suspected to be infecting the subject to the biological sample; (c) detecting a T-cell interferon gamma (IFN-γ) response by detecting the IFN-γ produced by the biological sample; (d) comparing the levels of the IFN-γ produced by the biological sample to levels of IFN-γ produced in a control sample that contains no antigen; and wherein a significant difference between the levels of the IFN-γ produced by the biological sample to the levels of IFN-γ produced in the control sample indicates that the subject is infected with the invasive fungus.

In certain aspects, the presently disclosed subject matter provides a diagnostic kit for diagnosing an invasive fungal infection in a subject by detecting an interferon gamma (IFN-γ) response to a fungal antigen, the kit comprising: (a) at least one antigen from a fungus that is suspected of infecting the subject; and (b) at least one reagent for detecting the IFN-γ produced by a biological sample from the subject. In some aspects, the at least one reagent is an antibody that is specific for interferon gamma (IFN-γ). In yet other aspects, the at least one reagent also comprises a secondary detector antibody that can recognize the antibody that is specific for interferon gamma (IFN-γ).

Certain aspects of the presently disclosed subject matter having been stated hereinabove, which are addressed in whole or in part by the presently disclosed subject matter, other aspects will become evident as the description proceeds when taken in connection with the accompanying Examples and Figures as best described herein below.

BRIEF DESCRIPTION OF THE FIGURES

Having thus described the presently disclosed subject matter in general terms, reference will now be made to the accompanying Figures, which are not necessarily drawn to scale, and wherein:

FIG. 1 shows a schematic diagram of the biology of histoplasmosis (from the Centers for Disease Control and Prevention, Atlanta, GA); FIG. 2 shows a schematic diagram of the immunological basis of TST and IGRA, two commercially available IGRAs for TB: (A) upon TB infection, phagocytosis of the mycobacterium in the lung and presentation of antigens by APCs in the hilar lymph node leads to priming of antigen-specific T-cells; (B) the traditionally used TST detects a hypersensitivity reaction in vivo following intradermal injection of TB antigens; and (C, D) IGRAs detect a T-cell IFN-γ response in vitro following overnight stimulation of peripheral blood mononuclear cells (PBMCs) or whole blood with TB Ag (from Whitworth et al, 2013);

FIG. 3 shows an embodiment of a Histoplasma-specific ELISPOT assay: (A) ELISPOT plate showing samples utilizing human PBMCs and crude yeast-phase extracts from two H. capsulatum isolates (G186AS and G217B); and (B) ELISPOT counts represented as mean antigen-specific spot forming units (SFU);

FIG. 4 shows another embodiment of a Histoplasma-specific ELISPOT assay from one subject using two samples separated 2.5 months apart;

FIG. 5 shows another embodiment of a Histoplasma-specific ELISPOT assay illustrating repeated positivity to yeast cell lysate (YCL) from different species (indicated), but not to alternative antigen preparations from H. capsulatum (e.g. C- antigen, C-Ag) in people with known histoplasmosis and no responses in people without infection: VB9: healthy control, no infection; VB10: healthy control, with latent histoplasma infection; VB 11 : patient without histoplasmosis; VB 12: patient without histoplasmosis who has received non-specific T cell stimulating agent as cancer therapeutic (responses shown are non-specific and can be distinguished from specific responses seen in other infected subjects); VB15: healthy control, with latent histoplasma infection; VB16: patient without histoplasmosis;

FIG. 6 shows the optimization of H. capsulatum yeast cell lysate (YCL) concentration for robust response vis-a-vis mitogen (ΡΗΑ) after 24 hours of incubation (gray bar, 10 μg/mL YCL; striped bar, 50 μg/mL YCL, black bar, 2.5 μg/mL PHA);

FIG. 7 shows optimization of H. capsulatum yeast cell lysate (YCL) concentration and optimization of time of incubation of YCL for robust response visa-vis mitogen (PHA) after 24 hours and 48 hours of incubation (gray bar, 10 μg/mL YCL; striped bar, 50 μg/mL YCL, black bar, 2.5 μg/mL PHA); FIG. 8 shows the optimization of input PBMCs for robust response vis-a-vis mitogen (PHA) after 24 hours and 48 hours of incubation (gray bar, 10 μg/mL YCL; striped bar, 50 μg/mL YCL, black bar, 2.5 μg/mL PHA);

FIG. 9 shows the change in YCL and mitogen (PHA) response of PBMC from healthy volunteer VB005 over time;

FIGS. 10A-10D show the frequency distribution of SFU/le5 cells: (A) in the absence of antigenic stimulus after 24 hours of incubation; (B) in the absence of antigenic stimulus after 48 hours of incubation; (C) using a mitogenic positive control after 24 hours of incubation; and (D) using a mitogenic positive control after 48 hours of incubation; (mitogen 1, PHA; mitogen 2, anti-CD3 MAb);

FIG. 1 1 shows three representative ELISPOT wells: top well, 10 μg/mL yeast cell lysate (YCL); middle well, 2.5 μg/mL of phytohemagglutinin (PHA); bottom well, no antigen;

FIG. 12 shows the distribution of spot count in ELISPOT-positive and - negative clinical samples after 24 or 48 hours of incubation; and

FIG. 13 shows an IFN- γ ELISPOT assay of clinical samples (10 μg/mL yeast cell lysate (YCL) by protein) obtained from people with known latent histoplasmosis ("+") and without ("-"). DETAILED DESCRIPTION

The presently disclosed subject matter now will be described more fully hereinafter with reference to the accompanying Figures, in which some, but not all embodiments of the presently disclosed subject matter are shown. Like numbers refer to like elements throughout. The presently disclosed subject matter may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Indeed, many modifications and other embodiments of the presently disclosed subject matter set forth herein will come to mind to one skilled in the art to which the presently disclosed subject matter pertains having the benefit of the teachings presented in the foregoing descriptions and the associated Figures. Therefore, it is to be understood that the presently disclosed subject matter is not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims.

Some invasive fungal infections that are problematic to humans include those that are difficult to diagnose. This difficulty is particularly true when fungal antigens are hard to detect and/or culture does not reveal the cause of infection, as with infections that have become chronic, or 'latent' in the host. The presently disclosed subject matter provides methods for diagnosing an invasive fungal infection in a subject by detecting or measuring the release of interferon gamma by the infected subject upon cell exposure to specific microbial antigens. It is believed that the presently disclosed subject matter is the first instance of diagnosing a latent invasive fungal infection in a subject by using cellular specific immunity.

In some embodiments, the presently disclosed methods allow for the diagnosis of an invasive fungal infection by combining a biological sample, such as blood comprising a peripheral blood mononuclear cell (PBMC), from a subject and an antigen from an invasive fungus suspected to be infecting the subject. If the PBMC has previously encountered the antigen, an interferon-gamma (IFN-γ) response will occur, which can be detected by means of an assay. Preferably, the peripheral blood mononuclear cell (PBMC) is a CD3+ T cell, which produces IFN-γ.

As used herein, a "fungus" is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds. These organisms are classified as a kingdom, fungi, which is separate from plants, animals, protists and bacteria.

As used herein, an "antigen" is a molecule or part of a molecule that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor. Examples of antigens include, but are not limited to, proteins or polypeptides, peptides, polysaccharides, lipids, microbial structures, such as bacterial and fungal cell walls, protozoan cell membranes, bacterial and fungal capsules, viral capsids, viral glycoproteins, microbial toxins, allergens, such as dust mites, pollen, hair, dander, bee venom, drugs, and other agents causing allergic reactions, foreign tissue or cells, and the body's own cells that the body fails to recognize as normal, such as cancer cells, infected cells, and cells involved in autoimmune diseases.

As used herein, the term "infection" refers to the invasion of a host organism's bodily tissues by disease-causing organisms, their multiplication, and the reaction of host tissues to these organisms and the toxins they produce. By "invasive fungal infection," it is meant an infection where fungus has invaded into the deep tissues of a subject and has established itself, resulting in prolonged illness. As used herein, a "latent fungal infection" is a type of fungal infection that lays dormant in a host. Usually a latent infection is an asymptomatic infection capable of manifesting symptoms under particular circumstances or if activated. Many fungal pathogens can remain latent in the body, appearing only when Thl immunity is depressed because of age, disease, or medical therapies. In general, the presently disclosed subject matter is useful for diagnosing invasive fungal infections, and is particularly useful for diagnosing invasive, latent infections.

The presently disclosed diagnostic methods, kits, and devices are applicable to the detection of invasive fungi. In some embodiments, the fungus is selected from the group consisting of the genus Histoplasma, Coccidioides, Blastomyces,

Paracoccidioides, and Cryptococcus. In other embodiments, the fungus is selected from the group consisting of Histoplasma capsulatum, Coccidioides immitis, Coccidioides posadasii, Blastomyces dermatitidis , Paracoccidioides brasiliensis, Cryptococcus neoformans, and Cryptococcus gattii. In still other embodiments, the fungus is Histoplasma capsulatum, a fungus that infects a subject through the respiratory route and becomes dormant in phagocytic cells that exist in the reticuloendothelial system.

I. METHODS FOR DIAGNOSING AN INVASIVE FUNGAL INFECTION

Accordingly, the presently disclosed subject matter provides a method for diagnosing an invasive fungal infection in a subject, the method comprising: (a) obtaining a biological sample comprising at least one peripheral blood mononuclear cell (PBMC) from a subject; (b) adding at least one antigen from an invasive fungus suspected to be infecting the subject to the biological sample; (c) detecting a T-cell interferon gamma (IFN-γ) response by detecting the IFN-γ produced by the biological sample; (d) comparing the levels of the IFN-γ produced by the biological sample to levels of IFN-γ produced in a control sample that contains no antigen; and wherein a significant difference between the levels of the IFN-γ produced by the biological sample to the levels of IFN-γ produced in the control sample indicates that the subject is infected with the invasive fungus. In some embodiments, at least one peripheral blood mononuclear cell (PBMC) is at least one CD3+ T cell. As used herein, a PBMC is a blood cell having a round nucleus that is a component of the immune system, such as a lymphocyte, a monocyte, and the like. A T cell or T lymphocyte is a lymphocyte that plays a central role in cell-mediated immunity. Different types of T cells include, but are not limited to, T helper cells, cytotoxic T cells, memory T cells, regulatory T cells (also known as suppressor cells), and natural killer T cells. A T cell can be distinguished from other lymphocytes by the presence of a T cell receptor (TCR) on its cell surface. The CD3 complex is a group of cell surface molecules that associates with the TCR and functions in the cell surface expression of TCR and in the signaling transduction cascade that originates when a peptide: major histocompatibility complex (MHC) ligand binds to the TCR. As used herein, a "CD3+ T cell" is a T cell that is associated with the CD3 complex. In particular embodiments, the biological sample comprises at least one T cell, and in more particular embodiments, the T cell is a CD3+ T cell.

The terms "sample," "patient sample," "biological sample," and the like, encompass a variety of sample types obtained from a patient, individual, or subject and can be used in a diagnostic or monitoring assay. The patient sample may be obtained from a healthy subject, a diseased patient or a patient having associated symptoms of an active invasive fungal infection. Moreover, a sample obtained from a patient can be divided and only a portion may be used for diagnosis. Further, the sample, or a portion thereof, can be stored under conditions to maintain sample for later analysis. As used herein, the term "sample" refers to any sampling of cells, tissues, or bodily fluids in which IFN-γ can be detected. In a specific embodiment, a sample comprises a blood sample. In another specific embodiment, the sample comprises peripheral blood mononuclear cells. The definition also includes samples that have been manipulated in any way after their procurement, such as by centrifugation, filtration, precipitation, dialysis, chromatography, treatment with reagents, washed, or enriched for certain cell populations.

A biological sample comprising at least one PBMC can be taken from any part of the subject that comprises at least one PBMC. In a particular embodiment, the biological sample is peripheral blood. By "peripheral blood," it is meant blood that has circulated through the body and comprises platelets, lymphocytes, granulocytes, and erythrocytes. In still other embodiments, at least one PBMC is extracted from peripheral blood after the peripheral blood is taken from the subject by using, for example, a method to separate blood into layers, such as a density gradient. Accordingly, in some embodiments, the methods further comprise fractionating the peripheral blood to obtain at least one peripheral blood mononuclear cell (PBMC), such as by using a Ficoll-Hypaque density gradient. In other embodiments, the biological sample is selected from the group consisting of peripheral blood, fractionated blood and components thereof. In still other embodiments, the biological sample is peripheral blood.

As used herein, the term "control sample," "corresponding control," or "appropriate control" means any control or standard familiar to one of ordinary skill in the art useful for comparison purposes. For example, the control sample may be one that contains no antigen. In another example, the control sample may be one that contains a non-specific mitogen. As used herein, a "mitogen" refers to a chemical substance that encourages a cell to commence cell division, triggering mitosis. A "non-specific mitogen" refers to a mitogen that triggers mitosis selectively in various populations, such as lymphocytes. An example of a non-specific mitogen is phytohemagglutinin (PHA).

"Obtaining" may mean taking a biological sample directly from the subject or patient, or taking a biological sample from the subject indirectly, such as if blood is taken from the subject and then stored, fractionated, or in some other way handled before being used in the presently disclosed methods.

Interferon gamma is a dimerized soluble cytokine that is a member of the type

II class of interferons. In humans, the IFN-γ protein (UniProt Accession No. P01579) is encoded by the IFNG gene. In some embodiments, by "T-cell IFN-γ response," it is meant that a CD3+ T-cell responds to an environmental stimulus, such as the presence of an antigen, by producing IFN-γ. A positive T-cell IFN-γ response indicates that the subject has been exposed to, and is at least latently infected with the fungus. A subject that has not had prior exposure to a specific fungus does not have a biological sample that responds to a specific antigen from the fungus by producing IFN-γ.

The subject treated by the presently disclosed methods in their many embodiments is desirably a human subject, although it is to be understood that the methods described herein are effective with respect to all vertebrate species, which are intended to be included in the term "subject." Accordingly, a "subject" can include a human subject for medical purposes, such as for treating an existing condition or disease or the prophylactic treatment for preventing the onset of a condition or disease, or an animal (non-human) subject for medical, veterinary purposes, or developmental purposes. Suitable animal subjects include mammals including, but not limited to, primates, e.g., humans, monkeys, apes, and the like; bovines, e.g., cattle, oxen, and the like; ovines, e.g., sheep and the like; caprines, e.g., goats and the like; porcines, e.g., pigs, hogs, and the like; equines, e.g., horses, donkeys, zebras, and the like; felines, including wild and domestic cats; canines, including dogs; lagomorphs, including rabbits, hares, and the like; and rodents, including mice, rats, and the like. An animal may be a transgenic animal. In some embodiments, the subject is a human including, but not limited to, fetal, neonatal, infant, juvenile, and adult subjects. Further, a "subject" can include a patient afflicted with or suspected of being afflicted with a condition or disease. Thus, the terms "subject" and "patient" are used interchangeably herein. In some embodiments of the presently disclosed subject matter, the subject is human. In other embodiments, the subject is non-human.

As used herein, the terms "measuring" and "detecting" refer to methods which include detecting the T-cell IFN-γ response to a fungal antigen by detecting the level of IFN-γ or number of IFN-γ producing cells in a sample or subject. In some embodiments, the presently disclosed methods are performed in a reference laboratory.

After obtaining a biological sample from a subject, the biological sample is added to and/or mixed with at least one antigen from an invasive fungus that is suspected of infecting the subject. In some embodiments, at least one antigen from more than one fungus is added in the methods. In other embodiments, multiple different microbial antigens are used in the presently disclosed subject matter. These multiple antigens can be from one species of fungus or from multiple species of fungi. Using more than one species of fungal antigen may be beneficial if it is desirable to eliminate the possibility of more than one type of fungal infection simultaneously or if the therapy for an infected subject will be the same for related fungal infections. It is preferred that the antigens used are immunodominant or recognized significantly by human T-cells after natural infection.

In some embodiments, at least one antigen is added to a biological sample in the form of a fungal extract or lysate. As used herein, an "extract" or "lysate" refers to a solution of cellular proteins resulting when cells are lysed or broken apart, such as by shearing cells. A "crude extract" or "crude lysate" refers to the solution formed when cells are lysed or broken apart with only minimal purification of the cell antigens away from the rest of the cell components. A "partially purified extract" refers to an extract in which antigens have been extracted or purified away from some of the other components of the cell. A "purified antigen" refers to an antigen that has been almost completely or completely separated from the other cell components, including being separated from other types of antigens in the cell extract. Methods for purifying antigens are known in the art, and in the case of protein antigens, include the use of detergents or chaotropic agents to disrupt particles followed by differential extraction and separation of the polypeptides by ion exchange chromatography, affinity chromatography, sedimentation according to density, and gel electrophoresis, for example. Accordingly, in some embodiments, at least one antigen is in a crude fungal extract when it is added to the biological sample. In other embodiments, at least one antigen is in a partially purified fungal extract when it is added to the biological sample.

Antigens used in the presently disclosed subject matter include polypeptides, peptides, polysaccharides, and the like. In some embodiments, at least one antigen comprises at least one protein or fragment thereof, such as the immunogenic part of the protein that is recognized by a T cell. In other embodiments, at least one protein or fragment thereof is at least one purified protein or fragment thereof. In still other embodiments, at least one protein or fragment thereof is at least one recombinant protein or fragment thereof. In further embodiments, the antigen is a Histoplasma- specific protein recognized by the T-cells of latently infected subjects. Whole genome analysis has documented differential expression of multiple products in both yeast and conidial morphologies, such as CDF1, CBP1, SID4, YPS21, YPS3, SID3, CATB, GAD1, CATA, ALD1, and WHC2. In still further embodiments, at least one protein is selected from the group consisting of CDF 1, CBP1, SID4, YPS21, YPS3, SID3, CATB, GAD1, CATA, ALD1, and WHC2. In some embodiments, these proteins can be used as antigens in a standardized assay to test a biological sample for its ability to secrete IFN-γ.

FIG. 1 shows the life cycle of the Histoplasma capsulatum organism. In some embodiments, the fungal extract or protein used in the presently disclosed subject matter is from Histoplasma capsulatum. In other embodiments, at least one antigen is a yeast-phase antigen from Histoplasma capsulatum. The presently disclosed subject matter also includes antigens from other invasive fungi. After adding at least one antigen to a biological sample, the T-cell IFN-γ response is detected and/or measured. In particular embodiments, the T-cell IFN-γ response is detected by using an immunoassay. Immunoassays require biospecific capture reagents, such as antibodies to capture the IFN-γ. In some embodiments, the immunoassay comprises an antibody. Examples of immunoassays include, but are not limited to, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunosorbent spot (ELISPOT) assays, fluorescence-based immunoassays, immunoblots, Western blots, immunoprecipitation, immunofluorescence, and immunocytochemistry. In addition to antibodies, the presently disclosed subject matter comprises any other suitable agent (e.g., a peptide, an aptamer, or a small organic molecule) that specifically binds to an antigen.

Commonly used immunoassays in diagnostic and research use include radioimmunoassays and enzyme-linked immunosorbent assays (ELISAs). Many of these elaborately configured immunoassays use monoclonal antibodies (MAbs) that possess the ability to bind specifically to the analyte being tested, thereby enhancing the accuracy of the assay. Various approaches have been described for carrying out enzyme immunoassays. A considerable number of these approaches, starting with the earliest of ELISAs, are solid-phase immunoassays in which the analyte to be detected is bound to a solid matrix directly (Direct ELISA) or indirectly (Sandwich ELISA), in which the analyte is captured on a primary reagent. The choice of the solid matrix depends on procedural considerations. A common matrix is the polystyrene surface of multi-well microtiter plates. In some embodiments, the diagnostic device measures secreted IFN-γ levels using an ELISA assay or an ELISPOT assay.

As used herein, the term "antibody" refers to a polypeptide or group of polypeptides which are comprised of at least one binding domain, where an antibody binding domain is formed from the folding of variable domains of an antibody molecule to form three-dimensional binding spaces with an internal surface shape and charge distribution complementary to the features of an antigenic determinant of an antigen, which allows an immunological reaction with the antigen. Antibodies include recombinant proteins comprising the binding domains, as wells as fragments, including Fab, Fab', F(ab)2, and F(ab¾ fragments. An "antigenic determinant" is the portion of an antigen molecule that determines the specificity of the antigen-antibody reaction. An "epitope" refers to an immunological determinant of an antigen that serves as an antibody -binding site, such as the antigenic determinant of a polypeptide. In some embodiments, when the epitope is an amino acid sequence, an epitope can comprise as few as 3 amino acids in a spatial conformation which is unique to the epitope. Generally an epitope consists of at least 6 such amino acids, and more usually at least 8-10 such amino acids. Many antibodies are available commercially and in addition, antibodies also can be produced by methods well known in the art, e.g., by immunizing animals with the antigens. Antigens can be isolated from samples based on their binding characteristics. Alternatively, if the antigen is a protein and the amino acid sequence is known, the protein can be synthesized and used to generate antibodies by methods well-known in the art.

In the presently disclosed subject matter, the IFN-γ produced by the biological sample is secreted. By "secreted," it is meant that the IFN-γ is transferred from inside the cell to outside the cell. In some embodiments, the IFN-γ is detected by using an enzyme-linked immunosorbent assay (ELISA) or an enzyme-linked immunosorbent spot (ELISPOT) assay.

In some embodiments, the method further comprises comparing the levels of

IFN-γ produced by a biological sample to a negative control. In other embodiments, the method further comprises comparing the levels of the IFN-γ produced by the biological sample to levels of IFN-γ produced in a positive control sample. In still other embodiments, a significant difference means at least about a 5-fold difference between the levels of the IFN-γ produced by the biological sample to the levels of IFN-γ produced in the control sample that does not contain any antigen.

As used herein, the term "comparing" refers to making an assessment of how the proportion or level of IFN-γ, or number of IFN-γ producing cells in a fungal antigen-treated sample from a subject relates to the proportion or level of IFN-γ or number of IFN-γ producing cells in a subject's sample that has not been treated with antigen ("control sample"). A significant difference between the sample with antigen and the sample without antigen shows that the subject is infected with the fungus.

As used herein, the terms "significantly different" or "significant difference" mean a level of IFN-γ in a sample that is higher than the level of expression of IFN-γ in a control sample by at least 1.5 fold, 2.0 fold, 3.0 fold, 4.0 fold, 5.0 fold or more. In other embodiments, the terms "significantly different" or "significant difference" mean a level of IFN-γ in a sample that is higher than the level of IFN-γ in a control sample by at least 10 fold, 20 fold, or more. The presently disclosed subject matter also can be used to diagnose invasive fungal infections that are no longer latent, but are in the active phase. A subject with an active infection caused by a fungus can show symptoms of infection, such as febrile illness, lesions, rash, pneumonia, and the like. In some embodiments, the presently disclosed subject matter can be used to confirm an active fungal infection or can be used to determine the type of fungus that is causing the active infection.

Accordingly, in some embodiments, the presently disclosed subject matter includes invasive fungal infections, wherein the invasive fungal infection is active.

In some embodiments, the presently disclosed methods can be used to diagnose, for the prognosis, or the monitoring of a disease state or condition involving an invasive fungal infection. For example, a subject that is going to undergo immunosuppression before a transplant or requires biological inhibitors of immunity can be tested before treatment for latent invasive infections that may reactivate after immusuppression. If the subject is known to harbor a latent invasive infection, treatment can be given to prevent reactivation of the infection.

As used herein, the term "diagnosis" refers to a predictive process in which the presence, absence, severity or course of treatment of a disease, disorder or other medical condition is assessed. For purposes herein, diagnosis also includes predictive processes for determining the outcome resulting from a treatment. Likewise, the term "diagnosing," refers to the determination of whether a sample specimen exhibits one or more characteristics of a condition or disease. The term "diagnosing" includes establishing the presence or absence of, for example, a target antigen or reagent bound targets, or establishing, or otherwise determining one or more characteristics of a condition or disease, including type, grade, stage, or similar conditions. As used herein, the term "diagnosing" can include distinguishing one form of a disease from another. The term "diagnosing" encompasses the initial diagnosis or detection, prognosis, and monitoring of a condition or disease. The term "prognosis," and derivations thereof, refers to the determination or prediction of the course of a disease or condition. The course of a disease or condition can be determined, for example, based on life expectancy or quality of life. "Prognosis" includes the determination of the time course of a disease or condition, with or without a treatment or treatments. In the instance where treatment(s) are contemplated, the prognosis includes determining the efficacy of a treatment for a disease or condition. The term "monitoring," such as in "monitoring the course of a disease or condition," refers to the ongoing diagnosis of samples obtained from a subject having or suspected of having a disease or condition.

In some embodiments, the presently disclosed subject matter enables detection of reactive circulating T-cells (latent infection) in subjects with mild-moderate immunosuppression, supplementing antigen detection in the setting of disease, and/or enabling development of prevention strategies in subjects with impending biological immunosuppression. Based on the results of the presently disclosed subject matter, further procedures may be indicated, including additional diagnostic tests or therapeutic procedures.

II. KITS FOR DIAGNOSING AN INVASIVE FUNGAL INFECTION

The presently disclosed subject matter also relates to kits for practicing the methods of the presently disclosed subject matter. In general, a presently disclosed kit contains some or all of the components, reagents, supplies, and the like to practice a method according to the presently disclosed subject matter. In some embodiments, the term "kit" refers to any intended any article of manufacture (e.g., a package or a container) comprising a fungal antigen and a set of particular instructions for practicing the methods of the presently disclosed subject matter.

Accordingly, in some embodiments, the presently disclosed subject matter provides a diagnostic kit for diagnosing an invasive fungal infection in a subject by detecting an interferon gamma (IFN-γ) response to a fungal antigen, the kit comprising: (a) at least one antigen from a fungus suspected to be infecting the subject; and (b) at least one reagent for detecting the IFN-γ produced by a biological sample from the subject. In particular embodiments, the at least one reagent is an antibody that is specific for interferon gamma (IFN-γ). In yet more particular embodiments, the at least one reagent also comprises a secondary detector antibody that can recognize the antibody that is specific for interferon gamma ((IFN-γ).

Secondary detector antibodies suitable for use with the presently disclosed methods include, but are not limited to, enzyme labeled antibodies (e.g., peroxidase, alkaline phosphatase (AP), fluorescence labeled antibodies (e.g., FITC, Alexa-Fluor, Qdot), biotin conjugated antibodies, and the like. More generally, in some embodiments, the means for detecting the T-cell IFN-γ response can comprise one or more reagents for performing an immunoassay, such as an ELISA or ELISPOT assay.

In other embodiments, the diagnostic kit further comprises a receptacle for collecting a biological sample from the subject, such as a syringe, tube, a blood collection tube, and the like. In further embodiments, the kit may also include a means for separating at least one PBMC from some of the other blood components, including reagents, columns, and the like.

III. GENERAL DEFINITIONS

Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this presently described subject matter belongs.

Following long-standing patent law convention, the terms "a," "an," and "the" refer to "one or more" when used in this application, including the claims. Thus, for example, reference to "a subject" includes a plurality of subjects, unless the context clearly is to the contrary (e.g., a plurality of subjects), and so forth.

Throughout this specification and the claims, the terms "comprise,"

"comprises," and "comprising" are used in a non-exclusive sense, except where the context requires otherwise. Likewise, the term "include" and its grammatical variants are intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that can be substituted or added to the listed items.

For the purposes of this specification and appended claims, unless otherwise indicated, all numbers expressing amounts, sizes, dimensions, proportions, shapes, formulations, parameters, percentages, quantities, characteristics, and other numerical values used in the specification and claims, are to be understood as being modified in all instances by the term "about" even though the term "about" may not expressly appear with the value, amount or range. Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are not and need not be exact, but may be approximate and/or larger or smaller as desired, reflecting tolerances, conversion factors, rounding off, measurement error and the like, and other factors known to those of skill in the art depending on the desired properties sought to be obtained by the presently disclosed subject matter. For example, the term "about," when referring to a value can be meant to encompass variations of, in some embodiments, ± 100% in some embodiments ± 50%, in some embodiments ± 20%, in some embodiments ± 10%, in some embodiments ± 5%, in some embodiments ±1%, in some embodiments ± 0.5%, and in some embodiments ± 0.1% from the specified amount, as such variations are appropriate to perform the disclosed methods or employ the disclosed compositions.

Further, the term "about" when used in connection with one or more numbers or numerical ranges, should be understood to refer to all such numbers, including all numbers in a range and modifies that range by extending the boundaries above and below the numerical values set forth. The recitation of numerical ranges by endpoints includes all numbers, e.g., whole integers, including fractions thereof, subsumed within that range (for example, the recitation of 1 to 5 includes 1, 2, 3, 4, and 5, as well as fractions thereof, e.g., 1.5, 2.25, 3.75, 4.1, and the like) and any range within that range.

EXAMPLES

The following Examples have been included to provide guidance to one of ordinary skill in the art for practicing representative embodiments of the presently disclosed subject matter. In light of the present disclosure and the general level of skill in the art, those of skill can appreciate that the following Examples are intended to be exemplary only and that numerous changes, modifications, and alterations can be employed without departing from the scope of the presently disclosed subject matter. The synthetic descriptions and specific examples that follow are only intended for the purposes of illustration, and are not to be construed as limiting in any manner to make compounds of the disclosure by other methods.

EXAMPLE 1

Histoplasma-Specific ELISPOT Assays

Materials and Methods: The Histoplasma-specific ELISPOT assay utilized

PBMC harvested from human volunteers with, and without known histoplasmosis, testing reactivity to crude yeast-phase extract from two isolates. Ly sates from H. capsulatum isolates G186AS and G217B (which lacks a-glucan) were prepared by cell shearing, with protein concentrations measured prior to use using the

bicinchoninic acid assay (BCA assay). PBMCs were separated by Ficoll-Hypaque density gradients from multiple subjects, including one patient being treated for documented disseminated histoplasmosis, and other laboratory volunteers. Cells in RPMI media (supplemented with 10% FBS) were enumerated by hemacytometer, mixed with YCL and positive control antigens (phytohemagglutinin, PHA), for indicated time durations and plates (Mabtech) were processed according to manufacturer specifications.

IFN- γ production was measured using a commercially available kit. Briefly, plates were incubated at 37 °C for 24 hrs, washed, and AP-conjugated secondary antibodies to IFN-γ were added. Wells were washed, plates were dried overnight, and spots were visualized and enumerated. Results are represented as mean antigen- specific spot forming units (SFU) after subtraction of background control wells containing no antigen. Results were measured as positive, negative, or indeterminate (lacking a positive control response).

Results: Prior studies had shown that ELISPOT assays could detect fungal antigen-specific T-cells in human blood (Chaudhary et al, 2010). Fungus-specific T- cells (CD4 and CD8) could be successfully detected both by quantifying released IFN-γ and with ELISPOT technology, specifically in the setting in which healthy subjects have developed cellular immune responses to Aspergillus fumigatus (Chaudhary et al, 2010). Although fungus-specific T-cells could be detected for a non-latent fungus such as Aspergillus, however, diagnosis of latent infection with a pathogenic fungus, such as Histoplasma, has been limited.

For the development of a Histoplasma-specific ELISPOT assay, PBMC were harvested from human volunteers with and without known histoplasmosis and reactivity to crude yeast-phase extract from two isolates was tested. Representative results are shown visually in FIG. 3. In these data, volunteer blood ("VB") from subjects are listed across the top, after exposure to both yeast lysates (G186AS left, G217B right), diluted as indicated. Positive controls included anti-CD3 MAb and the mitogen, phytohemagglutinin (PHA). The anti-CD3 MAb acts as a positive control by cross-linking the CD3 on a T cell, thereby causing secretion of IFN-γ by the CD3+ T cell. One donor (VB5) responded with a vigorous spot forming units (SFU) response to all dilutions of both yeast antigens. This donor was a healthy infectious diseases physician and lifetime resident of a highly endemic region (Tennessee) who had known granulomatous disease (as seen by chest X-rays) that is representative of latent histoplasmosis. This donor had tested negative for TB exposure with occupational performed TB-Quantiferon assays. Other volunteers (VB2, 4, 6, and 7) had no known granulomatous disease and had not resided in Histoplasma-endemic regions. The one volunteer who was being treated for disseminated histoplasmosis (VB 1) actually had a weak positive mitogenic response, but not enough CD3+ T-cells to measure a Histoplasma specific response.

Repeat results using the same methodology show that the positive results from one donor are reproducible although separated by time (FIG. 4). Responses assessed from other volunteers (FIG. 5) show repeated positivity in people with known histoplasmosis (subject VB10 and VB15), and no responses in people without infection (VB9, VB11, VB16) (repeated experiments not shown). This also shows one subject who had non-specific reactivity caused by receipt of a T cell stimulating agent for cancer chemotherapy (VB12).

These results show that a latent fungal infection, such as latent histoplasmosis, is detectable by measurement of reactive CD3+ T-cells after exposure to crude yeast phase antigen. There was remarkably little non-specific reactivity in other healthy volunteers. Without wishing to be bound to any one particular theory, dilution studies did suggest that there was an inhibitory molecule in the crude yeast lysate, but this was less well appreciated in the lysate from the yeast that lacked a-glucan (G217B), which generated more robust responses at all dilutions. These studies demonstrate that T-cells reactive to fungal antigens can be effectively measured in human peripheral blood mononuclear cells, and that this can be used as a diagnostic assay for latent fungal infection.

EXAMPLE 2

Histoplasma-Sveciiic ELISPOT Assay Optimization Materials and Methods: To perform assay optimization, healthy volunteers from endemic areas and patients with suspected infection were recruited to provide blood. Lysates from H. capsulatum isolate G217B were prepared as disclosed in

Example 1. Peripheral blood mononuclear cells (PBMCs) were harvested, separated, counted and used in assays to measure IFNy release after exposure to multiple Histoplasma antigen preparations, using ELISA and ELISPOT, with

phytohemagglutinin (ΡΗΑ) as a positive control. Antigen-specific spot- forming units or concentration of IFNy (pg/mL) were calculated for cells tested. One volunteer with known latent histoplasmosis had a very robust response and was used for optimization and reproducibility studies.

Results: IFNy release assays were optimized by varying yeast cell lysate (YCL) concentrations, time of incubation, and the number of PBMCs added to the assay. Results showed that the optimal YCL concentration was lC^g/ml (FIG. 6) and the optimal time of incubation was 48 hours (FIG. 7). The minimum cell input per well was found to be 10 ⁵ PBMCs (FIG. 8). The signals were enhanced by 48 hour incubation (FIG. 8) and this length of incubation also appeared to stabilize the positive control (mitogen PHA) and YCL responses in serial samples from healthy volunteer VB5 (FIG. 9; serial samples were taken initially and then approximately 2 months and 9 months after the initial assay). FIG. 10 shows the spot count in control wells with no antigen added after 24 hours of incubation (Panel A) and 48 hours of incubation (Panel B), as well as the spot count when positive controls PHA (mitogen 1) or anti-CD3 MAb (mitogen 2) were added and incubated for 24 hours (Panel C) and 48 hours (Panel D). FIG. 1 1 shows representative ELISPOT wells from a yeast cell lysate sample, positive control PHA, and no antigen. FIG. 12 shows the distribution of spot count in ELISPOT-positive and -negative clinical samples after 24 - 48 hours of incubation. It was demonstrated that there is a reasonably large variability in spot forming units (SFU) in people who have latent infection, but people who don't have latent infection have relatively few measurable SFU.

The IFNy release assays were used to screen volunteers (Table 1). Two of the volunteers exhibited robust responses to yeast cell lysate (YCL) from H. capsulatum strain G217B, with less response to YCL from a different strain and C-antigen. Assay optimization produced reproducible measurements of approximately 100 spot- forming units/10 ⁵ cells with ELISPOT and measureable quantities (25-50 pg/mL) of IFN-γ released by ELISA. Positive responses were reproducible with repeated assay and differential blood draws. Controls with no known exposure or latent disease demonstrated no response to Histoplasma YCL.

FIG. 13 shows an IFN- γ ELISPOT assay of all the clinical samples obtained from people with known latent histoplasmosis ("+") and without ("-")· The results show that the presently disclosed methods can be used to diagnose people with latent histoplasmosis. Table 1. Study Subjects

Pulmonary cryptococcosis

cryptococcus

Patient MD AML, Possible fungal 0 Negative pulmonary pneumonia

nodules, skin (all negative)

lesions

VB1 Patient TN Disseminated Proven 0 3

IND

histoplasmosis Histoplasmosis

after TNF-a (Culture, urine

inhibitor Ag)

1, ASC = Adjusted Spot Count (Antigen Well Spot count - No Antigen Well Spot count) per 10 ⁵ cells; 2. Cut-off: 10 spots; 3. IND = Indeterminate; PHA response <100 spots.

EXAMPLE 3

Discussion

Lack of sensitive diagnostic tests for histoplasmosis currently delays treatment of symptomatic disease, and limits the ability to prevent disease progression in the setting of latency. Unlike TB, no commercial tests are available to detect skin hypersensitivity; the equivalent of the "histo PPD" does not exist. Even with active disease, diagnosis is difficult, and clinicians are often misled by the variety of clinical manifestations. Even in the setting of active disease, sensitivity of culture is less than 60% (Hage and Wheat, 2010). Similarly, detection of the organism by cytopathology is rare. For these reasons, current standards rely on immunodiagnostics, with detection of circulating antibodies, and/or the presence of cellular antigen in serum or urine. These tests are run by only a couple of reference laboratories in the U.S. and are not available in less developed areas of the world. Performance of assays is variable, and dependent on the population studied. For instance, antibodies are detected only late after infection and are unreliable; the sensitivity of Ab detection in AIDS patients are estimated at only 10% (Hage and Wheat, 2010). In the setting of active disease having high fungal burden, antigen can be detected. Reported sensitivities of antigen assays range between 50-80%, depending on the host, disease, and type of assay (Hage and Wheat, 2010). As this only occurs with late and advanced disease, outcomes of treatment are poor. There is currently no reliable way to devise preventative algorithms in subjects who have high risks for reactivation of latent disease due to impending immune suppression; this is a critical clinical gap given the increasing population of subjects in the U.S. who are exposed to medical therapies that suppress defenses, and aging of the population. As used herein, the term "risk" refers to a predictive process in which the probability of a particular outcome is assessed.

Histoplasmosis develops after microconidia of the organism that grows in the environment are inhaled into the lung (FIG. 1). The organism is ingested by resident and recruited phagocytes, such as macrophages, dendritic cells and neutrophils.

Intracellular yeasts can remain viable inside macrophages, where they are transported to local lymph nodes, spleen and organs of the reticuloendothelial system. There, the yeast is kept in check by an interferon gamma dependent Thl response (Kroetz and Deepe, 2012). A critical feature that supports development of T-cell diagnostics is that, like Mycobacterium tuberculosis, which causes TB, H. capsulatum exists in a latent state, with T-cell immunity limiting progressive disease. Measurement of the T-cell response itself thus serves as a very useful adjunctive diagnostic; only subjects with latent disease harbor T-cells reactive to specific antigens. Quantitative results also potentially serve as markers to predict risks for progressive disease. This concept has propelled development of two commercially available IGRAs for TB (FIG. 2), which have essentially revolutionized current diagnostic approaches over the last 10 years. The assays provide enhanced sensitivity and specificity compared to PPDs (Cattamanchi et al, 201 1 ; Whitworth et al, 2013).

The presently disclosed subject matter provides novel technology for diagnosing an invasive fungal infection in a subject by measuring the release of interferon gamma (IFN-γ) by the infected subject upon cell exposure to specific microbial antigens.

REFERENCES

All publications, patent applications, patents, and other references mentioned in the specification are indicative of the level of those skilled in the art to which the presently disclosed subject matter pertains. All publications, patent applications, patents, and other references are herein incorporated by reference to the same extent as if each individual publication, patent application, patent, and other reference was specifically and individually indicated to be incorporated by reference. It will be understood that, although a number of patent applications, patents, and other references are referred to herein, such reference does not constitute an admission that any of these documents forms part of the common general knowledge in the art.

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Although the foregoing subject matter has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be understood by those skilled in the art that certain changes and modifications can be practiced within the scope of the appended claims.