Patent Grant
10675339
The present invention relates to methods for the recombinant expression of Chlamydia antigen MOMP and translocation to the outer membrane of E. coli, pharmaceutical compositions comprising recombinant MOMP and uses of the recombinant MOMP and pharmaceutical compositions of the invention in methods for the prevention of Chlamydia infection and/or the clinical manifestations thereof.
The sequence listing of the present application is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file name “23870WOPCT-SEQLIST.txt”, creation date of Oct. 29, 2018, and a size of 53 kB. This sequence listing submitted via EFS-Web is part of the specification and is herein incorporated by reference in its entirety.
Chlamydia trachomatis is an obligate intracellular Gram-negative bacterium responsible for a number of pathologies, including ocular trachoma and several sexually transmitted diseases. There are many different strains of C. trachomatis, which are separated into multiple serovars based on serological differences in the chlamydial major outer membrane protein (MOMP). C. trachomatis serovars A, B, Ba, and C are responsible for ocular trachoma which can cause conjunctivitis, conjunctival scarring and corneal scarring. C. trachomatis serovars D, Da, E, F, G, H, I, Ia, J, Ja and K are responsible for oculogenital disease which can cause cervicitis, urethritis, endometritis, pelvic inflammatory disease, tubal infertility, ectopic pregnancy, neonatal conjunctivitis and infant pneumonia. Chlamydia trachomatis serovars L1, L2 and L3 are responsible for lymphogranuloma venereum, which can cause submocosa and lymph-node invasion, with necrotizing granulomas and fibrosis. (Reviewed in Brunham et al., Nature Reviews Immunology 5:149-161, 2005; Montoya, Chlamydia, p. 694-702, In Wilson et al., Eds. Current Diagnosis & Treatment in Infectious Diseases, The McGraw-Hill Companies, Inc. 2001.) Asymptomatic genital Chlamydia infections are also common, which may lead to infertility in women that are left untreated.
Chlamydia trachomatis infects mucosal epithelial cells. Like other Chlamydia, C. trachomatis undergoes a biphasic development cycle in which it begins the cycle as a metabolically inactive infectious elementary body (EB) and transforms into a metabolically active reticulate body (RB). The bacterium exists outside the host cell as an EB, which is internalized by a host cell and surrounded by an endosomal membrane forming an inclusion body, where the EB transforms into a metabolically active RB. The RB can divide by binary fusion. Within about 40-48 hours, the RB transforms back to an EB, which is released by the host cell and can infect neighboring cells. (Id.)
Chlamydia MOMPs are part of a larger family of genetically related outer membrane proteins (the OmpA family) that are heat-modifiable, surface exposed porin proteins. OmpA proteins have a structurally similar N-terminal domain that is embedded in the bacterial outer membrane. OmpA proteins have been targeted for vaccine development because of their surface exposure, high immunogenicity, and role in the interaction between the bacteria and their host cells. Specifically, Chlamydia MOMP has been a vaccine target for many researchers (Cambridge et al., Int. J. Nanomedicine 8:1759-71 (2013); Farris et al., Infection and Immunity 79(3): 986-996 (2011); Hickey et al., Vaccine 22:4306-4315 (2004); Kalbina et al., Protein Expression and Purification 80: 194-202 (2011); O'Meara et al., PLOS One 8(4): 1-14; Skelding et al., Vaccine 24:355-366 (2006), Tifrea et al., Infection and Immunity 81(5): 1741-1750 (2013)). However, a safe and effective Chlamydia vaccine remains unavailable to reduce the risk of Chlamydia infection or its associated pathogenic effects. Additional vaccine candidates and methods for making them are therefore needed.
The present invention is related to a method for the recombinant expression of Chlamydia major outer membrane protein (MOMP) comprising: (a) transforming a population of E. coli host cells with an expression vector comprising a nucleic acid molecule comprising a sequence of nucleotides that encode a leader sequence for targeting the MOMP to the outer membrane of the cell and a sequence of nucleotides that encode Chlamydia MOMP, wherein the nucleic acid molecule is operatively linked to a promoter; (b) culturing the transformed cells under conditions that permit expression of the nucleic acid molecule and translocation to the outer membrane of the cells to produce a recombinant Chlamydia MOMP; and (c) optionally purifying the MOMP. The method of the invention allows recombinant expression of MOMP in the outer membrane of the cell, which leads to protein folding that is more like native MOMP relative to a recombinant MOMP protein that is expressed intracellularly.
In some embodiments of the invention, the nucleotide sequence encoding MOMP and/or the nucleotide sequence encoding the leader sequence is codon harmonized. In alternative embodiments, the nucleotide sequence encoding MOMP and/or the nucleotide sequence encoding the leader sequence is codon optimized.
In some embodiments of the invention, the leader sequence comprises the Shigella flexneri SopA sequence, the Salmonella enterica PgtE sequence, the Yersinia pestis Pla, the E. coli OmpP sequence, the E. coli OmpA sequence, or the pectate lysase B (PelB) sequence. In further embodiments, expression of the recombinant MOMP is optimized by using a low or moderate strength promoter. In additional embodiments, optimized expression is achieved through using a vector that is characterized by a transcription/translation rate that is constrainable to low or moderate.
Also provided herein are recombinant MOMPs produced by the methods of the invention and pharmaceutical compositions comprising an effective amount of a recombinant MOMP of the invention and a pharmaceutically acceptable carrier.
In a further aspect, the invention provides methods for the treatment or prophylaxis of Chlamydia in a patient by administering a recombinant MOMP or a pharmaceutical composition of the invention to the patient.
As used throughout the specification and in the appended claims, the singular forms “a,” “an,” and “the” include the plural reference unless the context clearly dictates otherwise.
As used throughout the specification and appended claims, the following definitions and abbreviations apply:
As used herein, the term “recombinant” refers to a polypeptide or nucleic acid that does not exist in nature. The term “recombinant” polypeptide refers to a polypeptide that is prepared, expressed, created, or isolated by recombinant means, such as polypeptides expressed using a recombinant expression vector transfected into a host cell. A recombinant polynucleotide mal also include two or more nucleotide sequences artificially combined and present together in a longer polynucleotide sequence, wherein the two sequences are not found together (e.g. attached or fused) in nature, e.g. a promoter and a heterologous nucleotide sequence encoding a polypeptide that are normally not found together in nature or a vector and a heterologous nucleotide sequence.
As used herein, the terms “isolated” or “purified” refer to a molecule (e.g., nucleic acid, polypeptide, bacterial strain, etc.) that is at least partially separated from other molecules normally associated with it in its native state. An “isolated or purified polypeptide” is substantially free of other biological molecules naturally associated with the polypeptide such as nucleic acids, proteins, lipids, carbohydrates, cellular debris and growth media. An “isolated or purified nucleic acid” is at least partially separated from nucleic acids which normally flank the polynucleotide in its native state. Thus, polynucleotides fused to regulatory or coding sequences with which they are not normally associated, for example as the result of recombinant techniques, are considered isolated herein. Such molecules are considered isolated even when present, for example in the chromosome of a host cell, or in a nucleic acid solution. Generally, the terms “isolated” and “purified” are not intended to refer to a complete absence of such material or to an absence of water, buffers, or salts, unless they are present in amounts that substantially interfere with experimental or therapeutic use of the molecule.
As used herein, “homology” refers to sequence similarity between two polynucleotide sequences or between two polypeptide sequences when they are optimally aligned. When a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit, e.g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position. The percent of homology is the number of homologous positions shared by the two sequences divided by the total number of positions compared ×100. For example, if 6 of 10 of the positions in two sequences are matched or homologous when the sequences are optimally aligned then the two sequences are 60% homologous. Generally, the comparison is made when two sequences are aligned to give maximum percent homology. Gaps (in either of the two sequences being matched) are allowed in maximizing matching; gap lengths of 5 or less are preferred with 2 or less being more preferred. Alternatively and preferably, two protein sequences (or polypeptide sequences derived from them of at least 30 amino acids in length) are homologous, as this term is used herein, if they have an alignment score of at more than 5 (in standard deviation units) using the program ALIGN with the mutation data matrix and a gap penalty of 6 or greater. See Dayhoff, M. O., in Atlas of Protein Sequence and Structure, pp. 101-110 (Volume 5, National Biomedical Research Foundation (1972)) and Supplement 2 to this volume, pp. 1-10.
Sequence identity refers to the degree to which the amino acids of two polypeptides are the same at equivalent positions when the two sequences are optimally aligned. Sequence identity can be determined using a BLAST algorithm wherein the parameters of the algorithm are selected to give the largest match between the respective sequences over the entire length of the respective reference sequences. The following references relate to BLAST algorithms that are often used for sequence analysis: BLAST ALGORITHMS: Altschul, S. F., et al., (1990) J. Mol. Biol. 215:403-410; Gish, W., et al., (1993) Nature Genet. 3:266-272; Madden, T. L., et al., (1996) Meth. Enzymol. 266:131-141; Altschul, S. F., et al., (1997) Nucleic Acids Res. 25:3389-3402; Zhang, J., et al., (1997) Genome Res. 7:649-656; Wootton, J. C., et al., (1993) Comput. Chem. 17:149-163; Hancock, J. M. et al., (1994) Comput. Appl. Biosci. 10:67-70; ALIGNMENT SCORING SYSTEMS: Dayhoff, M. O., et al., “A model of evolutionary change in proteins.” in Atlas of Protein Sequence and Structure, (1978) vol. 5, suppl. 3. M. O. Dayhoff (ed.), pp. 345-352, Natl. Biomed. Res. Found., Washington, D.C.; Schwartz, R. M., et al., “Matrices for detecting distant relationships.” in Atlas of Protein Sequence and Structure, (1978) vol. 5, suppl. 3.” M. O. Dayhoff (ed.), pp. 353-358, Natl. Biomed. Res. Found., Washington, D.C.; Altschul, S. F., (1991) J. Mol. Biol. 219:555-565; States, D. J., et al., (1991) Methods 3:66-70; Henikoff, S., et al., (1992) Proc. Natl. Acad. Sci. USA 89:10915-10919; Altschul, S. F., et al., (1993) J. Mol. Evol. 36:290-300; ALIGNMENT STATISTICS: Karlin, S., et al., (1990) Proc. Natl. Acad. Sci. USA 87:2264-2268; Karlin, S., et al., (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877; Dembo, A., et al., (1994) Ann. Prob. 22:2022-2039; and Altschul, S. F. “Evaluating the statistical significance of multiple distinct local alignments.” in Theoretical and Computational Methods in Genome Research (S. Suhai, ed.), (1997) pp. 1-14, Plenum, N.Y.
The term “cassette” refers to a nucleic acid molecule which comprises at least one nucleic acid sequence that is to be expressed, along with its transcription and translational control sequences. Changing the cassette, will cause the vector into which is incorporated to direct the expression of different sequence or combination of sequences. In the context of the present invention, the nucleic acid sequences present in the cassette will usually encode any polypeptide of interest such as an immunogen. Because of the restriction sites engineered to be present at the 5′ and 3′ ends, the cassette can be easily inserted, removed or replaced with another cassette.
The term “promoter” refers to a recognition site on a DNA strand to which an RNA polymerase binds. The promoter forms an initiation complex with RNA polymerase to initiate and drive transcriptional activity. The complex can be modified by activating sequences such as enhancers, or inhibiting sequences such as silencers.
“MAA” means an amorphous aluminum hydroxyphosphate sulfate adjuvant.
As used herein, an “ISCOM-type adjuvant” is an adjuvant comprising an immune stimulating complex (ISCOM), which is comprised of a saponin, cholesterol, and a phospholipid, which together form a characteristic caged-like particle, having a unique spherical, caged-like structure that contributes to its function (for review, see Barr and Mitchell, Immunology and Cell Biology 74: 8-25 (1996)). This term includes both ISCOM adjuvants, which are produced with an antigen and comprise antigen within the ISCOM particle and ISCOM matrix adjuvants, which are hollow ISCOM-type adjuvants that are produced without antigen.
As used herein, the term “derivative” refers to a polypeptide having one or more alterations, which can be changes in the amino acid sequence (including additions and deletions of amino acid residues) and/or chemical modifications, relative to a reference sequence (e.g., a leader sequence and/or MOMP sequence described herein). In preferred embodiments, the derivative is at least 85%, at least 90%, at least 95%, at least 97%, at least 99% identical to the original reference sequence prior to alteration. In general, derivatives retain the activity of the reference sequence, e.g. inducing an immune response. As used herein, the term “derivative” is not limited to derivatives of a wild-type or native reference sequence, but includes derivatives of a mutant sequence as a reference sequence. In preferred embodiments, any specified mutations of the mutant reference sequence are maintained, but alterations/modifications relative to the mutant reference sequence are included in the derivative sequence at amino acid residues other than the specified mutations of the reference sequence. As used herein, the term “derivative” also includes polynucleotides that have one or more alterations relative to a reference nucleotide sequence.
In one embodiment, a derivative is a polypeptide that has an amino acid sequence which differs from the base sequence from which it is derived by one or more amino acid substitutions. Amino acid substitutions may be “conservative” (i.e. the amino is replaced with a different amino acid from the same class of amino acids (e.g., non-polar, polar/neutral, acidic and basic), an amino acid with broadly similar properties, or with similar structure (aliphatic, hydroxyl or sulfur-containing, cyclic, aromatic, basic, and acidic)) or “non-conservative” (i.e. the amino acid is replaced with an amino acid of a different type). Broadly speaking, fewer non-conservative substitutions will be possible without altering the biological activity of the polypeptide. Some embodiments of the invention include derivatives that include substitution of no more than 25 amino acid residues, 20 amino acid residues, 15 amino acid residues, 12 amino acid residues, 11 amino acid residues, 10 amino acid residues, 9 amino acid residues, 8 amino acid residues, 7 amino acid residues, 6 amino acid residues, 5 amino acid residues, 4 amino acid residues, 3 amino acid residues, 2 amino acid residues, or 1 amino acid residue that is/are substituted relative to a reference sequence.
In another embodiment, a derivative is a polypeptide that has an amino acid sequence which differs from the base sequence from which it is derived by having one or more amino acid deletions and/or additions in any combination. Deleted or added amino acids can be either contiguous or individual residues. In some embodiments, no more than 25 amino acid residues, no more than 20 amino acid residues, no more than 15 amino acid residues, no more than 12 amino acid residues, no more than 10 amino acid residues, no more than 8 amino acid residues, no more than 7 amino acid residues, no more than 6 amino acid residues, no more than 5 amino acid residues, no more than 4 amino acid residues, no more than 3 amino acid residues, no more than 2 amino acid residues, or no more than 1 amino acid residue is/are deleted or added relative to a reference sequence.
In another embodiment, a derivative is a polypeptide that has an amino acid sequence which differs from the base sequence from which it is derived by having one or more chemical modifications of the protein. Chemical modifications include, but are not limited to, modification of functional groups (such as alkylation, hydroxylation, phosphorylation, thiolation, carboxylation and the like), incorporation of unnatural amino acids and/or their derivatives during protein synthesis and the use of crosslinkers and other methods which impose conformational constraints on the polypeptides.
As used herein, the term “conservative substitution” refers to substitutions of amino acids in a protein with other amino acids having similar characteristics (e.g. charge, side-chain size, hydrophobicity/hydrophilicity, backbone conformation and rigidity, etc.), such that the changes can frequently be made without altering or substantially altering the biological activity of the protein. Those of skill in this art recognize that, in general, single amino acid substitutions in non-essential regions of a polypeptide do not substantially alter biological activity (see, e.g., Watson et al. (1987) Molecular Biology of the Gene, The Benjamin/Cummings Pub. Co., p. 224 (4th Ed.)). In addition, substitutions of structurally or functionally similar amino acids are less likely to disrupt biological activity. Exemplary conservative substitutions are set forth in Table 1.
As used herein, the expressions “cell,” “cell line,” and “cell culture” are used interchangeably and all such designations include progeny. Thus, the words “transformants” and “transformed cells” include the primary subject cell and cultures derived therefrom without regard for the number of transfers. It is also understood that not all progeny will have precisely identical DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Where distinct designations are intended, it will be clear from the context.
The term “treatment” refers to both therapeutic treatment and prophylactic or preventative measures. Individuals “in need of” treatment include those already with a Chlamydia infection, whether or not manifesting any clinical symptoms, as well as those at risk of being infected with Chlamydia. Treatment of a patient with the pharmaceutical compositions of the invention includes one or more of the following: inducing/increasing an immune response against Chlamydia in the patient, inducing/increasing a virus neutralizing antibody response against one or more Chlamydia viruses, preventing, ameliorating, abrogating, or reducing the likelihood of the clinical manifestations of Chlamydia in patients who have been infected with Chlamydia, preventing or reducing the likelihood of developing oculogenital disease, cervicitis, urethritis, endometritis, pelvic inflammatory disease, tubal infertility, ectopic pregnancy, neonatal conjunctivitis, infant pneumonia and/or other disease or complication associated with Chlamydia infection, reducing the severity or duration of the clinical symptoms of Chlamydia infection and/or other disease or complication associated with Chlamydia, and preventing or reducing the likelihood of Chlamydia infection.
The term “therapeutically effective amount” or “effective amount” means sufficient pharmaceutical composition comprising recombinant MOMP is introduced to a patient to produce a desired effect, including, but not limited to: inducing/increasing an immune response against Chlamydia in the patient, inducing/increasing a neutralizing antibody response against Chlamydia in a patient, preventing or reducing the likelihood of Chlamydia infection, preventing or reducing the likelihood of Chlamydia recurrent infection, preventing, ameliorating or abrogating the clinical manifestations of Chlamydia infection in patients who have been infected with Chlamydia, preventing one or more of ocular trachoma, conjunctivitis, conjunctival scarring, corneal scarring, oculogenital disease, cervicitis, urethritis, endometritis, pelvic inflammatory disease, tubal infertility, ectopic pregnancy, neonatal conjunctivitis, infant pneumonia, and lymphogranuloma venereum; reducing the severity or duration of disease associated with Chlamydia. One skilled in the art recognizes that this level may vary.
“An immunologically effective amount” refers to the amount of an immunogen that can induce an immune response against the heterologous polypeptide when administered to a patient that can protect the patient from infection by the pathogen that expresses the heterologous polypeptide (including primary, recurrent and/or super-infections) and/or ameliorate at least one pathology associated with infection and/or reduce the severity/length of infection in the patient. The amount is sufficient to significantly reduce the likelihood or severity of an infection. Animal models known in the art can be used to assess the protective effect of administration of immunogen. For example, immune sera or immune T cells from individuals administered the immunogen can be assayed for neutralizing capacity by antibodies or cytotoxic T cells or cytokine producing capacity by immune T cells. The assays commonly used for such evaluations include but not limited to viral neutralization assay, anti-viral antigen ELISA, interferon-gamma cytokine ELISA, interferon-gamma (IFN-γ) ELISPOT, intracellular multi-cytokine staining (ICS), and 51Chromium release cytotoxicity assay. Animal challenge models can also be used to determine an immunologically effective amount of immunogen.
The term “immune response” refers to a cell-mediated (T-cell) immune response and/or an antibody (B-cell) response.
The term “patient” refers to any human being that is to receive the pharmaceutical compositions described herein, including both immunocompetent and immunocompromised individuals. As defined herein, a “patient” includes those already infected with Chlamydia, either through natural infection or vaccination or those that may subsequently be exposed.
Additional abbreviations employed herein include the following: CI is confidence interval; Cm is Chlamydia muridarium; CtD is Chlamydia trachomatis Serovar D, CtE is Chlamydia trachomatis Serovar E, FACS is fluorescent activated cell sorting; GFI is geometric mean fluorescence intensity; IPTG is isopropyl β-D-1-thiogalactopyranoside; LPS is lipopolysaccharide MOMP is major outer membrane protein; rMOMP is recombinant MOMP; rCmMOMP is recombinant Chlamydia muridarium MOMP; nOMV is a native outer membrane vesicle from E. coli that does not contain a recombinant MOMP gene and OM is outer membrane.
Chlamydia major outer membrane protein (MOMP) is a target for vaccine development to reduce the risk of Chlamydia infection or its associated clinical manifestations due to its surface exposure and high immunogenicity. Native MOMP can be purified from an infected cell line, but development of a robust, cost-effective commercial manufacturing process based on the use of native MOMP can be challenging. Recombinant expression of vaccine antigens is an alternative method to purification of native antigen, which may be easier to scale-up to a commercial manufacturing level. However, previous attempts to recombinantly express Chlamydia MOMP intracellularly have resulted in insoluble MOMP protein, which is not useful as a vaccine antigen.
To that end, one aspect of the invention provides a method for the recombinant expression of Chlamydia MOMP wherein the MOMP protein is recombinantly expressed and translocated to the outer membrane of an E. coli cell. Without wishing to be bound by theory, it is thought that expression of MOMP in the outer membrane of E. coli results in a MOMP protein that is folded in a manner that more closely resembles native MOMP, which is normally expressed on the cell membrane. Accordingly, the method of the invention comprises: (a) transforming a population of E. coli host cells with an expression vector comprising a nucleic acid molecule comprising a sequence of nucleotides that encode a leader sequence for targeting the MOMP to the outer membrane of the cell and a sequence of nucleotides that encode Chlamydia MOMP, wherein the nucleic acid molecule is operatively linked to a promoter; (b) culturing the transformed cells under conditions that permit expression of the nucleic acid molecule and translocation to the outer membrane of the cells to produce a recombinant Chlamydia MOMP; and (c) optionally purifying the MOMP. The E. coli outer membrane expressed recombinant MOMP produced by the method of the invention is shown herein to elicit comparable protection relative to native MOMP in a Chlamydia animal challenge model (see Examples 10-13).
Heterologous protein expression systems may produce inadequate expression or formation of insoluble protein aggregates due to differences between the codon usage of the recombinant host cell and the natural cell type. A “triplet” codon of four possible nucleotide bases can exist in over 60 variant forms. Because these codons provide the message for only 20 different amino acids (as well as translation initiation and termination), some amino acids can be coded for by more than one codon, a phenomenon known as codon redundancy. For reasons not completely understood, alternative codons are not uniformly present in the endogenous DNA of differing types of cells. Indeed, there appears to exist a variable natural hierarchy or “preference” for certain codons in certain types of cells. As one example, the amino acid leucine is specified by any of six DNA codons including CTA, CTC, CTG, CTT, TTA, and TTG. Exhaustive analysis of genome codon use frequencies for microorganisms has revealed endogenous DNA of E. coli most commonly contains the CTG leucine-specifying codon, while the DNA of yeasts and slime molds most commonly includes a TTA leucine-specifying codon. To that end, embodiments of the invention provide methods for the heterologous expression of Chlamydia MOMP in the OM of an E. coli host cell, wherein the gene sequence encoding the MOMP is either (1) codon harmonized or (2) codon optimized for optimal expression in an E. coli host cell.
Thus, in accordance with one aspect of this invention, MOMP-encoding genes were converted to sequences having identical translated sequences but with harmonized codon usage as described by Angov et al. (Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host. PLOS one 3(5): 1-10 (2008)). Codon harmonization relies on known relationships between secondary protein structure and codon usage frequencies to modulate translation rates at domain boundaries (i.e. link/end segments). The methodology generally consists of identifying slowly translated regions in the wild-type mRNA that are associated with domain boundaries and replacing codons in said region with synonymous codons having usage frequencies in the recombinant host cell that are less than or equal to the usage frequencies of the codons in the native expression host. Id. For regions outside of the domain boundaries, codons are selected that have usage frequencies that are closely matched to the native expression system. Id. It is shown herein that expression of a codon-harmonized DNA sequence encoding Chlamydia MOMP results in a higher expression level relative to a codon-optimized DNA sequence encoding the same MOMP polypeptide.
Thus, the invention relates to codon harmonized nucleic acid molecules encoding Chlamydia MOMP or a derivative thereof, or encoding Chlamydia MOMP plus a leader sequence for targeting the MOMP to the outer membrane of the cell, as discussed, infra. Also provided by the invention are methods for the recombinant expression of Chlamydia MOMP, as described in any embodiment herein, wherein the nucleotide sequence encoding MOMP and/or the nucleotide sequence encoding the leader for targeting the MOMP to the OM of the cell are codon harmonized.
In alternative embodiments of the invention, the MOMP-encoding gene is codon-optimized for high levels of expression in the intended host cell, e.g. E. coli. The process of codon optimization generally consists of identifying codons in the wild-type sequence that are not commonly associated with highly expressed genes in the intended host cell and replacing them with optimal codons for high expression in the intended host (i.e. codons that are frequently associated with high levels of expression in the recombinant expression host). The new gene sequence is then inspected for undesired sequences generated by these codon replacements (e.g., “ATTTA” sequences, inadvertent creation of intron splice recognition sites, unwanted restriction enzyme sites, high GC content, presence of transcription termination signals that are recognized by yeast, etc.). Undesirable sequences are eliminated by substitution of the existing codons with different codons coding for the same amino acid. The synthetic gene segments are then tested for improved expression.
The methods described above were used to create synthetic genes encoding MOMP, resulting in a gene comprising codons that are harmonized or optimized for improved expression in the intended host, e.g. E. coli. While the above procedures provide a summary of the methodology for designing codon harmonized and codon-optimized genes for use in the methods of the invention, it is understood by one skilled in the art that similar expression of genes may be achieved by minor variations in the procedure or by minor variations in the sequence. For example, the procedure for codon optimization, as described herein, may comprise replacement of all of the codons in a given sequence with synonymous codons associated with high levels of expression in the host cell, or comprise replacement of only some of the codons in the wild-type sequence, for example, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more of the wild-type codons can be replaced. For example, in some instances, codons in the wild-type sequence may naturally match that of the preferred codon in the intended host cell and a replacement with a synonymous codon may not be necessary and/or desired.
As discussed, supra, the methods of the invention utilize an expression vector comprising a nucleic acid molecule comprising a sequence of nucleotides that encode a leader sequence for targeting the MOMP to the outer membrane of the cell and a sequence of nucleotides that encode Chlamydia MOMP, wherein the nucleic acid molecule is operatively linked to a promoter. In embodiments of the invention, the leader sequence is operatively linked to the N-terminus (i.e. amino or NH2 terminus) of the MOMP. In preferred embodiments, the leader sequence is directly adjacent to the MOMP sequence. In alternative embodiments, additional amino acid residues may be present between the leader and the MOMP, e.g. a single amino acid residue, two amino acid residues, three amino acid residues, four amino acid residues, or five or more amino acid residues. In embodiments wherein additional amino acid residues are present between the leader and the MOMP, such amino acid residues form a fusion protein with the MOMP in the protein product. After expression of the nucleic acid molecule in the E. coli OM, the leader sequence is preferably cleaved from the MOMP protein or MOMP fusion protein, although in some cases, the leader sequence is not cleaved.
As noted above, the methods of the invention are useful for expression of MOMP fusion proteins in the OM of an E. coli host cell. To that end, in some embodiments the nucleic acid molecule, as described above, further comprises a sequence of nucleotides that encodes an additional polypeptide attached to the MOMP, wherein the polypeptide is selected from the group consisting of: a linker, an additional antigen, a polypeptide having adjuvant properties, a polypeptide for facilitating purification, a polypeptide for enhancing stability of the MOMP, a carrier protein, and a marker protein.
In embodiments of the invention directed to expression of MOMP fusion proteins in the OM of an E. coli cell, the additional polypeptide can be attached to the N-terminus of the MOMP or the C-terminus of the MOMP. In some embodiments of the invention, the additional polypeptide is attached to the C-terminus of the MOMP. In additional embodiments, the additional polypeptide is attached to the N-terminus of the MOMP. In preferred embodiments, the nucleic acid molecule comprises, from 5′ to 3′, a sequence of nucleotides that encodes a secretion leader for targeting the protein to the E. coli OM, a sequence of nucleotide that encodes Chlamydia MOMP, or a derivative thereof, and a sequence of nucleotides that encodes an additional polypeptide having the attributes described above. However, the invention also contemplates use of nucleic acid molecules that encode, from 5′ to 3′, a leader sequence, an additional polypeptide, and a MOMP or derivative thereof. One of skill in the art can readily determine whether a MOMP fusion protein made by the methods of the invention is expressed in the E. coli OM and whether the resulting fusion protein has the desired properties by using procedures known in the art of molecular and cell biology.
In embodiments of any of the methods of the invention described herein, the MOMP comprises, consists, or consists essentially of the Chlamydia trachomatis MOMP amino acid sequence set forth in SEQ ID NO:23 (serovar E), SEQ ID NO: 25 (serovar D), SEQ ID NO:26 (serovar G), SEQ ID NO:27 (serovar F), SEQ ID NO: 28 (serovar I), SEQ ID NO:29 (serovar J), or SEQ ID NO:30 (serovar H). In additional embodiments, the MOMP comprises, consists, or consists essentially of the Chlamydia muridarium MOMP amino acid sequence set forth in SEQ ID NO:31.
In additional embodiments of the invention, the methods comprise expression of Chlamydia MOMP derivatives in the E. coli OM. In some embodiments, such Chlamydia MOMP derivatives are derivatives of the sequences set forth in SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 or SEQ ID NO:31, wherein the derivative is at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% identical to the reference sequence provided in SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 or SEQ ID NO:31.
In some embodiments, the MOMP derivative comprises amino acid residues that are deleted, inserted or substituted relative to the sequence of amino acids set forth in the MOMP sequences set forth in SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 or SEQ ID NO:31. In particular embodiments, the MOMP derivative comprises a number of amino acid substitutions, deletions or additions relative to the MOMP sequences disclosed herein, wherein the MOMP derivative comprises no more than 25 amino acid residues, no more than 20 amino acid residues, no more than 15 amino acid residues, no more than 12 amino acid residues, no more than 11 amino acid residues, no more than 10 amino acid residues, no more than 9 amino acid residues, no more than 8 amino acid residues, no more than 7 amino acid residues, no more than 6 amino acid residues, no more than 5 amino acid residues, no more than 4 amino acid residues, no more than 3 amino acid residues, no more than 2 amino acid residues, or 1 amino acid residue that is/are substituted, deleted or added relative to the MOMP sequences set forth in SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 or SEQ ID NO:31. In a particular embodiment, the Chlamydia MOMP derivative is a Chlamydia trachomatis (serovar D) derivative set forth in SEQ ID NO:24, which comprises a 2-amino acid substitution relative to SEQ ID NO:25, which was modified in order to increase Barn-site binding.
In embodiments of any of the methods of the invention, the leader sequence comprises the Shigella flexneri SopA sequence set forth in SEQ ID NO:8, the Salmonella enterica PgtE sequence set forth in SEQ ID NO:9, the Yersinia pestis Pla set forth in SEQ ID NO:10, the E. coli OmpP sequence set forth in SEQ ID NO:11, the E. coli OmpA sequence set forth in SEQ ID NO:12, or the pectate lysase B (PelB) sequence set forth in or SEQ ID NO:13 or derivative thereof. Thus, in embodiments of the invention, the leader sequence comprises a sequence of amino acids selected from the group consisting of: SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 and SEQ ID NO:13.
In alternative embodiments, the leader sequence comprises a sequence of amino acids that shares at least 90%, at least 95%, at least 97%, at least 98%, or at least 99% sequence identity with the amino acid sequence set forth in any of SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, or SEQ ID NO:13.
As stated above, the nucleic acid molecule used in the methods of the invention is operatively linked to a promoter. It is preferable that a low or moderate strength promoter is used in the methods of the invention. In some embodiments, the promoter is λTL or T7. It is also preferred that the expression vector is associated with a rate of transcription and/or translation that is constrainable to low or moderate. As used herein a constrainable to low or moderate transcription/translation rate can result from either elements in the vector itself or elements in the host cell. In some embodiments of the invention, the expression vector is pAVE029 or pACYDuet-1.
In any of the embodiments of any of the methods of the invention, the method may further comprise a step of inducing the transformed host cell with IPTG for from about 4 hours to about 6 hours. In additional embodiments, the step of inducing with IPTG is carried out for about 3.5 hours, about 4 hours, about 4.5 hours, about 5 hours, about 5.5 hours, about 6 hours or about 6.5 hours.
In some embodiments of the invention, the induction step described above is carried out at about 30° C.
In further embodiments, the cell density (OD590) is allowed to reach about 0.4 to about 0.8 before the induction step is carried out.
The invention also relates to a recombinant MOMP produced by any embodiment of any of the methods of the invention. The invention further relates to a recombinant MOMP derivative produced by the methods of the invention. In some embodiments, the MOMP derivative is a MOMP fusion protein or chimeric MOMP.
Pharmaceutical Compositions
The invention also relates to pharmaceutical compositions comprising a therapeutically or immunologically effective amount of a recombinant MOMP as described herein, formulated together with a pharmaceutically acceptable carrier or diluent.
To prepare pharmaceutical or sterile compositions of the invention, one or more recombinant Chlamydia MOMP is admixed with a pharmaceutically acceptable carrier or excipient. See, e.g., Remington's Pharmaceutical Sciences and U.S. Pharmacopeia: National Formulary, Mack Publishing Company, Easton, Pa. (1984). Pharmaceutically acceptable carriers include any and all solvents, dispersion media, isotonic and absorption delaying agents, and the like that are physiologically compatible, i.e. suitable for administration to humans. The carriers can be suitable for intravenous, intramuscular, subcutaneous, parenteral, rectal, spinal, or epidermal administration (e.g., by injection or infusion).
As used herein, the term “pharmaceutically acceptable carrier” refers to a substance, as described above, which is admixed with the recombinant MOMP (or derivative) of the invention that is suitable for administration to humans. In embodiments of the invention, the pharmaceutically acceptable carrier does not occur in nature in the same form, e.g. the substance is man-made, either because it does not exist in nature or the purity and/or sterility of the substance is not the same as the corresponding natural substance. For example, sterile water for injection, which is a sterile, bacteria-free, solute-free preparation of distilled water for injection, does not occur in nature in the same form and is considered a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical compositions of the invention comprise one or more recombinant MOMP or derivative thereof disclosed herein and sterile water for injection. In further embodiments, the pharmaceutically acceptable carrier may be another form of water that is appropriate for pharmaceutical or biological preparations and is not the same as water that occurs in nature, including purified water, water for injection, sterile purified water, and bacteriostatic water for injection.
In additional embodiments, the pharmaceutical compositions of the invention include a buffer as a pharmaceutically acceptable carrier. When a buffer is employed, the pH of the buffer is preferably in the range of about 5.5 to about 8.0. In additional embodiments, the pH is about 5.5 to about 7.5, about 5.5 to about 7.0, about 5.5 to about 6.5, about 6.0 to about 8.0, about 6.0 to about 7.5, about 6.0 to about 7.0, about 6.5 to about 7.0, about 6.0 to 6.5, about 6.0 to about 6.9, about 6.2 to about 6.75, or about 6.0 to about 6.75.
Pharmaceutical compositions typically should be sterile and stable under the conditions of manufacture and storage. Formulations of therapeutic and diagnostic agents may be prepared by mixing with acceptable carriers, excipients, or stabilizers in the form of, e.g., lyophilized powders, slurries, aqueous solutions, suspensions, microemulsions, dispersions, or liposomes, (see, e.g., Hardman, et al. (2001) Goodman and Gilman's The Pharmacological Basis of Therapeutics, McGraw-Hill, New York, N.Y.; Gennaro (2000) Remington: The Science and Practice of Pharmacy, Lippincott, Williams, and Wilkins, New York, N.Y.; Avis, et al. (eds.) (1993) Pharmaceutical Dosage Forms: Parenteral Medications, Marcel Dekker, N.Y.; Lieberman, et al. (eds.) (1990) Pharmaceutical Dosage Forms: Tablets, Marcel Dekker, N.Y.; Lieberman, et al. (eds.) (1990) Pharmaceutical Dosage Forms: Disperse Systems, Marcel Dekker, N.Y.; Weiner and Kotkoskie (2000) Excipient Toxicity and Safety, Marcel Dekker, Inc., New York, N.Y.).
Sterile injectable solutions can be prepared by incorporating the active compound (i.e., one or more recombinant MOMP and optionally additional protein antigen) in the required therapeutically effective amount in an appropriate solvent with one or a combination of ingredients, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients. In the case of sterile powders for the preparation of sterile injectable solutions, the useful methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prolonged absorption of injectable pharmaceutical compositions can be brought about by including in the pharmaceutical composition an agent that delays absorption, for example, monostearate salts and gelatin. Additional agents, such as polysorbate 20 or polysorbate 80, may be added to enhance stability.
Toxicity and therapeutic efficacy of the pharmaceutical compositions of the invention, administered alone or in combination with another agent, can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index (LD50/ED50). In particular aspects, pharmaceutical compositions exhibiting high therapeutic indices are desirable. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage in such pharmaceutical compositions lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration.
In some embodiments of the invention, the pharmaceutical compositions of any embodiment herein can further comprise one or more additional rMOMP antigens produced by the methods of the invention, or derivative thereof, and/or one or more additional non-MOMP Chlamydia antigens. In specific embodiments, the pharmaceutical composition comprises, in addition to a pharmaceutically acceptable carrier, at least one recombinant MOMP comprising a sequence of amino acids as set forth in SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, or SEQ ID NO:30, or derivative thereof, wherein the rMOMP is produced by the methods of the invention. In additional embodiments, the pharmaceutical composition comprises two rMOMP of the invention, or derivatives thereof. In additional embodiments, the pharmaceutical composition comprises three, four, five, six, seven, eight, or more rMOMP of the invention, or derivatives thereof. The pharmaceutical compositions of the invention can comprise more than one rMOMP as set forth herein, more than one rMOMP derivative, or a combination of one or more rMOMP of the invention and one or more rMOMP derivative of the invention. In additional embodiments, the pharmaceutical composition comprises at least one rMOMP produced by the methods herein, or derivative thereof, and at least one additional Chlamydia antigen that is not a MOMP or derivative.
In further embodiments of this aspect of the invention, the pharmaceutical compositions comprise one or more recombinant MOMP or derivative thereof produced by the methods disclosed herein, a pharmaceutically acceptable carrier, and an adjuvant. The inclusion of adjuvants may augment the immune response elicited by administration of the vaccine antigens (e.g. rMOMP or rMOMP derivative and optionally additional Chlamydia antigens) to a patient, in order to induce long lasting protective immunity. In addition to increasing the immune response, adjuvants may be used to decrease the amount of antigen necessary to provoke the desired immune response or decrease the number of injections needed in a clinical regimen to induce a durable immune response and to provide protection from disease and/or induce regression of disease caused by Chlamydia infection.
Adjuvants that may be used in conjunction with the pharmaceutical compositions of the invention, include, but are not limited to, montanide, adjuvants containing CpG oligonucleotides, or other molecules acting on toll-like receptors such as TLR4 and TLR9 (for reviews, see, Daubenberger, C. A., Curr. Opin. Mol. Ther. 9(1):45-52 (2007); Duthie et al., Immunological Reviews 239(1): 178-196 (2011); Hedayat et al., Medicinal Research Reviews 32(2): 294-325 (2012)), including lipopolysaccharide, monophosphoryl lipid A, and aminoalkyl glucosaminide 4-phosphates. Additional adjuvants useful in the pharmaceutical compositions of the invention include immunostimulatory oligonucleotides (IMO's; see, e.g. U.S. Pat. Nos. 7,713,535 and 7,470,674, such as IMO-2055, as disclosed in the Examples herein); T-helper epitopes, lipid-A and derivatives or variants thereof, liposomes, calcium phosphate, cytokines, (e.g. granulocyte macrophage-colony stimulating factor (GM-CSF) IL-2, IFN-α, Flt-3L), CD40, CD28, CD70, IL-12, heat-shock protein (HSP) 90, CD134 (OX40), CD137, CoVaccine HT, non-ionic block copolymers, incomplete Freund's adjuvant, chemokines, cholera toxin; E. coli heat-labile enterotoxin; pertussis toxin; muramyl dipeptide, muramyl peptide analogues, MF59, SAF, immunostimulatory complexes, biodegradable microspheres, polyphosphazene; and polynucleotides.
Additional adjuvants for use with the pharmaceutical compositions described herein are adjuvants containing saponins (e.g. QS21), either alone or combined with cholesterol and phospholipid in the characteristic form of an ISCOM (“immune stimulating complex,” for review, see Barr and Mitchell, Immunology and Cell Biology 74: 8-25 (1996); and Skene and Sutton, Methods 40: 53-59 (2006)). Such adjuvants are referred to herein as “saponin-based adjuvants”. In specific embodiments of the pharmaceutical compositions and methods provided herein, the recombinant MOMP antigens are combined with an ISCOM-type adjuvant or “ISCOM”, which is an ISCOM matrix particle adjuvant, such as ISCOMATRIX™, which is manufactured without antigen (ISCOM™ and ISCOMATRIX™ are the registered trademarks of CSL Limited, Parkville, Australia).
Additionally, aluminum-based compounds, such as aluminum hydroxide (Al(OH)3), aluminum hydroxyphosphate (AlPO4), amorphous aluminum hydroxyphosphate sulfate (AAHS) or so-called “alum” (KAl(SO4).12H2O) (see Klein et al., Analysis of aluminum hydroxyphosphate vaccine adjuvants by Al MAS NMR., J. Pharm. Sci. 89(3): 311-21 (2000)), may be combined with the pharmaceutical compositions provided herein.
In some embodiments described herein, the adjuvant is an aluminum salt adjuvant. In alternative embodiments, the adjuvant is a saponin-based adjuvant or a toll-like receptor agonist adjuvant. In exemplary embodiments of the invention provided herein, the aluminum adjuvant is aluminum hydroxyphosphate or AAHS, alternatively referred to as “MAA”. In alternative embodiments, the adjuvant is aluminum hydroxide. In further embodiments, the adjuvant is aluminum phosphate.
Adjuvants may be combined to provoke the desired immune response. For example, the pharmaceutical compositions of the invention may comprise at least one rMOMP produced by the methods described herein, a pharmaceutically acceptable carrier and a combination of two or more adjuvants. In some embodiments of the invention, the pharmaceutical compositions comprise an aluminum salt adjuvant and a second adjuvant. In other embodiments, the compositions comprise an aluminum salt adjuvant and a second adjuvant selected from a saponin adjuvant and a toll-like receptor agonist.
Methods of Use
Embodiments of the invention also include one or more of the recombinant MOMP, or derivative thereof, or pharmaceutical compositions comprising said recombinant MOMP or derivative, or a vaccine comprising said recombinant MOMP or pharmaceutical compositions (i) for use in, (ii) for use as a medicament or composition for, or (iii) for use in the preparation of a medicament for: (a) therapy (e.g., of the human body); (b) medicine; (c) inhibition of Chlamydia replication; (d) treatment or prophylaxis of infection by Chlamydia; (e) prevention of recurrence of Chlamydia infection; (f) reduction of the progression, onset or severity of pathological symptoms associated with Chlamydia infection and/or reduction of the likelihood of a Chlamydia infection or, (g) treatment, prophylaxis of, or delay in the onset, severity, or progression of Chlamydia-associated disease(s), including, but not limited to: oculogenital disease, cervicitis, urethritis, endometritis, pelvic inflammatory disease, tubal infertility, ectopic pregnancy, neonatal conjunctivitis, and infant pneumonia. In the uses set forth herein, the recombinant MOMP or derivatives thereof, pharmaceutical compositions and/or vaccines comprising or consisting of said recombinant MOMP can optionally be employed in combination with one or more additional therapeutic agents, for example, a second vaccine for a different pathogen.
Thus, the invention relates to a method as set forth above, which method comprises administration of an immunologically or therapeutically effective amount of any rMOMP or rMOMP derivative produced by the methods of the invention, or pharmaceutical composition or vaccine thereof, to a patient in need thereof, whereby administration to the patient results in any of (c) through (g) above.
The mode of administration to the patient can vary and may include oral, rectal, transmucosal, intestinal, parenteral; intramuscular, subcutaneous, intradermal, intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, intraocular, inhalation, insufflation, topical, cutaneous, transdermal, or intra-arterial. In embodiments of the invention, the route of administration is parenteral. In specific embodiments of the invention, the mode of administration is subcutaneous or intraperitoneal. In additional embodiments of the invention, the route of administration is intramuscular, intradermal, or subcutaneous.
The rMOMP, derivatives, or pharmaceutical compositions of the invention can be administered with medical devices known in the art. For example, a pharmaceutical composition of the invention can be administered by injection with a hypodermic needle, including, e.g., a prefilled syringe or autoinjector.
The pharmaceutical compositions disclosed herein may also be administered with a needleless hypodermic injection device; such as the devices disclosed in U.S. Pat. Nos. 6,620,135; 6,096,002; 5,399,163; 5,383,851; 5,312,335; 5,064,413; 4,941,880; 4,790,824 or 4,596,556.
Codon-Harmonized MOMP Nucleotide Sequences
One aspect of the invention relates to codon harmonized nucleic acid molecules encoding Chlamydia MOMP or a derivative thereof, or encoding Chlamydia MOMP plus a leader sequence for targeting the MOMP to the outer membrane of the cell. In particular embodiments, the invention provides a nucleic acid molecule that encodes the Chlamydia trachomatis MOMP set forth in SEQ ID NO:23, SEQ ID NO: 25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO: 28, SEQ ID NO:29, SEQ ID NO:30, wherein the nucleic acid molecule is codon-harmonized. The invention also provides a codon-harmonized nucleic acid molecule that encodes the Chlamydia muridarium MOMP set forth in SEQ ID NO:31.
In additional embodiments, the invention provides codon-harmonized nucleic acid molecules that encode variants or derivatives of the Chlamydia MOMP amino acid sequences described herein. Thus, the invention relates to codon-harmonized nucleic acid molecules encoding derivatives of the Chlamydia MOMP sequences set forth in SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 or SEQ ID NO:31, wherein the derivative is at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% identical to the reference sequence provided in SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 or SEQ ID NO:31.
In some embodiments, the codon-harmonized nucleic acid molecule encodes a MOMP derivative that comprises amino acid residues that are deleted, inserted or substituted relative to the sequence of amino acids set forth in the MOMP sequences set forth in SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 or SEQ ID NO:31. In particular embodiments, the MOMP derivative comprises a number of amino acid substitutions, deletions or additions relative to the MOMP sequences disclosed herein, wherein the MOMP derivative comprises no more than 25 amino acid residues, no more than 20 amino acid residues, no more than 15 amino acid residues, no more than 12 amino acid residues, no more than 11 amino acid residues, no more than 10 amino acid residues, no more than 9 amino acid residues, no more than 8 amino acid residues, no more than 7 amino acid residues, no more than 6 amino acid residues, no more than 5 amino acid residues, no more than 4 amino acid residues, no more than 3 amino acid residues, no more than 2 amino acid residues, or 1 amino acid residue that is/are substituted, deleted or added relative to the MOMP sequences set forth in SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 or SEQ ID NO:31. In a particular embodiment, the codon-harmonized nucleic acid molecule encodes the Chlamydia trachomatis (serovar D) derivative set forth in SEQ ID NO:24, which comprises a 2-amino acid substitution relative to SEQ ID NO:25, which was modified in order to increase Barn-site binding.
The invention further relates to nucleic acid molecules that encode a Chlamydia MOMP polypeptide and a leader sequence for targeting the MOMP to the OM of the cell, wherein the nucleic acid molecules are codon-harmonized.
In some embodiments, the Chlamydia MOMP is any MOMP polypeptide sequence or MOMP derivative polypeptide sequence disclosed herein, and the leader sequence comprises the Shigella flexneri SopA sequence set forth in SEQ ID NO:8, the Salmonella enterica PgtE sequence set forth in SEQ ID NO:9, the Yersinia pestis Pla set forth in SEQ ID NO:10, the E. coli OmpP sequence set forth in SEQ ID NO:11, the E. coli OmpA sequence set forth in SEQ ID NO:12, or the pectate lysase B (PelB) sequence set forth in or SEQ ID NO:13. In particular embodiments, the codon-harmonized nucleic acid molecule encodes a Chlamydia MOMP+leader sequence set forth in SEQ ID NO:16, SEQ ID NO:19, or SEQ ID NO:22. In additional particular embodiments, the nucleic acid molecule that encodes the Chlamydia MOMP+leader sequence comprises a sequence of nucleic acids as set forth in SEQ ID NO:15, SEQ ID NO:18, or SEQ ID NO:21, or a nucleic acid derivative thereof.
All publications mentioned herein are incorporated by reference for the purpose of describing and disclosing methodologies and materials that might be used in connection with the present invention.
Having described preferred embodiments of the invention with reference to the accompanying drawings, it is to be understood that the invention is not limited to those precise embodiments, and that various changes and modifications may be effected therein by one skilled in the art without departing from the scope or spirit of the invention as defined in the appended claims.
Expression of Recombinant Chlamydia MOMP.
A. Codon Harmonization.
β-barrel membrane protein expression directed to the E. coli outer membrane (OM expression) is typically challenging. We evaluated the effect of codon selection on the surface expression of full length recombinant Chlamydia MOMP (rMOMP). We performed codon harmonization and standard codon optimization on the recombinant MOMP gene and evaluated outer membrane expression with a whole cell flow cytometry binding assay using anti-Chlamydial EB mouse sera. Both genes were expressed in a pET vector expression system and with a native Chlamydia muridarium (Cm) MOMP leader sequence (Tables 2 and 3). We observed that codon harmonization resulted in ˜2 fold increase in outer membrane expression of recombinant Chlamydia muridarium MOMP, compared to the standard host codon optimized gene (
B. Expression Vector Optimization.
A panel of E. coli expression vectors were evaluated to further increase the surface expression level of rMOMP (Table 2). The key elements that could affect the OM expression include promoter strength and vector copy number. We compared vectors with high, medium or low copy numbers, with promoters of high, moderate or titratable strength. We found that either a strong promoter or a high vector copy number limited the surface expression of rMOMP (Table 2). Higher rMOMP surface expression was achieved with a combination of moderate promoter and a low vector copy number (such as pAVE029), suggesting that lower transcription level is preferred. Consistently, reasonable rMOMP OM expression level can be obtained with a pACYDuet vector when we used a host strain with a controllable RNA polymerase level to reduce the rMOMP mRNA transcription rate. We hypothesized that slower transcription and therefore slower translation is optimal for rMOMP OM expression as it provides ample time to allow the newly synthesized protein to properly fold and translocate onto the outer membrane, resulting in an increased level of surface expression. This result is also consistent with our observations on the effect of gene codon usage harmonization described above.
C. Secretion Leader Sequence Optimization.
In order to better direct the OM localization of rMOMP, we evaluated different secretion leader sequences which might help the OM localization of the target protein (Table 3). Among tested leader sequences, E. coli OmpA leader and OmpP leader resulted in the highest rMOMP OM expression. However, incomplete cleavage of the OmpP leader was observed and heterologous forms of rMOMP were generated (data not shown). Omptins leader family and PelB leader resulted in similar levels of moderate surface expression of rMOMP. Native Cm MOMP leader is able to direct the OM expression for CmMOMP, but not for CtD or CtE MOMP. Neither native CtD or CtE MOMP leaders result in the surface expression of rMOMP.
enterica (PgtE)
E. coli. OmpP
E. coli. OmpA
Erwinia carotovora
D. Optimization of Expression Conditions.
We evaluated many expression conditions with the pAVE029 expression system that could impact rMOMP OM expression, including cell culture medium, cell density at induction, induction time and temperature (
Seven different cell culture media were evaluated for their effect on expression level: 1-LB (Luria broth), 2-2YT (2× yeast extract and tryptone)+1% Glu, 3-Mg, 4-ProGro™ (Expression Technologies, Inc., San Diego, Calif.), 5—Azura, 6—Cinnabar, and 7—Auto induction medium). Interestingly, we observed very different rMOMP OM expression (
In summary, the most optimized conditions we have obtained for rMOMP OM expression is to perform induction for 4 hrs at 30° C. when cell density (OD590) reaches ˜0.5 (
Purification of Recombinant Chlamydia MOMP.
Harvested E. coli cells expressing recombinant MOMP were disrupted by microfluidization and membrane fraction containing rMOMP was pelleted by ultra-centrifugation, while soluble cellular proteins were largely separated. Washing the membrane fraction with high salt buffer further removed residual soluble cellular proteins. Subsequent wash with a buffer containing 1% triton X-100 detergent removed the bacterial inner membrane and wash with a buffer containing 3% beta-octyl-glucoside detergent removed certain bacterial outer membrane proteins other than recombinant MOMP. After these steps, rMOMP became the most abundant protein in the membrane fraction. A variety of detergents were evaluated for extraction of rMOMP from the outer membrane. We found that sarkosyl (an anionic detergent) was the most efficient, followed by foscholine-14 (a lipid like zwitterionic detergent) and zwittergent 3-12. DTT was required for extraction of rMOMP. The extraction contained ˜60% rMOMP. Extracted rMOMP was further purified by size exclusion and ion exchange chromatography. The purified rMOMP migrates very similarly to the native MOMP (nMOMP) protein that was purified from Chlamydia elementary body (EB) on a SDS-PAGE gel, with slightly higher amounts of dimeric and oligomeric forms (
Mouse Immunogenicity and Challenge Study
Female C57BL/6 mice (32 per group) were immunized by subcutaneous (s.c.) routes with purified nMOMP or rMOMP (10 μg/mouse/immunization) in combination with an adjuvant containing IMO-2055 and Montanide ISA 720 VG. Two preparations of rCtE-MOMP were evaluated: one with a PelB leader sequence and the other one with an OmpA leader sequence. A positive control group was immunized with 1×106 live EB in SPG per mouse by intraperitoneal (i.p.) route. A negative control group (adjuvant control) was administered with a combination of IMO-2055 and Montanide ISA 720 VG only.
Post-immunization mouse serum was analyzed by ELISA with CtD EBs as the coating antigen (
Two weeks following the last immunization, mice were challenged intravaginally with CtD EBs. The vaginal vault and ectocervix were swabbed on multiple time points following challenge and Chlamydia copy numbers were evaluated by real-time PCR. For each animal, qPCR values were log transformed at each time point and AUC (area under curve) value was calculated for the time period (
Our data suggested that the recombinant MOMP expressed on and purified from the outer membrane of E. coli elicits protective serum antibody responses in a mouse challenge model, therefore, can be evaluated as a potential candidate for a vaccine against Chlamydia.
Materials and Methods:
Codon Harmonization of the Chlamydia MOMP Gene for Recombinant Expression
Nucleotide sequences of the gene encoding the Major Outer Membrane Protein (MOMP) were retrieved from Merck internal website CMR (Comprehensive Microbial Resources) for the following strains: C. muridarum Nigg (strain MoPn) ORF TC0052 (GenBank Gene ID: 1245581; Protein Accession No. P75024.1); C. trachomatis strain D/UW-3/CX CT ORF TC_681 Serovar D (GenBank Gene ID: 884473; Protein Accession No. NP_220200.1); and C. trachomatis strain E/12-94 ORF O175_03780 Serovar E (GenBank Gene ID: 16635280; Protein Accession No. P17451). Amino acid sequences consisting of a secretion leader and the mature MOMP protein (Table 3) were codon harmonized (Angov et al., Plos One 3(5):1-10 (2008)). In brief, the codon usage data for Chlamydia (native host) and E. coli (expression host) was obtained from the Codon Usage Database (tabulated from NCBI-Genbank, Kazusa DNA Res. Inst., Kisarazu, Japan). For each species, the strain with the most codon usage data available was selected as a representative. The codon usage frequency for both native and expression hosts was then calculated and a reference database was generated. We first identified the amino acid residues for which the rare codons were used in the native host, and the corresponding rare codon in the expression host was selected for those residues. For the remaining residues, the codon in the expression host that has the closest frequency (less than 15% difference) to the corresponding codon in the native host was selected. If a codon in E. coli could not be identified that had less than 15% difference relative to the frequency of the native codon, a codon with 15% or more lower frequency was chosen if the residue was in a “linker/hinge” region in order to slow down the translation speed and a codon with 15% or more higher frequency was selected if the residue was outside the linker region to achieve higher expression. Once the harmonized gene sequence for Chlamydia MOMP was generated, NdeI and XhoI restriction enzyme sites were mutated for subsequent cloning.
Cloning and Expression of Recombinant Chlamydia MOMP
The harmonized gene sequences with flanking NdeI and XhoI restriction enzyme sites were synthesized and cloned into the PUC57 cloning vector. The synthesized genes were excised from PUC57 vector through NdeI and XhoI restriction sites. The excised DNA fragments were ligated into the pAVE029 expression vector (MSD Biologics UK) using T4 DNA ligase (Promega Corp., Madison, Wis.) for 4 hours at 16° C. Ligated plasmids were transformed into competent cells DH5α (Invitrogen, Carlsbad, Calif.) and grown in LB agar plates with 10 μg/mL tetracycline. Colonies harboring the recombinant plasmid were identified by PCR and confirmed by sequencing using pAVE029 vector specific primers for 5′ end of the gene (ppop40 primer ATT CTG CAT TCA CTG GCC GAG G (SEQ ID NO:1)) and 3′ end of the gene (T7 Term standard sequencing primer GCT AGT TAT TGC TCA GCG G (SEQ ID NO:2)). The sequence-confirmed positive colonies were propagated in LB medium with 10 μg/mL of tetracycline and plasmid DNA was isolated from the cell cultures with a HiSpeed Maxi Kit (QIAGEN, Venlo, Netherlands).
The recombinant plasmid DNA was transformed by electroporation into an expression host strain E. coli K12 W25113 using a Bio-Rad GenePulser (Bio-Rad Laboratories, Inc., Hercules, Calif. Transformed cells were plated on LB Agar plates with 10 μg/mL tetracycline and grown overnight at 37° C. Single colonies were picked and inoculated into Cinnabar media (Teknova, Hollister, Calif.) with 10 μg/mL of tetracycline and grown at 37° C. with shaking at 250 RPM until OD600 reaches to mid log phase (˜0.5). 0.4 mM IPTG was added into the cell culture for induction and the cell culture was incubated for 4 hours at 30° C. with shaking. The cell cultures were then characterized by whole cell flow cytometry binding assay, SDS-PAGE, and Western Blot analysis.
Whole Cell Flow Cytometry Binding
50 μL of E. coli cell culture (at ˜1×109 cells/mL) that recombinantly expressed Chlamydia MOMP was incubated with 50 μL of mouse sera against Chlamydia elementary body (EB) at a dilution of 1:250 for 1 hour at room temperature in a 96 well plate. After incubation, the cells were washed with 1 mL phosphate buffered saline (PBS) and stained with 100 μL of a fluorescence labeled secondary antibody (Alexa Fluo-488 F(ab)′2 fragment of goat anti-mouse IgG (H+L), Life Technologies, Carlsbad, Calif.) at a dilution of 1:100. The stained cells were washed twice and re-suspended in PBS for flow cytometric analysis (Guava Technologies, EMD Millipore, Billerica, Mass.). Data analyses were performed with CytoSoft 5.3 software (Guava Technologies).
SDS-PAGE and Western Blot
E. coli cell culture (˜1˜109 cells) that recombinantly expresses Chlamydia MOMP was treated with SDS loading buffer with reducing agent (Invitrogen, Carlsbad, Calif.). Samples were applied to NuPAGE (Invitrogen) gel electrophoresis. NuPAGE gel was stained with Gel code blue staining solution (Pierce Biotechnology, Rockford, Ill.). For Western Blot, samples were applied to gel electrophoresis and then electro-transferred onto nitrocellulose membranes (Life Technologies, Carlsbad, Calif.). The membranes were incubated with mouse sera against Chlamydia EB (or other specific primary antibodies) followed by a fluorescence conjugated goat anti-mouse secondary antibody (IRDye 680LT, Licor). Image was acquired and analyzed by LICOR ODYSSEY® (Li-Cor Biosciences, Lincoln Nebr.).
Purification of Recombinant Chlamydia MOMP
E. coli cell culture was grown in Cinnabar media (Teknova, Hollister, Calif.) and induced by IPTG as described above. Cell culture was harvested by centrifugation at 12,000 g for 15 min. Cell pellets were weighed and resuspended in 9 volumes (v/w) of 50 mM Tris-Cl pH 8.0 buffer with EDTA free protease inhibitor (Roche, Basel, Switzerland, 1 tab per 100 mL buffer). Cells were disrupted by microfluidization and undisrupted cells were pelleted and removed by centrifugation at 9700 g for 15 min. Membrane fraction was pelleted by centrifugation of the cleared disrupted cells at 23800 g for 90 min and washed with high salt buffer (1M NaCl, 0.05% tween20) followed by another centrifugation at 23800 g for 90 min. To remove the bacterial inner membrane, washed membrane fraction was resuspended in buffer A (20 mM Tris-Cl pH 8.0, 1 mM EDTA) with 1% triton X-100, incubated at room temperature for 15 min followed by ultracentrifugation at 120,000 g for 40 min. To remove bacterial outer membrane proteins other than recombinant MOMP (rMOMP), pellets were resuspended by buffer A (20 mM Tris-Cl pH 8.0, 1 mM EDTA) with 3% beta-octyl-glucoside, incubated at room temperature for 1 hour followed by ultracentrifugation at 120,000 g for 40 min. rMOMP was extracted by resuspending the pellets in buffer A (20 mM Tris-Cl pH 8.0, 1 mM EDTA) with 1% sarkosyl, incubated at room temperature for 2 hour followed by ultracentrifugation at 120,000 g for 40 min. Extracted rMOMP was subjected to size exclusion chromatography (Sephacryl 5300, GE healthcare) in a buffer containing 10 mM Hepes pH 7.3, 150 mM NaCl, 0.1% zwittergent 3-14. Eluted rMOMP was further purified with ion exchange chromatography (Hitrap Q FF, GE healthcare). Purified rMOMP fractions were pooled and stored at 4° C.
Cell Culture and Propagation of Chlamydiae
All cell lines and Chlamydia strains were obtained from ATCC (Manassas, Va.). HeLa 229 cells were used for propagation all strains. HeLa 229 cells were grown in Eagle's Minimal Essential Medium (ATCC) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone), 50 μg/mL vancomycin (Sigma-Aldrich, St. Louis, Mo.), and 10 μg/mL gentamicin (Gibco). Host cells were seeded into tissue culture flasks at a cell density of 5×105 cells/mL and incubated overnight at 37° C. in 5% CO2 to achieve a confluent monolayer. Cell monolayers were infected with C. trachomatis (Ct) strain D/UW-2/Cx stock diluted in sucrose-phosphate-glutamate (SPG) buffer and cultured for 72 hours. The Chlamydiae were harvested from the infected cells and purified by centrifugation through 30% Renograffin (Bracco Diagnostics, Milan Italy) and stored frozen at −80° C.
Mouse Immunization
Female C57BL/6 mice (Taconic Farms) were used at 6 to 8 weeks of age, and food and water were provided ad libitum. All animal procedures were in accordance with government and institutional guidelines for animal health and well-being, and were approved by the Merck Institutional Animal Care and Use Committee.
Animals were immunized by subcutaneous (s.c.) routes with rMOMP (1 to 10 μg/mouse/immunization) in combination with an adjuvant containing IMO-2055 and Montanide ISA 720 VG (SEPPIC Inc., Coley Pharmaceutical Group Inc., Wellesley, Mass.) at a ratio of 70:30 (v/v). Live EB groups were immunized with 1×106 EB in SPG per mouse by intraperitoneal (i.p.) route. Adjuvant control groups were administered with a combination of IMO-2055 and Montanide ISA 720 VG only Immunizations were administered on days 0, 20 and 30.
Prior to the first immunization and two weeks following the final immunization, tail bleeds were performed with blood collected in BD Microtainer® Serum Separator Tubes (Becton, Dickinson and Company, Franklin Lakes, N.J.). Blood samples were centrifuged at 6,000 rpm for 5 min and serum was transferred to a microcentrifuge tube.
Murine Challenge Study
At approximately 2 weeks following the last immunization, progesterone (medroxyprogesterone acetate, Depo-Provera; Pfizer, New York, N.Y.) was administered subcutaneously (2.5 mg/dose) at 10 and 3 days before challenge. Mice were challenged intravaginally (approximately 1 month following the last immunization) by direct instillation of 10 μL of SPG containing 1×105 Ct serovar D EBs. The vaginal vault and ectocervix were swabbed using a microfiber swab (Fisher, Hampton, N.H.) on days 7, 11, 14, 18, and 21 (or a combination of these time points) following challenge.
Swabs were placed into a 1.5-mL tube containing 2 sterile glass beads (5 mm diameter) and 300 μL of Chlamydia isolation medium (Trinity Biotech, Bray, Ireland) on ice. Bacteria were eluted from the swabs and separated from cells by vortexing for 60 seconds. 100 μL of eluted cells/bacteria were plated onto a processing cartridge containing 100 μL of PBS and stored at −70° C. until DNA extraction.
Primer, Probe and Real-Time PCR
DNA from genital swab samples was extracted using the MagNA Pure 96 DNA and Viral NA small volume kit (Roche, Basel, Switzerland) on the MagNA pure machine (Roche) according to the manufacturer's instructions.
The oligonucleotide primer set was designed for detection of all species of Chlamydiae. The sense primer, 16S DIR 5′-CGC CTG AGG AGT ACA CTC GC-3′ (SEQ ID NO:3), and anti-sense primer, 16S Rev 5′-CCA ACA CCT CAC GGC ACG AG-3′ (SEQ ID NO:4), were designed to amplify a 208-bp fragment of the chlamydial 16S ribosomal subunit gene, conserved across Chlamydia strains and serovars. Primers were obtained from Sigma Genosys (The Woodlands, Tex.), and the probe, 16S Fam-5′-CAC AAG CAG TGG AGC ATG TGG TTT AA-3′ Tamra (SEQ ID NO:5), was synthesized by Applied Biosystems, (Foster City, Calif.).
The 50-μL, reaction mixtures consisted of 1× QuantiTect Multiplex PCR master mix without ROX (Qiagen, venlo, netherlands), 100 nmol/L 16S probe, 200 nmol/L primer 16S DIR, 400 nmol/L primer 16S Rev, 30 nmol/L ROX reference dye, and 5 μL of sample DNA. Nontemplate controls consisting of the reaction master mix, primers, and probe, but no DNA, were included in each assay run. Reaction conditions were set as follows: 1 cycle at 95° C. for 15 min, followed by 40 cycles at 94° C. for 1 min and at 60° C. for 1 min. Thermal cycling, fluorescent data collection, and data analysis were performed using the Stratagene Mx3005P system (Stratagene, La Jolla, Calif.) according to the manufacturer's instructions.
Detection of Serum Antibody and Isotype Levels by ELISA
Serum was analyzed by an enzyme-linked immunosorbent assay (ELISA). Nunc™ C96 Maxisorp Immunoplates (Thermo Scientific, Waltham, Mass.) were coated with 50 uL of 1 ug/ml C. trachomatis Serovar D EBs in PBS and refrigerated overnight. The plates were washed three times with 0.05% Tween-20 (Fisher Scientific) in PBS (PBS-T). The wells were blocked with 5% HyClone® Fetal Bovine Serum (FBS) (Thermo Scientific) in PBS at 200 μL/well for 1 hour at room temperature and washed three times with PBS-T. Serum was diluted in 5% FBS in PBS at a 1:500 dilution. Serially diluted sera were added to the plate, incubated for 2 hours at room temperature and the plates were washed three times with PBS-T. HRP-conjugated secondary antibodies (Goat anti-mouse IgG, Fcγ fragment specific; Goat Anti-mouse IgG, Fcγ Subclass 1 specific; or Goat Anti-mouse IgG, Fcγ Subclass 2c specific; Jackson ImmunoResearch Laboratories, Inc., West Grove, Pa.) were diluted in 5% FBS in PBS at 1:6,000, 1:6,000, or 1:2,000 dilution, respectively. The diluted secondary antibodies were added at 100 μL/well, incubated for 1 hour at room temperature and the plates were washed three times with PBS-T followed by three times with PBS. Room temperature BD Opt EIA™ TMB Substrate Reagent Set (BD Biosciences, Franklin Lakes, N.J.) was mixed and filtered through a 0.22 um CA filter unit (Corning, Inc., Corning N.Y.), and 100 μL was added to each well and incubated for 10 min at room temperature. The reaction was stopped with 100 μL/well of 2M H2SO4 (Fisher Scientific). The optical density (OD) was read at 450 nm on a SpectraMax® M5 (Molecular Devices). The cutoff OD for each post-imunization serum was calculated as two times of the OD450 of the corresponding pre-immunization serum. ELISA titers were determined by linearly interpolating between the sequential log dilutions that bracket the cutoff OD, where the dependent variable is the OD response and the independent variable is the log dilution. The resulting dilution is then back transformed to obtain the reported titer. The reported titer is the estimated dilution of serum that results in a response equivalent to the cutoff OD.
This application claims the benefit of U.S. Provisional Application No. 62/082,889, filed Nov. 21, 2014, the contents of which are hereby incorporated by reference in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2015/060780 | 11/16/2015 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2016/081327 | 5/26/2016 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 20020136742 | Kousoulas et al. | Sep 2002 | A1 |
| 20090214582 | Dean | Aug 2009 | A1 |
| Number | Date | Country |
|---|---|---|
| 0192033 | Aug 1986 | EP |
| WO2008040757 | Apr 2008 | WO |
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| Number | Date | Country | |
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| 20190046626 A1 | Feb 2019 | US |
| Number | Date | Country | |
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| 62082889 | Nov 2014 | US |
