Patent Application
20210030852
Candida auris is a pathogenic yeast species that poses a newly emerging global health threat. The yeast can enter the bloodstream and spread throughout the body, causing serious invasive infections. Additionally, C. auris is known to cause severe wound, ear, respiratory, and urinary infections. C. auris infections can be difficult to treat because they are often resistant to commonly used antifungal drugs. Accordingly, new methods of treatment for and prevention of C. auris infections are needed.
Disclosed herein are compositions and methods for treating and immunizing against C. auris infection. Featured are polypeptides, antibodies, and methods of use thereof for providing active and passive immunoprotection against C. auris infection.
In one aspect, featured is a method of treating a subject (e.g., a human subject) for, or immunizing a subject (e.g., a human subject) against, a C. auris infection by administering to the subject an immunogenic amount of an Als3 polypeptide or fragment or homolog thereof or an anti-Als3 antibody or antigen-binding fragment thereof. Also featured is a method of preventing C. auris infection in a subject by administering to the subject an immunogenic amount of an Als3 polypeptide or fragment or homolog thereof or an anti-Als3 antibody or antigen-binding fragment thereof. Also featured is a method of inducing an immune response to C. auris or production of antibodies to C. auris in a subject by administering to the subject an immunogenic amount of an Als3 polypeptide or fragment or homolog thereof. The methods may further include identifying the subject as having a C. auris infection prior to administration. The methods may further include identifying the subject as being colonized with C. auris prior to administration. The methods may further include identifying the subject as at risk of becoming colonized and/or infected with C. auris prior to administration. The subject may have, is suspected of having, or is at risk of having a C. auris infection. The subject may have been exposed to, or is suspected of being exposed to C. auris. The identifying step may include obtaining a sample from the subject. The sample may be obtained with a swab of the skin or mucous membranes (e.g., subject's mouth, throat, esophagus, rectum, or vagina).
In some embodiments, the method of administration inhibits or reduces C. auris burden or biofilm formation (e.g., by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, or substantially eliminates) in the subject, relative to C. auris burden or biofilm formation in an untreated subject.
The subject may be immunocompromised, suffer from a comorbidity, and/or have a risk factor for C. auris infection. The comorbidity may be a bacterial infection, a fungal infection, a viral infection, an immune disorder, or diabetes. The fungal infection may be candidiasis (e.g., of a mucous membrane such as the mouth, throat, or esophagus), vulvovaginal candidiasis (e.g., recurrent vulvovaginal candidiasis), and/or invasive candidiasis. Exemplary risk factors are surgery, a stay in an intensive care unit, habitation in a nursing home, use of a breathing tube or a feeding tube, treatment with a broad-spectrum antibiotic or antifungal agent, or presence of a catheter (e.g., a central venous catheter).
The subject may be one that is being treated at, has been treated at, or will be treated at a hospital or health center. The subject may also be one that works at, has worked at, or will work at a hospital or health center.
The subject may be at least 50, 60, 70, 80, or 90 years old. Alternatively, the subject may be a newborn, infant, or toddler (e.g., less than 3 years old).
In some embodiments, the C. auris may be multi-drug resistant.
The methods described herein may reduce C. auris colonization (e.g., by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, or substantially eliminate colonization). The methods may increase survival of the subject (e.g., by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 100%, or more), relative to an untreated subject with C. auris infection or colonization. The methods may reduce the number of days of active C. auris infection in the subject (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), reduce the number of days of hospitalization of the subject (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), reduce the number of days requiring antifungal therapy of the subject (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), and/or reduce the dose and/or frequency of antifungal therapy needed by the subject, each relative to an untreated subject.
In some embodiments, the Als3 polypeptide or fragment or homolog thereof or anti-Als3 antibody or antigen-binding fragment thereof is administered subcutaneously, intramuscularly, intradermally, transdermally, intranasally, orally, or via an infusion. Preferably, the Als3 polypeptide or fragment is administered by intradermal or intramuscular injection. Preferably, the anti-Als3 antibody or antigen-binding fragment thereof is administered by infusion (e.g., intravenous infusion).
The Als3 polypeptide or fragment or homolog thereof or anti-Als3 antibody or antigen-binding fragment thereof may be administered with an additional therapeutic agent, such as an antifungal drug. The antifungal drug may be an azole (e.g., triazole (e.g., fluconazole, albaconazole, efinaconazole, epoxiconazole, isavuconazole, itraconazole, posaconazole, propiconazole, ravuconazole, terconazole, or voriconazole), an imidazole (e.g., bifonazole, butoconazole, clotrimazole, eberconazole, econazole, fenticonazole, flutrimazole, isoconazole, ketoconazole, luliconazole, miconazole, omoconazole, oxiconazole, sertaconazole, sulconazole, or tioconazole), or a thiazole (e.g., abafungin)), a polyene (e.g., amphotericin B, candicidin, filipin, hamycin, natamycin, nystatin, or rimocidin), an allylamine (e.g., amorolfin, butenafine, naftifine, or terbinafine), an echinocandin (e.g., anidulafungin, biafungin, caspofungin, or micafungin), a lanosterol demethylase inhibitor (e.g., VT-1161), benzoic acid, ciclopirox oamine, enfumafungin, 5-flucytosin, griseofulvin, haloprogin, tolnaftate, aminocandin, chlordantoin, chlorphenesin, nifuroxime, undecylenic acid, or crystal violet.
The additional therapeutic agent and the Als3 polypeptide or fragment or homolog thereof or anti-Als3 antibody or antigen-binding fragment thereof and the additional therapeutic agent can be administered within 1 month, 2 weeks, 1 week, 1 day, 12 hours, 6 hours, or 1 hour of each other, or at substantially the same time (e.g., serially in any order). The Als3 polypeptide or fragment thereof may be administered as an admixture with the additional therapeutic agent (e.g., antifungal drug).
The Als3 polypeptide or fragment or homolog thereof may have at least 85% (e.g., 90%, 95%, 97%, 99%, or 100%) identity to any one of SEQ ID NOs: 1-7. The anti-Als3 antibody or antigen-binding fragment thereof may be an antibody or antigen-binding fragment thereof that specifically binds to an epitope within a polypeptide having the amino acid sequence set forth in any one of SEQ ID NOs: 1-7 (e.g., with a KD of 100 nM or less, such as a KD of between about 1 pM and 100 nM, inclusive of the endpoints).
A dose of about 5 micrograms to about 5 milligrams (e.g., 10 to about 600 micrograms, about 20 to about 300 micrograms, about 30 to about 90 micrograms, 30 to 300, or about 200 to about 300 micrograms) of the Als3 polypeptide or fragment or homolog thereof may be administered to the subject in a single dose or diluted into one or more separate doses. The dose may be administered in a volume of about 2 mL or less (e.g., about 1 mL or less, about 0.75 mL or less, about 0.5 mL or less, or about 0.25 mL or less). Preferably, the Als3 polypeptide or fragment thereof is administered at a dose of 300 micrograms/0.5 mL.
The Als3 polypeptide or fragment or homolog thereof may be formulated with an adjuvant (e.g., Freund's adjuvant, lipopolysaccharide, aluminum phosphate, aluminum hydroxide, or alum). Preferably, the adjuvant is alum. The adjuvant may be present at a concentration about 0.1-10 mg/mL (e.g., 0.2 mg/mL, 0.3 mg/mL, 0.4 mg/mL, 0.5 mg/mL, 0.6 mg/mL, 0.7 mg/mL, 0.8 mg/mL, 0.9 mg/mL, 1 mg/mL, 2 mg/mL, 3 mg/mL, 4 mg/mL, 5 mg/mL, 6 mg/mL, 7 mg/mL, 8 mg/mL, 9 mg/mL, or 10 mg/mL) and about 5%-90% (e.g., 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%) of the solution. Preferably, about 600 micrograms Als3 polypeptide is formulated with about 0.5 mg aluminum hydroxide in phosphate-buffered saline.
The Als3 polypeptide or fragment or homolog thereof may be administered to the subject more than once (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more times, e.g., at the same or at a different dose). The second dose may be administered between about 7 and 90 days (e.g., between about 21 and 60 days) after administration of the first dose.
In some embodiments, the anti-Als3 antibody or antigen-binding fragment thereof can be administered at a dose of about 0.5 grams to about 5 grams. For example, the anti-Als3 antibody or antigen-binding fragment thereof may be administered at a dose of about 1 mg/kg to about 20 mg/kg and/or in a volume of about 1000 mL or less (e.g., 900 mL, 800 mL, 700 mL, 600 mL, 500 mL, 400 mL, 300 mL, 200 mL, 100 mL, 50 mL, or 10 mL or less, or a volume between about 1000 mL and 10 mL). In particular, the anti-Als3 antibody or antigen-binding fragment thereof may be administered at a concentration of about 0.5 mg/mL (e.g., 2 mg/mL) to about 500 mg/mL (e.g., up to 200 mg/mL). The anti-Als3 antibody or antigen-binding fragment thereof may be administered as an infusion, such as a continuous infusion or a bolus infusion. The anti-Als3 antibody or antigen-binding fragment thereof may be prepared as a lyophilized composition that is hydrated prior to administration. The anti-Als3 antibody or antigen-binding fragment thereof may be administered to the subject more than once (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more times, e.g., at the same or at a different dose). The second dose may be administered to the subject within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months or more after the first dose, or in the event the C. auris infection has not resolved after administration of the first (or a subsequent) dose.
As used herein, “adjuvant” refers to one or more substances that cause and/or enhance stimulation of the immune system. In this context, an adjuvant is used to enhance an immune response to one or more vaccine antigens (e.g., one or more of the Als3 polypeptides described herein). An adjuvant may be administered to a subject before, in combination with, or after administration of a vaccine. Examples of chemical compounds used as adjuvants include, but are not limited to, aluminum compounds (e.g., alum, aluminum hydroxide, aluminum phosphate, ALHYDROGEL®, ADJU-PHOS®), oils, block polymers, immune stimulating complexes, vitamins and minerals (e.g., vitamin E, vitamin A, selenium, and vitamin B12), Quil A (saponins), bacterial and fungal cell wall components (e.g., lipopolysaccarides, lipoproteins, and glycoproteins), hormones, cytokines, and co-stimulatory factors.
As used herein, a “conservative substitution” in an amino acid sequence refers to substitution of an amino acid with an amino acid having similar charge, polarity, and/or size. Preferably, a conservative substitution does not alter the structure or function of the protein or polypeptide.
As used herein, “fusion protein” refers to a protein that includes a polypeptide of the invention (e.g., an Als3 polypeptide, including fragments, homologs, and variants thereof) and a fusion partner (e.g., a heterologous polypeptide).
As used herein, “Als3 polypeptide” refers to any polypeptide, fragment, or variant, thereof sharing substantial sequence identity with C. albicans Als3. This includes, for example, the polypeptides of SEQ ID NOs: 1-5 and fragments thereof. Variants of an Als3 polypeptide have at least 50% (e.g., 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%) sequence identity to the sequence of, e.g., any one of SEQ ID NOs: 1-5.
As used herein, “Als3 homolog” refers to a polypeptide derived from a common ancestral gene as Als3. Homologs include orthologs, which are genes in different species that evolved from a common ancestral gene. Als3 orthologs include, e.g., C. auris hypothetical proteins QG37_06265 (Genbank Accession No. XP 018167572.1) and QG37_05979 (Genbank Accession No. XP_018167307.1). A homolog or ortholog may share at least 10% sequence identity and/or sequence similarity to an Als3 polypeptide (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity and/or sequence similarity to an Als3 polypeptide; such as at least 50% or greater sequence identity to an Als3 polypeptide having the sequence of any one of SEQ ID NOs: 1-5).
As used herein, “immunogenic” refers any substance that is capable of inducing an immune response in a subject (e.g., as determined by an increase in antibody titer in the subject, such as determined by ELISA, antibody subclass determination, an opsonophagocytosis assay (see, e.g., Dwyer and Gadjeva, Methods Mol. Biol. 1100:373-379, 2014), or the presence of cellular anamnesis, e.g., CD4+ and/or CD8+ cellular responses, e.g., using flow cytometry or MHC tetramer staining).
As used herein, “immunogenic amount” in the context of an immunogenic composition or vaccine refers to an amount of the composition that induces an immune response in a subject (e.g., as determined by an increase in antibody titer in the subject, such as determined by ELISA, antibody subclass determination, an opsonophagocytosis assay (see, e.g., Dwyer and Gadjeva, Methods Mol. Biol. 1100:373-379, 2014), or the presence of cellular anamnesis, e.g., CD4+ and/or CD8+ cellular responses, e.g., using flow cytometry or MHC tetramer staining).
As used herein, “immunogenic composition” refers to a composition that elicits an immune response in a subject to which it is administered (e.g., as determined by an increase in antibody titer in the subject, such as determined by ELISA, antibody subclass determination, an opsonophagocytosis assay (see, e.g., Dwyer and Gadjeva, Methods Mol. Biol. 1100:373-379, 2014), or the presence of cellular anamnesis, e.g., CD4+ and/or CD8+ cellular responses, e.g., using flow cytometry or MHC tetramer staining).
By “isolated” or “purified” is meant separated from other naturally accompanying components. Typically, a compound (e.g., nucleic acid, polypeptide, antibody, or small molecule) is substantially isolated when it is at least 60% (e.g., 70%, 80%, 85%, 90%, 95%, 97%, 99%, or 100%) by weight, free from the proteins and/or naturally occurring organic molecules with which it is naturally associated.
As used herein, a “patient” or “subject” refers to a mammal, including, but not limited to, a human or non-human mammal, such as a bovine, equine, canine, ovine, or feline.
The terms “polypeptide,” and “protein” as used interchangeably herein, refer to any chain of two or more natural or unnatural amino acids, regardless of post-translational modification (e.g., glycosylation or phosphorylation), constituting all or part of a naturally-occurring or non-naturally occurring polypeptide or peptide, as is described herein.
As used herein, “pharmaceutical composition” refers to a composition containing a polypeptide or antibody as described herein, formulated with a pharmaceutically acceptable excipient or carrier. Pharmaceutically acceptable excipients or carriers are auxiliary substances that do not induce an immune response in the individual receiving the composition and do not deleteriously affect the properties of the composition.
As used herein, “specifically binds” refers to a binding reaction which is determinative of the presence of an antigen (e.g., an Als3 polypeptide) in a heterogeneous population of proteins and other biological molecules that is recognized, e.g., by an antibody or antigen-binding fragment thereof, with particularity. An antibody or antigen-binding fragment thereof that specifically binds to an antigen will bind to the antigen with a KD of less than 100 nM. For example, an antibody or antigen-binding fragment thereof that specifically binds to an antigen will bind to the antigen with a KD of up to 100 nM (e.g., between 1 μM and 100 nM). An antibody or antigen-binding fragment thereof that does not exhibit specific binding to a particular antigen or epitope thereof will exhibit a KD of greater than 100 nM (e.g., greater than 500 nm, 1 μM, 100 μM, 500 μM, or 1 mM) for that particular antigen or epitope thereof. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein (e.g., an Als3 polypeptide), such as solid-phase ELISA immunoassays.
As used herein, “substantially identical” refers to an amino acid sequence or nucleic acid sequence that exhibits at least 50% sequence identity to a reference sequence. Such a sequence is generally at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical at the amino acid level or nucleic acid level to a reference amino acid or nucleic acid sequence, respectively. In general, for polypeptides, the length of comparison sequences can be at least five amino acids, e.g., 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or more amino acids, up to the entire length of the polypeptide (see, e.g., SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 7). Preferably the comparison is up to the entire length of the polypeptide.
As used herein, when a polypeptide or nucleic acid sequence is referred to as having “at least X % sequence identity” to a reference sequence, it is meant that at least X percent of the amino acids or nucleotides in the polypeptide or nucleic acid, respectively, are identical to those of the reference sequence when the sequences are optimally aligned. An optimal alignment of sequences can be determined in various ways that are within the skill in the art, for instance, using the Smith Waterman alignment algorithm (Smith et al., J. Mol. Biol. 147:195-7, 1981) and BLAST (Basic Local Alignment Search Tool; Altschul et al., J. Mol. Biol. 215: 403-10, 1990). These and other alignment algorithms are accessible using publicly available computer software such as “Best Fit” (Smith and Waterman, Advances in Applied Mathematics, 482-489, 1981) as incorporated into GeneMatcher Plus™ (Schwarz and Dayhof, Atlas of Protein Sequence and Structure, Dayhoff, M. O., Ed pp 353-358, 1979), BLAST, BLAST-2, BLAST-P, BLAST-N, BLAST-X, WU-BLAST-2, ALIGN, ALIGN-2, CLUSTAL, or Megalign (DNASTAR). In addition, those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve optimal alignment over the length of the sequences being compared.
As used herein, the terms “treatment” or “treating” refer to reducing, decreasing, decreasing the progression of, or decreasing the side effects of (e.g., by 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 99%, or about 100%) a C. auris infection. To determine whether the treatment is effective, a comparison can be made between the treated subject and a similarly-situated subject (e.g., one with, or at risk of, a C. auris infection) who did not receive the treatment. A comparison can also be made between the treated subject and a control, a baseline, or a known level or measurement. Treating a C. auris infection includes one or more of reducing C. auris colonization, infection burden, and biofilm formation (e.g., by 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 99%, or about 100%), as well as reducing the number of days of active C. auris infection in the subject (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), reducing the number of days of hospitalization of the subject (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), reducing the number of days requiring antifungal therapy of the subject (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), and/or reducing the dose of antifungal therapy needed by the subject.
As used herein, the term “preventing” means decreasing the risk of (e.g., by 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 99%, or about 100%) contracting a C. auris infection. To determine whether the prevention is effective, a comparison can be made between the subject who received the composition (e.g., Als3 polypeptide or fragment or homolog thereof or anti-Als3 antibody or antigen-binding fragment thereof) and a similarly-situated subject (e.g., one at risk of a C. auris infection) who did not receive the composition. A comparison can also be made between the subject who received the composition and a control, a baseline, or a known level or measurement.
We have surprisingly discovered that polypeptides and fragments derived from the Candida albicans agglutinin-like sequence 3 (Als3) protein and antibodies or antigen-binding fragments thereof that bind these polypeptides and fragments promote treatment of and confer resistance against C. auris infection. Als3 is a protein normally expressed on the cell surface of the hyphal form of C. albicans. C. auris does not exhibit a hyphal form, nor is it known to express an Als3 protein. Nonetheless, we discovered that C. auris has two previously uncharacterized surface proteins with homology to Als3 that cross-react with anti-Als3 antibodies. Consequently, targeting C. auris with anti-Als3 antibodies or antigen-binding fragments thereof provides protection against infection and/or colonization of this yeast species. Disclosed herein are compositions and methods for treating and immunizing against C. auris infection and colonization. Als3 protein-containing compositions may be administered as immunogenic compositions and vaccines to human subjects to treat, prevent, or reduce the risk of a C. auris infection. Similarly, compositions containing anti-Als3 antibodies and antigen-binding fragments thereof may be administered as immunotherapy compositions to human subjects to treat or reduce the risk of a C. auris infection.
The compositions and methods described herein can be used to treat a subject (e.g., a human) that is at risk of C. auris infection or prone to a C. auris infection (e.g., due to a history of past infection, has been exposed to, or is suspected of being exposed to C. auris), or a subject with (or suspected of having) an active C. auris infection. For example, a patient with a compromised immune system, a comorbidity, or a risk factor is one that is susceptible to, or at greater risk of, a C. auris infection. Some comorbidities that increase the risk of C. auris infections are, for example, a bacterial infection, a fungal infection, a viral infection, and immune disorder, or diabetes. The fungal infection may be candidiasis (e.g., infection with one or more Candida species (e.g., C. albicans), e.g., other than C. auris), such as candidiasis infection of a mucous membrane (e.g., mouth, throat, esophagus, rectum, or vagina). The candidiasis may be vulvovaginal candidiasis (e.g., recurrent vulvovaginal candidiasis (RVVC)) or invasive candidiasis. Other risk factors for C. auris infection are surgery, a stay in an intensive care unit, habitation in a nursing home, use of a breathing tube or feeding tube, treatment with a broad-spectrum antibiotic or antifungal agent, or a catheter, such as a central venous catheter.
Certain patients may also be at greater risk for a C. auris infection. These include people who have been treated at, are being treated at, or will be treated at a hospital or health center. Furthermore, people who have worked, work at, or will work at a hospital or health center may be susceptible to infection. Elderly people (e.g., older than 50, 60, 70, 80, or 90 years old) or very young people, such as newborns, infants, or toddlers (e.g., under 3 years old) may be at increased risk due to an underdeveloped immune system or an immunocompromised immune system.
Assays for diagnosing a C. auris infection are known (see, e.g., Kordalewska et al., J. Clin. Microbiol. 55:2445-2452, 2017, and Leach et al., J. Clin. Microbiol. 2017) and can be used to identify a patient for treatment of the C. auris infection. C. auris can also be diagnosed by standard laboratory culture growth tests following a swab of, or collection from, a tissue suspected of being infected or containing C. auris, or a blood sample. Molecular methods using diagnostic devices based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry can differentiate C. auris from other Candida species. Another method includes sequencing the D1-D2 region of the 28s rDNA or the Internal Transcribed Region (ITS) of rDNA to identify C. auris. C. auris strains can also be further tested for antifungal susceptibility to determine an appropriate course of treatment.
The compositions and methods described herein are particularly useful for human subjects, both male and female. The methods may include first identifying a subject as having a risk factor or comorbidity, as described herein, that increases the likelihood of a C. auris infection or colonization. In some instances, the methods include first identifying a subject as having a C. auris infection or C. auris colonization prior to administration of a treatment described herein.
After the subject is diagnosed and/or receives a treatment, the subject can be monitored over time to track the treatment progress and monitor the subject for C. auris colonization and/or infection. The monitoring or identifying step may include determining a change (e.g., an increase or decrease) in C. auris colonization in the subject as compared to C. auris colonization in the subject prior to administration of the treatment. The monitoring or identifying step may involve taking a sample from the subject, such as with a swab of the skin or a mucous membrane of the subject. The mucous membrane may be from the mouth, throat, esophagus, rectum, or vagina of the subject. Then, the contents of the skin swab can be cultured or analyzed to identify the presence of, or progression of, the infection.
The compositions and methods may reduce C. auris colonization or infection by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, or 90%, or substantially eliminate colonization or infection. Furthermore, the compositions and methods described herein may be useful for inhibiting or reducing C. auris biofilm formation. For example, the compositions and methods may reduce or inhibit biofilm formation by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, or 90%, or substantially eliminate biofilm formation. In general, the compositions and methods described herein may increase the probability of survival of the subject as compared to a subject that does not receive the treatment. The compositions and methods may reduce the number of days of active C. auris infection in the subject (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), the number of days of hospitalization of the subject (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), the number of days the subject requires antifungal therapy (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more days), and/or the dose of antifungal therapy needed by the subject, e.g., each relative to an untreated subject.
C. Albicans Als3 is natively expressed as a 1119 amino acid pre-protein, which has the following amino acid sequence:
This protein includes an N-terminal signal sequence of 17 amino acids (underlined above), which is cleaved during production of the mature protein.
One of skill in the art would appreciate that Als3 is a surface expressed, membrane-bound protein and, thus, includes a hydrophobic transmembrane domain. Therefore, robust expression of the full length protein may be difficult to achieve in order to obtain large quantities of the protein to produce a useful yield for the creation of an immunogenic or vaccine composition. Accordingly, fragments of Als3 can be produced, which may be expressed at a higher yield than the native protein. Als3 polypeptides include, e.g., the Als3-2 fragment, which is a 416 amino acid N-terminal fragment that lacks the signal sequence has the following amino acid sequence:
Another Als3 polypeptide fragment is the Als3-1 fragment, which is similar to Als3-2, but is a 425 amino acid fragment that contains a 6×-His tag and a three amino acid GIQ linker at the N-terminus to facilitate protein purification. The amino acid sequence of Als3-1 is:
Another Als3 polypeptide fragment is a 307 amino acid fragment corresponding to residues 18-324 of Als3 and designated as Als3 (18-324). The amino acid sequence of Als3 (18-324) is:
A 108 amino acid Als3 fragment, designated as Als3 Ser/Thr-rich sequence, which contains residues 325-432, has the following amino acid sequence:
Exemplary polypeptides that may be used in conjunction with the compositions and methods as described herein include any polypeptide, fragment, homolog, or ortholog thereof of an Als3 polypeptide, such as the polypeptide fragments described above. Furthermore, fragments and variants of the Als3 homologs or orthologs may be used.
The C. auris genome is not believed to contain an Als3 gene, although genes encoding hypothetical proteins with homology to C. albicans Als3 have been identified. One protein is designated as C. auris hypothetical protein QG37_06265 (Genbank Accession No. XP 018167572.1) and has the following 861 amino acid sequence:
A second protein, designated as C. auris hypothetical protein QG37_05979 (Genbank Accession No. XP_018167307.1), has the following 714 amino acid sequence:
Polypeptides comprising any protein, fragment, or variant or modified version of any one of SEQ ID NOs: 1-7 can be prepared as an immunogenic composition or vaccine and used to treat or immunize against a C. auris infection in a subject (e.g., a human subject). The polypeptides of the invention may have, for example, at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity with any one of SEQ ID NOs: 1-7 or may have at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity with any fragment thereof of SEQ ID NOs: 1-7.
The full length native Als3 protein of SEQ ID NO: 1 consists of 1119 amino acids. Thus, fragments of Als3 that may be used to prepare compositions for use in the methods described herein include, e.g., fragments of Als3 that are fewer than 1119, 1118, 1117, 1116, 1115, 1114, 1113, 1112, 1111, 1110, 1100, 1090, 1080, 1070, 1060, 1050, 1040, 1030, 1020, 1010, 1000, 990, 980, 970, 960, 950, 940, 930, 920, 910, 910, 900, 890, 880, 870, 860, 850, 840, 830, 820, 810, 800, 790, 780, 770, 760, 750, 740, 730, 720, 710, 700, 690, 680, 670, 660, 650, 640, 630, 620, 610, 600, 590, 580, 570, 560, 550, 540, 530, 520, 510, 500, 490, 480, 470, 460, 450, 440, 430, 420, 410, 400, 390, 380, 370, 360, 350, 340, 330, 320, 310, 300, 290, 280, 270, 260, 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, 50, 40, 30, 25, 20, 15, or 10 amino acids in length.
The Als3 polypeptide of SEQ ID NO: 1 could also be truncated at either the N-terminus or the C-terminus, or at both termini, to produce an immunogenic fragment, e.g., for use in the methods described herein. For example, the N-terminus, the C-terminus, or both the N-terminus and the C-terminus may be truncated by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, or 1100 amino acids.
The C. auris Als3 homolog of SEQ ID NO: 6 contains 861 amino acids. Thus, fragments of SEQ ID NO: 6 can be used to produce an immunogenic composition or vaccine and used to treat or immunize against a C. auris infection in a subject (e.g., a human subject). Such fragments include, e.g., fragments of SEQ ID NO: 6 that are fewer than 861, 860, 859, 858, 857, 856, 855, 854, 853, 852, 851, 850, 840, 830, 820, 810, 800, 790, 780, 770, 760, 750, 740, 730, 720, 710, 700, 690, 680, 670, 660, 650, 640, 630, 620, 610, 600, 590, 580, 570, 560, 550, 540, 530, 520, 510, 500, 490, 480, 470, 460, 450, 440, 430, 420, 410, 400, 390, 380, 370, 360, 350, 340, 330, 320, 310, 300, 290, 280, 270, 260, 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, 50, 40, 30, 25, 20, 15, or 10 amino acids in length. The N-terminus, the C-terminus, or both the N-terminus and C-terminus may be truncated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, or 850 acids.
The C. auris Als3 homolog of SEQ ID NO: 7 consists of 714 amino acids. Thus, fragments of SEQ ID NO: 7 can be used to produce an immunogenic composition or vaccine and used to treat or immunize against a C. auris infection in a subject (e.g., a human subject). Such fragments of SEQ ID NO: 7 include fragments of SEQ ID NO: 7 that are fewer than 714, 713, 712, 711, 710, 700, 690, 680, 670, 660, 650, 640, 630, 620, 610, 600, 590, 580, 570, 560, 550, 540, 530, 520, 510, 500, 490, 480, 470, 460, 450, 440, 430, 420, 410, 400, 390, 380, 370, 360, 350, 340, 330, 320, 310, 300, 290, 280, 270, 260, 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, 50, 40, 30, 25, 20, 15, or 10 amino acids in length. The N-terminus, the C-terminus, or both the N-terminus and C-terminus may be truncated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, or 710 amino acids.
In some instances, a polypeptide as described herein (e.g., the polypeptides of SEQ ID NOs: 1-7 or fragments thereof) may comprise a modification (e.g., chemical modification, e.g., post-translational modification). Preferably, the modification does not substantially reduce the immunogenicity of the polypeptide. The modified polypeptide (e.g., the polypeptides of SEQ ID NOs: 1-7) may have or may optimize a characteristic of the polypeptide, such as in vivo stability, bioavailability, toxicity, immunological activity, immunological identity, or conjugation properties.
A polypeptide as described herein (e.g., the polypeptides of SEQ ID NOs: 1-7) can also include one or more amino acid insertions, deletions, or substitutions in the polypeptide sequence. For example, the addition of one or more residues (e.g., cysteine residues) to the N- or C-terminus of any of the polypeptides described herein (e.g., the polypeptides of SEQ ID NOs: 1-7) can facilitate conjugation of these polypeptides with a chemical moiety or fusion partner. Additional (e.g., 1, 2, 3, 4, 5, 6, and 7, 8, 9, 10, or more) residues may also be present at the N- or C-termini that not part of the native peptide sequence (e.g., the sequences of SEQ ID NOs: 1-7). Amino acid substitutions can be conservative (i.e., in which a residue is replaced by another with similar chemical properties) or non-conservative (i.e., in which a residue is replaced by an amino acid with different chemical properties).
Als3 polypeptides (e.g., the polypeptides of SEQ ID NOs: 1-5 and fragments thereof) and orthologs thereof (e.g., the polypeptides of SEQ ID NOs: 6-7 and fragments thereof) may be made synthetically, e.g., using methods known in the art, and can include, e.g., substitutions of amino acids not naturally encoded by DNA (e.g., non-naturally occurring or unnatural amino acid). Examples of non-naturally occurring amino acids include D-amino acids, an amino acid having an acetylaminomethyl group attached to a sulfur atom of a cysteine, a pegylated amino acid, the omega amino acids of the formula NH2(CH2)nCOOH wherein n is 2-6, neutral nonpolar amino acids, such as sarcosine, t-butyl alanine, t-butyl glycine, N-methyl isoleucine, and norleucine. Phenylglycine may substitute for Trp, Tyr, or Phe; citrulline and methionine sulfoxide are neutral nonpolar, cysteic acid is acidic, and ornithine is basic. Proline may be substituted with hydroxyproline.
The polypeptides described herein (e.g., the polypeptides of SEQ ID NOs: 1-7 and fragments, variants, and homologs thereof) can be obtained by chemical synthesis using a commercially available automated peptide synthesizer. The synthesized protein or polypeptide can be precipitated and further purified, for example by high performance liquid chromatography (HPLC). Alternatively, the proteins and polypeptides can be obtained by recombinant methods that are well-known in the art (e.g., expression in S. cerevisiae, E. coli, CHO cells, or insect cells).
The polypeptides described herein (e.g., the polypeptides of SEQ ID NOs: 1-7 and fragments, variants, and homologs thereof) may be conjugated or fused with another moiety (e.g., a heterologous protein or chemical moiety) to improve its physical properties (e.g., stability, immunogenicity, expression, purity).
Also featured are anti-Als3 antibodies and antigen binding fragments thereof. These antibodies may specifically bind an epitope present in an Als3 polypeptide or fragment thereof, such as the polypeptides of SEQ ID NOs: 1-5. The invention also features antibodies and antigen-binding fragments thereof directed to homologs or orthologs of Als3 and fragments of said homologs or orthologs, such as the C. auris Als3 orthologs of SEQ ID NOs: 6-7. The antibodies may bind any epitope present in an Als3 homolog or ortholog or a fragment or variant thereof (e.g., fragment or variant of SEQ ID NOs: 6-7).
The antibody may be a polyclonal, monoclonal, genetically engineered, and otherwise modified form of antibody, including but not limited to a chimeric antibody, human antibody, murine antibody, humanized antibody, heteroconjugate antibody (e.g., bi- tri- and quad-specific antibody, diabody, triabody, and tetrabody), and antigen binding fragments of such antibodies, including, for example, Fab′, F(ab′)2, Fab, Fv, rlgG, and scFv fragments. A monoclonal antibody (mAb) is meant to include both intact molecules, as well as antibody fragments (including, for example, Fab and F(ab′)2 fragments) that are capable of specifically binding to a target protein. Fab and F(ab′)2 fragments refer to antibody fragments that lack the Fc fragment of an intact antibody.
The antibody can be generated using an epitope present within any one of SEQ ID NOs: 1-7 or the antibody can be one that cross-reacts with an epitope present within any one of SEQ ID NOs: 1-7. The antibody may bind an epitope (e.g., an epitope present in any one of SEQ ID NOs: 1-7) with a KD of less than 100 nM (e.g., 90 nM, 80 nM, 70 nM, 60 nM, 50 nM, 40 nM, 30 nM, 20 nM, 10 nM, 9 nM, 8 nM, 7 nM, 6 nM, 5 nM, 4 nM, 3 nM, 2 nM, 1 nM, 900 μM, 800 μM, 700 μM, 600 μM, 500 μM, 400 μM, 300 μM, 200 μM, 100 μM, or less).
An antigen-binding fragment refers to one or more fragments of an antibody that retain the ability to specifically bind to a target antigen (e.g., an Als3 polypeptide or a polypeptide of any one of SEQ ID NOs: 1-7 or a fragment, variant, or homolog thereof). The antigen-binding function of an antibody can be performed by fragments of a full-length antibody. The antibody fragments can be, for example, a Fab, F(ab′)2, scFv, diabody, a triabody, an affibody, a nanobody, an aptamer, or a domain antibody. Examples of antigen-binding fragments include, but are not limited to: a Fab fragment, a monovalent fragment consisting of the VL, VH, CL, and CH1 domains, a F(ab′)2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region, a Fd fragment consisting of the VH and CH1 domains, a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, a dAb including VH and VL domains, a dAb fragment that consists of a VH domain (see, e.g., Ward et al., Nature 341:544-546, 1989), a dAb which consists of a VH or a VL domain, an isolated complementarity determining region (CDR), and a combination of two or more (e.g., two, three, four, five, or six) isolated CDRs which may optionally be joined by a synthetic linker. Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see, for example, Bird et al., Science 242: 423-426, 1988 and Huston et al., Proc. Natl. Acad. Sci. USA 85: 5879-5883, 1988). These antibody fragments can be obtained using conventional techniques known to those of skill in the art, and the fragments can be screened for utility in the same manner as intact antibodies. Antigen-binding fragments can be produced by recombinant DNA techniques, enzymatic or chemical cleavage of intact immunoglobulins, or, in certain cases, by chemical peptide synthesis procedures known in the art.
Monoclonal antibodies (e.g., anti-Als3 antibodies) may be made, for example, by using the hybridoma method first described by Kohler et al., Nature 256:495, 1975, or may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567). In the hybridoma method, a mouse or other appropriate host animal, such as a hamster or macaque monkey, is immunized, e.g., using a polypeptide described herein (e.g., the polypeptides of any one of SEQ ID NOs: 1-7), to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the polypeptide used for immunization. Alternatively, lymphocytes may be immunized in vitro. Lymphocytes then are fused with myeloma cells using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103, Academic Press, 1986). The antibody may also be made in an animal model that has been genetically modified to product human antibodies.
The polypeptides or fragments described herein (e.g., the polypeptides of any one of SEQ ID NOs: 1-7) and the antibodies or antigen-binding fragments thereof (e.g., antibodies and antigen-binding fragments thereof directed against an epitope present in any one of SEQ ID NOs: 1-7) may be formulated as a pharmaceutical composition for administration to a subject (e.g., a human subject).
Pharmaceutical compositions can be prepared using standard pharmaceutical formulation chemistries and methodologies that are readily available to the reasonably skilled artisan. For example, polypeptides and antibodies or antigen-binding fragments thereof described herein (e.g., the polypeptides of any one of SEQ ID NOs: 1-7 or fragments thereof, and antibodies or antigen-binding fragments thereof that specifically bind to an epitope within any one of SEQ ID NOs: 1-7) can be combined with one or more pharmaceutically acceptable excipients or vehicles. Auxiliary substances, such as wetting or emulsifying agents, pH buffering substances and the like, may be present in the excipient or vehicle. These excipients, vehicles and auxiliary substances are generally pharmaceutical agents that do not induce an immune response in the individual receiving the composition, and which may be administered without undue toxicity. Pharmaceutically acceptable excipients include, but are not limited to, liquids, such as water, saline, polyethyleneglycol, hyaluronic acid, glycerol and ethanol. Pharmaceutically acceptable salts can also be included therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of pharmaceutically acceptable excipients, vehicles and auxiliary substances is available in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991).
Such compositions (e.g., pharmaceutical compositions comprising an Als3 polypeptide or fragment or homolog thereof, e.g., of any one of SEQ ID NOs: 1-7, or an antibody or antigen-binding fragment thereof that specifically binds an epitope present in any one of SEQ ID NOs: 1-7) may be prepared, packaged, or sold in a form suitable for bolus administration or for continuous administration. Injectable compositions may be prepared, packaged, or sold in unit dosage form, such as in ampoules or in multi-dose containers containing a preservative.
Compositions may include, but are not limited to, suspensions, solutions, emulsions in oily or aqueous vehicles, pastes, and implantable sustained-release or biodegradable formulations. Such compositions may further comprise one or more additional ingredients including, but not limited to, suspending, stabilizing, or dispersing agents. In one embodiment of a composition for parenteral administration, the active ingredient is provided in dry (e.g., a powder or granules) form for reconstitution with a suitable vehicle (e.g., sterile pyrogen-free water) prior to parenteral administration of the reconstituted composition. The compositions may be prepared, packaged, or sold in the form of a sterile injectable aqueous or oily suspension or solution. This suspension or solution may be formulated according to the known art, and may comprise, in addition to the active ingredient, additional ingredients such as the dispersing agents, wetting agents, or suspending agents described herein. Such sterile injectable formulations may be prepared using a non-toxic parenterally-acceptable diluent or solvent, such as water or 1,3-butane diol, for example. Other acceptable diluents and solvents include, but are not limited to, Ringer's solution, isotonic sodium chloride solution, and fixed oils such as synthetic mono- or di-glycerides.
Other parentally-administrable compositions that are useful include those which comprise the active ingredient in microcrystalline form, in a liposomal preparation, or as a component of a biodegradable polymer system. Compositions for sustained release or implantation may comprise pharmaceutically acceptable polymeric or hydrophobic materials such as an emulsion, an ion exchange resin, a sparingly soluble polymer, or a sparingly soluble salt.
Alternatively, the polypeptides or fragments thereof and/or the antibodies or antigen-binding fragments thereof described herein (e.g., the polypeptides of any one of SEQ ID NOs: 1-7 and fragments thereof and antibodies or antigen-binding fragments thereof that bind to an epitope within any one of SEQ ID NOs: 1-7) may be encapsulated, adsorbed to, or associated with particulate carriers. Suitable particulate carriers include those derived from polymethyl methacrylate polymers, as well as PLG microparticles derived from poly(lactides) and poly(lactide-co-glycolides). See, e.g., Jeffery et al. (1993) Pharm. Res. 10:362-368. Other particulate systems and polymers can also be used, for example, polymers such as polylysine, polyarginine, polyornithine, spermine, spermidine, as well as conjugates of these molecules.
The anti-Als3 antibodies or fragments thereof (e.g., antibodies that specifically bind to an epitope within any one of SEQ ID NOs: 1-7) may be formulated as a composition with an excipient selected from a buffer, salt, surfactant, polyol/disaccharide/polysaccharide, amino acid, and/or antioxidant. For example, the composition may contain a buffer that keeps pH levels between 4.7 and 7.4, such as acetate, citrate, histidine, succinate, phosphate, and hydroxymethylaminomethane (Tris). If present, a surfactant may be selected from one or more of polysorbate 80 (Tween 80), polysorbate 20 (Tween 20), and poloxamer 188. Among those, 72% used polysorbate 80. For lyophilized or liquid compositions, one or a mixture of polyol/disaccharide/polysaccharide (e.g., mannitol, sorbitol, sucrose, trehalose, and dextran 40) may be present. The composition may also include sodium chloride (NaCl). Amino acids that may be included in an antibody formulation include, e.g., glycine and arginine. Finally, antioxidants that may be included in the compositions include ascorbic acid, methionine, and ethylenediaminetetraacetic acid (EDTA).
Substances that stimulate the immune response, e.g., adjuvants, may be included in the compositions that comprise polypeptides (e.g., Als3 polypeptides). Adjuvants are substances that cause and/or increase stimulation of the immune system. In this context, an adjuvant is used to enhance an immune response to one or more immunogenic peptides (e.g., one or more of the Als3 polypeptides described herein). An adjuvant may be administered to a subject before, in combination with, or after administration of an immunogenic composition, an Als3 peptide, fragment or homolog thereof, or a vaccine described herein. Examples of chemical compounds used as adjuvants include, but are not limited to, aluminum compounds (e.g., alum, aluminum hydroxide, aluminum phosphate, ALHYDROGEL®, ADJU-PHOS®), oils, block polymers, immune stimulating complexes, vitamins and minerals (e.g., vitamin E, vitamin A, selenium, and vitamin B12), Quil A (saponins), bacterial and fungal cell wall components (e.g., lipopolysaccarides, lipoproteins, and glycoproteins), hormones, cytokines, Freund's adjuvant, and co-stimulatory factors.
The polypeptides or fragments described herein (e.g., the polypeptides of any one of SEQ ID NOs: 1-7 or fragments thereof) may be formulated as an immunogenic composition or a vaccine. The formulated compositions will include an amount of one or more polypeptides described herein (e.g., the polypeptides of any one of SEQ ID NOs: 1-7 or fragments thereof) that is sufficient to mount an immunological response, e.g., as determined by antibody titer in the subject, such as by ELISA, antibody subclass determination, an opsonophagocytosis assay (see, e.g., Dwyer and Gadjeva, Methods Mol. Biol. 1100:373-379, 2014), or the presence of cellular anamnesis, e.g., CD4+ and/or CD8+ cellular responses, e.g., using flow cytometry or MHC tetramer staining. An immunogenic amount can be readily determined by one of skill in the art. The compositions may contain from about 0.1% to about 99.9% of the polypeptides (e.g., of SEQ ID NOs: 1-7 or a fragment thereof), and can be administered to the subject.
Immunogenic and vaccine compositions can include a mixture of distinct polypeptides as described herein. For example, immunogenic compositions or vaccines may include, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more distinct polypeptides as described herein, e.g., containing or consisting of the amino acid sequences of SEQ ID NOs: 1, 2, 3, 4, 5, 6, or 7, or a variant sequence thereof having up multiple (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) substitutions (e.g., conservative substitutions), deletions, or additions to the amino acid sequence of any one of SEQ ID NOs:1, 2, 3, 4, 5, 6, or 7.
Als3 polypeptides (e.g., the polypeptides of any one of SEQ ID NOs: 1-7), optionally in combination with an adjuvant (e.g., aluminum hydroxide; also see examples described above), can be formulated in compositions including, for example, a buffer and a salt. Such compositions can include, for example, sodium phosphate, sodium citrate, histidine, or sodium succinate (2-20 mM, e.g., 5-15 mM or 10 mM), pH 6.0-8.0 (e.g., pH 6.5-7.5 or pH 7.0), as well as sodium chloride (100-300 mM, e.g., 100-200 mM or 154 mM.
A specific example of a vaccine formulation that can be used in the invention is NDV-3, which includes Als3-1 (SEQ ID NO: 3) formulated in 10 mM sodium phosphate, pH 7.0, and 154 mM sodium chloride. Another example is NDV-3A, which includes Als3-2 (SEQ ID NO:2) formulated in 10 mM sodium phosphate, pH 6.5, and 154 mM sodium chloride. The NDV-3 and NDV-3A vaccines can optionally be filled in 2 mL glass vials with a 0.7 mL volume containing 600 μg Als3-1 (or Als3-2)/mL, 1.0 mg Al/mL as aluminum hydroxide and phosphate-buffered saline. When withdrawn from the vial with a needle and syringe for injection, approximately 0.5 mL can be injected (e.g., by the intramuscular route), resulting in a delivered dose of 300 μg of Als3-1 (or Als3-2).
The compositions described herein (e.g., the polypeptides of SEQ ID NOs: 1-7 or fragments thereof or antibodies or fragments thereof that specifically bind to an epitope within any one of SEQ ID NOs: 1-7) can be administered to a subject (e.g., a human patient) in a variety of ways. The compositions may contain a polypeptide or fragment thereof or an antibody or fragment thereof as the sole active agent or in combination with one or more additional active agents. Furthermore, the severity of the infection to be treated may affect the dosage administered, the route of administration, or the frequency of administration. The dosage regimen may be determined by the clinical indication being addressed, as well as by various patient variables (e.g., weight, age, sex) and clinical presentation (e.g., extent or severity of infection). The compositions may be administered orally, buccally, sublingually, parenterally, intravenously, subcutaneously, intramedullary, intranasally, as a suppository, using a flash formulation, topically, intradermally, intramuscularly, via pulmonary delivery, via intra-arterial injection, intrathecally, via an infusion (e.g., continuous infusion or Bolus infusion), or via a mucosal route. Furthermore, it is understood that the dosage(s) may be continuously given or divided into multiple dosages given over time. The composition may be administered, for example, one or more times every hour, day, week, month, or year.
In general, the dosage of a pharmaceutical composition described herein, or an active agent in a pharmaceutical composition described herein (e.g., the polypeptides of any one of SEQ ID NOs: 1-7 or fragments thereof and antibodies that bind an epitope within any one of SEQ ID NOs: 1-7), may be in the range of from about 1 pg to about 10 g (e.g., 1 pg-10 pg, e.g., 2 pg, 3 pg, 4 pg, 5 pg, 6 pg, 7 pg, 8 pg, 9 pg, 10 pg, e.g., 10 pg-100 pg, e.g., 20 pg, 30 pg, 40 pg, 50 pg, 60 pg, 70 pg, 80 pg, 90 pg, 100 pg, e.g., 100 pg-1 ng, e.g., 200 pg, 300 pg, 400 pg, 500 pg, 600 pg, 700 pg, 800 pg, 900 pg, 1 ng, e.g., 1 ng-10 ng, e.g, 2 ng, 3 ng, 4 ng, 5 ng, 6 ng, 7 ng, 8 ng, 9 ng, 10 ng, e.g., 10 ng-100 ng, e.g., 20 ng, 30 ng, 40 ng, 50 ng, 60 ng, 70 ng, 80 ng, 90 ng, 100 ng, e.g., 100 ng-1 μg, e.g., 200 ng, 300 ng, 400 ng, 500 ng, 600 ng, 700 ng, 800 ng, 900 ng, 1 μg, e.g., 1-10 μg, e.g., 1 μg, 2 μg, 3 μg, 4 μg, 5 μg, 6 μg, 7 μg, 8 μg, 9 μg, 10 μg, e.g., 10 μg-100 μg, e.g., 20 μg, 30 μg, 40 μg, 50 μg, 60 μg, 70 μg, 80 μg, 90 μg, 100 μg, e.g., 100 μg-1 mg, e.g., 200 μg, 300 μg, 400 μg, 500 μg, 600 μg, 700 μg, 800 μg, 900 μg, 1 mg, e.g., 1 mg-10 mg, e.g., 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, 10 mg, e.g., 10 mg-100 mg, e.g., 20 mg, 30 mg, 40 mg, 50 mg, 60 mg, 70 mg, 80 mg, 90 mg, 100 mg, e.g., 100 mg-1 g, e.g., 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, 1 g, e.g., 1 g-10 g, e.g., 2 g, 3 g, 4 g, 5 g, 6 g, 7 g, 8 g, 9 g, 10 g).
The Als3 polypeptide or anti-Als3 antibody, or fragments thereof, may also be administered in a unit dose form or as a dose per mass or weight of the patient from about 0.01 mg/kg to about 100 mg/kg (e.g., 0.01-0.1 mg/kg, e.g., 0.02 0.03 mg/kg, 0.04 mg/kg, 0.05 mg/kg, 0.06 mg/kg, 0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg, 0.1 mg/kg, e.g., 0.1-1 mg/kg, e.g., 0.2 mg/kg, 0.3 mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg, 0.8 mg/kg, 0.9 mg/kg, 1 mg/kg, e.g., 1-10 mg/kg, e.g., 1 mg/kg, 2 mg/kg, 3 mg/kg, 4 mg/kg, 5 mg/kg, 6 mg/kg, 7 mg/kg, 8 mg/kg, 9 mg/kg, 10 mg/kg, e.g., 10-100 mg/kg, e.g., 20 mg/kg, 30 mg/kg, 40 mg/kg, 50 mg/kg, 60 mg/kg, 70 mg/kg, 80 mg/kg, 90 mg/kg, 100 mg/kg).
Preferred embodiments for antibody administration (e.g., antibodies or fragments thereof that specifically bind to an epitope present in any one of SEQ ID NOs: 1-7) include infusions, such as continuous or bolus infusions. About 0.5 g to about 5 g of the anti-Als3 antibody may be administered. The anti-Als3 antibody may be administered in a suitable volume of about 1 mL to about 1 L (e.g., 10 mL-1 L, e.g., 900 mL, 800 mL, 700 mL, 600 mL, 500 mL, 400 mL, 300 mL, 200 mL, 100 mL, 50 mL, 10 mL, 5 mL, 4 mL, 3 mL, 2 mL, 1 mL, or less). The anti-Als3 antibody may be administered at a dosage of about 1 mg/kg to about 20 mg/kg. The dose may also be administered as a dose per mass or weight of the patient per unit day (e.g., 0.1-10 mg/kg/day).
Immunogenic compositions and vaccines comprising the polypeptides as described herein (e.g., the polypeptides of any one of SEQ ID NOs: 1-7 or fragments thereof) can be administered in multiple doses (e.g., 2, 3, 4, 5, or more), such as a primary dose and one or more (e.g., 2, 3, 4, 5, or more) subsequent booster doses. For example, an initial dose of the polypeptide may be administered, and a second dose may be administered between 1 and 100 days (e.g., 2 days, 3 days, 4 days, 5 days, 10 days, 15 days, 20 days, 25 days, 30 days, 35 days, 40 days, or 45 days, 50 days, 60 days, 70 days, 80 days, 90 days) later. The second dose may be administered about 7 to 90 days, 1 to 50 days, 21 to 60 days, or about 22 days after the first dose. In some preferred embodiments, about 5 μg to about 5 mg (e.g., about 10-600 μg, 20-300 μg, 30-300 μg, 30-90 μg. or 200-300 μg) of an Als3 polypeptide or fragment or homolog thereof (e.g., of any one of SEQ ID NOs: 1-7) is administered. These dosages may be administered in a suitable volume of 0.1 mL to about 1 L (e.g., 2 mL, 1 mL, 0.75 mL, 0.5 mL, or 0.25 mL, or less).
The methods described herein of treatment of or immunization against a C. auris infection may include administration of combination therapies comprising two or more pharmaceutical agents (e.g., an Als3 polypeptide (e.g., of any one of SEQ ID NOs: 1-5) or an anti-Als3 antibody or fragment thereof and an antifungal drug). The two or more agents may be administered sequentially (in any order, and including at substantially the same time) or as an admixture. For example, the agents may be administered within about 1 month, 2 weeks, 1 week, 1 day, 12 hours, 6 hours, or 1 hour of each other, or at substantially the same time. The two or more agents may be administered in the same formulation or as separate formulations.
The antifungal drug may be an azole, a polyene, an allylamine, an echinocandin, a lanosterol demethylase inhibitor, benzoic acid, ciclopirox oamine, enfumafungin, 5-flucytosin, griseofulvin, haloprogin, tolnaftate, aminocandin, chlordantoin, chlorphenesin, nifuroxime, undecylenic acid, or crystal violet. The azole may be a triazole, an imidazole, or a thiazole. The triazole may be fluconazole, albaconazole, efinaconazole, epoxiconazole, isavuconazole, itraconazole, posaconazole, propiconazole, ravuconazole, terconazole, or voriconazole. The imidazole may be bifonazole, butoconazole, clotrimazole, eberconazole, econazole, fenticonazole, flutrimazole, isoconazole, ketoconazole, luliconazole, miconazole, omoconazole, oxiconazole, sertaconazole, sulconazole, or tioconazole. The thiazole may be abafungin. The polyene may be amphotericin B, candicidin, filipin, hamycin, natamycin, nystatin, or rimocidin. The allylamine may be amorolfin, butenafine, naftifine, or terbinafine. The echinocandin may be anidulafungin, biafungin, caspofungin, or micafungin. The lanosterol demethylase inhibitor may be VT-1161. Any of the antifungal drugs may be a in the form of a pharmaceutically acceptable salt or ester thereof.
Also featured are kits that can be used to carry out the methods of treatment of or immunization against a C. auris infection, as described herein. Kits of the invention can include one or more Als3 polypeptides or fragments or homologs thereof (e.g., any one of SEQ ID NOs: 1-7), optionally in the form of an immunogenic or vaccine composition, such as a composition containing an adjuvant (for example, aluminum hydroxide). In an example, the Als3 polypeptide or fragment or homolog thereof (e.g., any one of SEQ ID NOs: 1-7) is present in a container (e.g., a glass vial) in liquid form (e.g., in water or a buffered salt solution, such as, e.g., 10 mM sodium phosphate, pH 6.5 or 7.0, and 154 mM sodium chloride; see above for other examples of buffer and salt conditions that can be used). In another example, the Als3 polypeptide or fragment or homolog thereof (e.g., any one of SEQ ID NOs: 1-7) is present in a container (e.g., a glass vial) in lyophilized form. In this example, the kit may optionally also include a diluent (e.g., water or a buffered salt solution) for reconstitution of the lyophilized polypeptide into liquid form prior to administration. The polypeptide may also be present in another formulation, as described herein, or as is known in the art. The amount of polypeptide and, optionally, adjuvant present in the compositions of the kits can be, for example, as described above. Thus, for example, the kits can include an Als3 polypeptide or fragment or homolog thereof (e.g., any one of SEQ ID NOs: 1-7) in an amount to facilitate the administration of a dose as described herein.
Also featured are kits with an anti-Als3 antibody or antigen-binding fragment thereof, such as those described above. The anti-Als3 antibody or antigen-binding fragment thereof may be present in a composition that is formulated for administration to a subject, or the composition may be present in the kit in lyophilized form. If so, the kit may also include a diluent for reconstituting the composition containing the anti-Als3 antibody or antigen-binding fragment thereof. The composition containing the anti-Als3 antibody or antigen-binding fragment thereof may be formulated as discussed above and may be present in the kit at one of the concentrations discussed above.
In addition to the Als3 polypeptide or fragment thereof or the anti-Als3 antibody or antigen-binding fragment thereof, the kits may also include one or more antifungal agents (e.g., fluconazole, ketoconazole, butoconazole, miconazole, terconazole, tioconazole, clotrimazole, and nystatin, or any of the other antifungal agents described above). In the case of, for example, fluconazole, the kits can include one or more doses in an amount as described herein, formulated in a tablet for oral administration (e.g., the fluconazole may be present in table form at a dosage of 50, 100, or 200 mg; the tablet may also include the following inactive ingredients: microcrystalline cellulose, dibasic calcium phosphate anhydrous, povidone, croscarmellose sodium, and magnesium stearate). The kit may include a single dose of the antifungal agent (e.g., fluconazole), or 2, 3, 4, 5, 6, 7, 8, 9, or 10 doses (e.g., at least 3 doses) of the antifungal agent (e.g., fluconazole). Other agents, such as butoconazole, miconazole, terconazole, tioconazole, and clotrimazole, may be present in the kits instead of, or in addition to, fluconazole. These agents may be in the form of a cream. Alternatively, clotrimazole, miconazole, and terconazole can be present in the form of a vaginal suppository, as is known in the art. These agents can be present in single or multiple doses. The antifungal agent may be packaged in a separate container within the kit so that a user (e.g., a physician) can provide the package containing the antifungal agent to a patient, or the antifungal agent may be present as an admixture with the Als3 polypeptide or fragment thereof or the anti-Als3 antibody or antigen-binding fragment thereof.
The kit components can be provided in dosage form to facilitate administration, and can optionally include materials required for administration and/or instructions for patient treatment consistent with, for example, the methods described herein.
For example, the kit can include instructions for use, which guides the user (e.g., the physician) with respect to the administration of the Als3 vaccine (e.g., the NDV-3 or NDV-3A vaccine, e.g., at the point of care location). The kit can also include instructions guiding the physician to administer a first dose of an antifungal agent (e.g., fluconazole). These instructions, or a separate set of instructions, in the kit may guide a user (e.g., a patient) with respect to the administration of the antifungal agent, which may be separately packaged in the kit so that the antifungal agent can be given to the patient for later home administration. For example, the instructions may guide the user (e.g., the physician or patient) to administer a first dose of the antifungal agent immediately and to administer a second and subsequent doses of the antifungal agent every 12 hours, 24 hours, 36 hours, 48 hours, or 72 hours, or until the antifungal agent consumed.
The kit may be packaged in materials suitable for storage at room temperature (e.g., about 70° F. (20° C.) or in a refrigerator at a temperature of between 35° F. and 46° F. (2° C. and 8° C.).
The following examples are intended to illustrate, rather than limit, the disclosure.
We examined the emerging multi-drug resistant (MDR) fungus C. auris for Als3 homologs and tested the efficacy of NDV-3A vaccination in protecting mice from hematogenously disseminated candidiasis due to C. auris. The NDV-3A vaccine used in this example contains the Als3 polypeptide of SEQ ID NO: 3 formulated with an aluminum hydroxide adjuvant in phosphate-buffered saline.
First, we identified homologs of Als3 in C. auris by blasting the Als3 sequence against the C. auris proteome. Two C. auris orthologs (hypothetical proteins QG37_06265 Genbank Accession No. XP_018167572.1; SEQ ID NO: 6 and QG37_05979 Genbank Accession No. XP 018167307.1; SEQ ID NO: 7), were identified to have 47% overall sequence identity with C. albicans Als3 protein (SEQ ID NO: 1). However, regions of higher sequence identities were identified in the N-terminus region believed to have the functional properties of Als3 protein. These had 72-82% overlapping sequence identity between C. auris proteins and Als3 (
Next, we studied the in vivo efficacy of the NDV-3A vaccine by vaccinating CD-1 male mice with 300 μg of the NDV-3A vaccine via subcutaneous injection on day 0. The mice were injected with a booster dose on days 21 and 35, and the mouse sera were obtained on day 42 to test for the development of anti-Als3 antibody titers by ELISA. The sera produced from these mice were able to bind C. auris at high affinity as determined by flow cytometry and immunofluorescence staining (
We tested the ability of antisera to prevent C. auris virulence traits (adhesion to plastic, biofilm formation, and sensitivity to neutrophil killing. Compared to placebo sera, sera (5%) from NDV-3A vaccinated mice enhanced neutrophil killing of C. auris ex vivo (p=0.002) (
To test the efficacy of NDV-3A vaccine, vaccinated mice were made neutropenic by cyclophosphamide (200 mg/kg) and cortisone acetate on day 47 and day 52. Mice were infected intravenously with 5×107 blastospores of C. auris on day 49. Mice were vaccinated with 300 μg NDV-3A vaccine and 200 μg alum, or just 200 μg alum. 18 days after infection, 40% of the vaccinated mice survived, as compared to 0% of the alum control (
Next, we measured the MIC for various antifungal drugs to test their efficacy in treating C. auris infection. In particular, we tested fluconazole, amphotericin B, posaconazole, micafungin, caspofungin, isavuconazole, and amplyx APX001, with DMSO or no drug media used as a control (
Additionally, we obtained sera from NDV-3A vaccinated female patients and tested the effect of the sera on binding to C. auris. The presence of cross-reactive antibodies was assessed in NDV-3A vaccinated women and in placebo women (that did not receive the NDV-3A vaccine) by ELISA against C. auris lysate supernatant. Cross-reactive antibodies were detected in NDV-3A vaccinated but not in the placebo group (
Biofilm formation by C. auris was also evaluated in the presence of 5% sera from NDV-3A vaccinated or placebo women. Percent reduction in biofilm formation was calculated for both vaccinated and placebo sera by dividing their respective pre-immunization serum OD values. As shown in
All publications, patents, and patent applications mentioned in the above specification are hereby incorporated by reference to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.
While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the invention that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the claims.
Other embodiments are within the claims.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2018/026889 | 4/10/2018 | WO | 00 |
