US20140275478A1 - Vaccines against Chlamydia sp. - Google Patents

Vaccines against Chlamydia sp. Download PDF

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US20140275478A1
US20140275478A1 US14/216,403 US201414216403A US2014275478A1 US 20140275478 A1 US20140275478 A1 US 20140275478A1 US 201414216403 A US201414216403 A US 201414216403A US 2014275478 A1 US2014275478 A1 US 2014275478A1
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amino acid
acid sequence
seq
momp
subsequence
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Frank Follmann
Ida Rosenkrands
Anja Olsen
Peter Andersen
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Statens Serum Institut SSI
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Statens Serum Institut SSI
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Priority to US15/956,731 priority patent/US10925954B2/en
Priority to US17/155,264 priority patent/US20210205433A1/en
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/118—Chlamydiaceae, e.g. Chlamydia trachomatis or Chlamydia psittaci
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/295—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Chlamydiales (O)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/60—Medicinal preparations containing antigens or antibodies characteristics by the carrier linked to the antigen
    • A61K2039/6031—Proteins
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/40—Fusion polypeptide containing a tag for immunodetection, or an epitope for immunisation

Definitions

  • the present invention relates to polypeptides of repetitive units of immunogenic fragments of surface exposed regions of outer membrane proteins of Chlamydia sp. and pharmaceutical compositions and vaccines comprising these fusion proteins.
  • Chlamydiae are intracellular bacterial pathogens responsible for a variety of infections. Chlamydia pneumoniae is responsible for human acute respiratory infection and believed to play a role in coronary heart disease. Chlamydia trachomatis is the causative agent of human sexually transmitted disease and eye infections (Trachoma). Also in animals, several infections with Chlamydia sp. are known, e.g. Chlamydia Suis infecting pigs, and Chlamydiaphila abortus which causes abortion in small ruminants (sheep and goats).
  • Ct Chlamydia trachomatis
  • Urogenital infections with Ct are of public health concern because of its high prevalence and the fact that it's a risk factor for ectopic pregnancy and infertility 2 .
  • Ct infections have been shown to facilitate the transmission of HIV 3 and act as a co-factor in HPV-induced cervical carcinoma 4 .
  • the duration of untreated genital Ct infection can be prolonged, and complete clearance is often not reached within the first 12 months 5 . From human studies it is known that some degree of protective immunity against genital re-infection develops, although it appears at best to be partial 6 .
  • the infection is effectively controlled by antibiotic therapy; however the high prevalence of asymptomatic cases suggests that sustainable disease control can only be envisaged if an effective Chlamydia vaccine is developed.
  • a vaccine against Ct needs to elicit protective T-cell and B-cell immunity in the genital tract mucosa 7 .
  • Immune mechanisms of clearance of infection and resistance to re-infection have been described in numerous studies.
  • a variety of animal models and chlamydial species have been used in attempts to identify protective and damaging immune responses.
  • a general consensus has emerged that, in mice, CD4+Th1 cell mediated immune responses plays a major role in the resolution of Ct infection 8, 9, 10 , whereas the role of humoral immunity in protection has remained less well defined.
  • guinea pigs immunity to chlamydial infection is mediated at least partly by secretory IgA at the mucosal surface 11, 12 and also in the mouse model there is increasing evidence to support a role for antibodies in protective immunity 9 .
  • Data from animal models that has emerged over the last years clearly demonstrate that if antibodies are formed after the infection is established they play a minimal role, whereas their presence at the time of infection (e.g. in a secondary response) promotes significant levels of protection, an effect that is however clearly amplified in the presence of Chlamydia specific CD4 + cells 9, 13, 14.
  • a strong cell mediated immune (CMI) response without antibodies may on the other hand control bacterial replication but can in the worst case exacerbate the pathology associated with Chlamydia infection 15 16 .
  • CMI cell mediated immune
  • identifying proteins as antigenic during an infection do not necessarily mean they are protective as vaccines 29 and despite the characterization of such a large number of antigens only very few of these have been demonstrated to mediate protection as vaccines in animal models 30 31, 32 .
  • the partial protection observed is mediated by T cells with no neutralizing antibodies. Therefore there is a lack of vaccine candidates that generate neutralizing antibodies that can cope with the infection in the initial phase and creating a balanced immune response.
  • MOMP is the classical target antigen for neutralizing antibodies and one of the first antigenic molecules described. It is a surface-exposed trans membrane protein which has structural (porin) properties 36, 37, 38 . MOMP is a 40 kDa protein making up roughly 60% of the protein in the Ct membrane and is a target for neutralizing antibodies with proven efficacy both in vitro and in vivo. MOMP consists of four variable surface exposed domains (VD-1 to VD-4) separated by five constant segments 36 39 and it is the molecular basis of the serovar ( ⁇ 15) grouping of Chlamydia ( FIG. 1 ).
  • MOMP is highly immunogenic in humans and animals and has therefore been studied in great detail as a vaccine candidate, both as a natively purified protein, recombinantly and as DNA-vaccine. These vaccination attempts gave variable results 17, 51, 52, 53, 54, 55, 56, 57 .
  • the reason for the relative inconsistency of MOMP as a vaccine is not fully understood, but the fact that the synthetic MOMP immunogens do not mimic the native structure of the protein has been the major concern 54 .
  • the structure of this membrane bound cysteine rich molecule and refolding various products to achieve native protein structure has been extremely challenging and is not suitable for large scale vaccine production 58 .
  • MOMP has so far not been a feasible vaccine candidate and several attempts have therefore been made to construct a vaccine based on selected epitopes (such as the highly conserved TTLNPTIAG (SEQ ID NO 76) in VD4 36, 59 ) or based on selected regions rich in neutralizing target epitopes (such as the VD's) from MOMP (WO9406827, U.S. Pat. No. 6,384,206) 60, 61 62, 63 64 51, 65 66 .
  • selected epitopes such as the highly conserved TTLNPTIAG (SEQ ID NO 76) in VD4 36, 59
  • selected regions rich in neutralizing target epitopes such as the VD's
  • VD1, VD2 and VD4 have been special focus on VD1, VD2 and VD4 because neutralizing monoclonal antibodies used for serotyping has been shown to map to these regions.
  • VD regions are targeted by antibodies during natural infection and in line with this, these regions have naturally been the focus of attempts to develop immuno-diagnostics.
  • Mygind et al. constructed different polyantigens containing VD regions from different serovariants in the search for a diagnostic tool based on ELISA 67 .
  • This analysis revealed that by increasing the number of serovariants and include the species specific TTLNPTIAG into one recombinant polyantigen, it was possible to increase the specificity and sensitivity of the assay compared to an assay based on a single serovariant antigen.
  • VD4 has attracted interest as an immunogen because this region was shown to contain the highly conserved species-specific epitope TTLNPTIAG embedded in the variable region. Importantly, this conserved epitope in the VD4 region can elicit a broadly cross-reactive immune response, which is able to neutralize multiple serovars, among them the most prevalent D, E and F ( FIG. 2 ). Peptides representing the VD4 region or the conserved epitope derived from this region have been used for immunization either alone, as chimeric peptides fused to other regions such as VD1 or mixed with T cell epitopes to potentiate the antibody response 60, 68 51, 65 64 69 . All these constructs generated antibodies with some functional capabilities of neutralizing the infection in vitro but in general these strategies suffer from a low immunogenicity and the titres did not translate into in vivo protective efficacy against genital chlamydial challenge.
  • VD4 based strategy furthermore suffers from the limitation that with the exception of the TTLNPTIAG (SEQ ID NO 76) epitope, these fragments as mentioned above are highly specific for one or two serovariants and a vaccine would accordingly have to be composed of several components to cover the most frequent serovariants causing human disease.
  • B-cell epitopes within the VD regions could function as a poly-epitope vaccine against Chlamydia psitattci serovar D in chickens; in the examples they describe the combination of up to three B-cell epitopes each derived from a VD region from different variable domains of the same serovariant together with several T-cell epitopes.
  • the use of repeats of a variable domain of a surface exposed region of MOMP and using different serovariants is not suggested and thus high titers and a broad response against different serovariants is not obtained.
  • the object of the current invention is to prepare recombinant fusion molecules that are capable of generating a high titered neutralizing antibody response that is protective against various Ct serovars in vivo.
  • Our invention furthermore describes the combination of these antibody promoting fragments with Ct antigens that are targets for T cells with the aim to provide a vaccine that activate both arms of the immune system.
  • the present invention discloses an efficient vaccine against a pathogen, e.g. Chlamydia trachomatis (Ct), that incorporates repeats of surface exposed fragments of Ct antigens (homologous immuno-repeats) for maximal antibody responses.
  • a pathogen e.g. Chlamydia trachomatis (Ct)
  • Ct antigens homologous immuno-repeats
  • these surface exposed fragments are extended to cover the flanking region of the surface exposed fragments that may contain T cell epitopes.
  • a defined large fragment representing an extended version of the VD1 or VD4 region from the Ct MOMP antigen and in the immuno-repeat format provides high levels of surface binding and neutralizing antibodies against Ct.
  • the immuno-repeat technology is used to obtain high titers and a broad response against different serovariants by the fusion of fragments that contain variable B and T cell epitopes from different serovariants (heterologous immuno-repeats).
  • these surface exposed repeats are recombinantly fused with fragments of other surface exposed antigens such as PMPs or OMPs.
  • our invention discloses combinations of these immuno-repeat constructs with strong T cell antigens, such as MOMP(CT681), CT043 or CT004 from Ct that together form a very efficient vaccine against the different infectious stages of Ct infection.
  • FIG. 1 Model of MOMP (Serovar D, strain: D/B-120) membrane topology adapted from Findlay et al 77 .
  • the VD1, VD2, VD3 and VD4 are marked by black lines in the AA sequence (SEQ ID NO: 68) and in the linear model MOMP depicted interspaced with 5 constant segments (CS).
  • FIG. 2 Alignment of amino acid sequence of Ct MOMP VD4 ext for serovars D, E, F, G, Ia and J.
  • the serovar D sequence is used as prototype, and conserved amino acids in other serovars are shown as “.”.
  • the variable domain VD4 according to Baehr et al (PNAS, 1988) 36 is shaded in gray and the conserved epitope TTLNPTIAG (SEQ ID NO: 76) is boxed.
  • SvD VD4 ext (SEQ ID NO: 23), SvE VD4 ext (SEQ ID NO: 24), SvF VD4 ext (SEQ ID NO: 25), SvG VD4 ext (SEQ ID NO: 26), SvI VD4 ext (SEQ ID NO: 27), and SvJ VD4 ext (SEQ ID NO: 26) are shown.
  • FIG. 3 Model of MOMP (Serovar D, strain: D/B-120) membrane topology adapted from Findlay et al.
  • the VD1ext and VD4ext described in this invention are shown as shaded in the figure.
  • Amino acid sequence shown is SEQ ID NO: 68.
  • FIG. 4 Illustration of the design of homologous and heterologous immuno-repeats.
  • the immuno-repeats are fusion proteins of e.g. four VD4 ext regions, either from the same serovar, homologous immuno-repeats, or from different serovars, heterologous immuno-repeats.
  • the variable VD4 region within each VD4 ext region is illustrated as hatched.
  • FIG. 5 Enhanced and broadened immune responses after immunization with homologous immuno-repeats of VD4 ext compared with a monomeric VD4 ext unit.
  • FIG. 6 A construct composed of heterologous immuno-repeats from SvD, E, F and G induced a stronger response to multiple serovars compared to homologous immuno-repeats from SvF.
  • FIGS. 7A-7D Fine specificity of the antibody responses after immunization with a heterologous immuno-repeat of the extended VD4 units from SvD, E, and F (CTH89) compared to constructs composed of a homologous immuno-repeat from (SvE ext VD4)*4 and from (SvF ext VD4)*4.
  • the Serovar E sequence shown is SEQ ID NO: 24, and the Serovar F sequence shown is SEQ ID NO: 25.
  • each set of overlapping peptides is NMFTPYIGV through MQIVSLQLN, corresponding to SEQ ID NO: 195 through SEQ ID NO: 254, respectively. (See Example 3).
  • FIG. 8 Immunization with heterologous immuno-repeats of extended VD4's from SvD, SvE and SvF (CTH89) generates early T cell independent protection after a SvD challenge.
  • FIG. 9 In vivo neutralization with CTH89 specific serum.
  • FIG. 10 Coupling of heterologous immuno-repeats to recombinant MOMP.
  • FIG. 11 Vaccination with heterologous immuno-repeats of VD1-VD4's regions from SvD, SvE and SvF (CTH88) compared to vaccination with a single VD1-VD4 unit from SvD (CTH87)
  • FIG. 12 Coupling of T cell antigens to immuno-repeats of VD4
  • FIG. 13 Immunization with a cocktail of a heterologous VD4 immuno-repeat and a T cell antigen fusion molecule
  • FIG. 14 Comparison of CAF01 and Alum as adjuvant delivery system.
  • FIG. 15 Vaccination with heterologous immuno-repeats composed of reduced length of the VD4 ext regions from SvD, SvE, SvF and SvG.
  • the CTH518 sequence shown is amino acids 1 through 68 of SEQ ID NO 53.
  • the CTH286 sequence shown is amino acids 21 through 64 of SEQ ID NO 53.
  • the CTH285 sequence shown is amino acids 28 through 57 of SEQ ID NO: 53.
  • FIG. 16 Vaccination with heterologous immuno-repeats composed of extended VD4 ext regions from SvD, SvE, SvF, SvG, SvIa and SvJ.
  • the CTH88 sequence shown is amino acids 60 through 127 of SEQ ID NO: 46.
  • the CTH69+CTH72 sequence shown is SEQ ID NO: 255.
  • the invention discloses a polypeptide comprising
  • an amino acid sequence comprising one or more surface exposed fragments of the same outer membrane protein expressed in a serotype of Chlamydia sp.; and b) two or more additional amino acid sequences which is either the same sequence as defined in a) or is the corresponding surface exposed fragments from a variant of said outer membrane protein expressed in a serotype of Chlamydia sp., which is different from the serotype in a).
  • polypeptides comprising immuno-repeats, which is 3 or more such as 4 or more repeats of an amino acid sequence comprising an immunogenic portion of a surface exposed region of an outer membrane protein of Chlamydia sp.
  • the invention can be described as a polypeptide comprising an amino acid sequence comprising one or more surface expose fragments of the same outer membrane protein expressed in a serotype of Chlamydia sp. and two or more such as three or more additional amino acid sequences which is either the same sequence as defined in a) or is the corresponding surface exposed fragments from a variant of said outer membrane protein expressed in a serotype of Chlamydia sp., which is different from the serotype in a).
  • the polypeptide comprises 3 or more different amino acid sequences, where said amino acid sequences each comprises one or more surface exposed fragments from different variants or isotypes of the same outer membrane protein that varies in different Chlamydia sp. serotypes, said amino acid sequences derived from different Chlamydia sp. serotypes (heterologous immuno-repeats in our terminology), but the invention also discloses a polypeptide comprising 3 or more repetitions of an amino acid sequence, where said amino acid sequence comprises one or more surface exposed fragments of the same outer membrane protein that varies in different Chlamydia sp. serotypes, said amino acid sequences derived from the same Chlamydia sp. serotype (homologous immuno-repeats in our terminology).
  • the outer membrane protein is preferable the major outer membrane protein (MOMP) from any Chlamydia sp. serotype and the surface exposed fragment is chosen from variable domain 1 (VD1), variable domain 2 (VD2), variable domain 3 (VD3) or variable domain 4 (VD4) of MOMP.
  • the surface exposed fragment can optionally be linearized by substitution of cysteine in the amino acid sequence to prevent disulfide bonds.
  • a preferred embodiment of the invention is polypeptides comprising immuno-repeats with 3 or more repeats of the variable domain 4 (VD4) of MOMP from any of serovars D, E, F, G, Ia and J of Chlamydia trachomatis , where each variable domain consists of an amino acid sequence, which corresponds to the position of amino acid residues Nos.
  • VD4 variable domain 4
  • variable domains in the immune-repeat is independently selected from the group consisting of the VD4 of serovar D, the VD4 of serovar E, the VD4 of serovar F, the VD4 of serovar G, the VD4 of serovar Ia and the VD4 of serovar J of Chlamydia trachomatis or has 80% sequence identity herewith.
  • VD4 from serovar D, E, F, G, Ia and J corresponds to SEQ ID NO 15-20 respectively.
  • Each variable domain can additionally be flanked/extended on the N-terminal side by either
  • variable domain On the C-terminal side the variable domain can additionally be flanked/extended by
  • polypeptides comprising 2-8 different amino acid sequences each derived from MOMP from Chlamydia trachomatis which comprises an amino acid sequence defined in formula I:
  • VD4 is independently selected from SEQ ID NO. 15-20 or an amino acid sequence which has at least 80% sequence identity herewith, and xx 1 consists of i) The amino acid sequence EWQASLALSYRLNMFTPYIGVKWSRASFDADTIRIAQPK (SEQ ID NO 21) or ii) A subsequence of the amino acid sequence in i) said subsequence comprising 1-38 amino acid residues, starting with the C-terminal K in the amino acid sequence in i) and xx 2 consists of iii) The amino acid sequence DTMQIVSLQLNKMKSRKSCGIAVGTTIVDA (SEQ ID NO 22)
  • fusion proteins comprising immuno-repeats of VD4 of MOMP is indicated by SEQ ID NO 49-59.
  • the polypeptide additionally comprises immuno-repeats of 3 or more variable domain 1 (VD1) of MOMP from any of serovars D, E, F, G, Ia and J of Chlamydia trachomatis , each variable domain consisting of an amino acid sequence, which corresponds to position of amino acid residues nos.
  • VD1 variable domain 1
  • variable domain can additionally be flanked/extended on the N-terminal side by either
  • variable domain On the C-terminal side the variable domain can additionally be flanked/extended by
  • polypeptides comprising 2-8 different amino acid sequences each derived from MOMP from Chlamydia trachomatis which comprises an amino acid sequence defined in formula I and additionally comprising an amino acid sequence defined in formula II:
  • VD1 is independently selected from SEQ ID NO. 1-6 or an amino acid sequence which has at least 80% sequence identity herewith, and yy 1 consists of v) The amino acid sequence DAISMRVGYYGDFVFDRVLKTDVNKEFQMG (SEQ ID NO 7) or vi) A subsequence of the amino acid sequence in v) said subsequence comprising 1-30 amino acid residues, starting with the C-terminal G in the amino acid sequence in v) and yy 2 consists of vii) The amino acid sequence NPAYGRHMQDAEMFTNAA (SEQ ID NO 8) or viii) A subsequence of the amino acid sequence in vii) said subsequence comprising 1-18 amino acid residues, starting with the N-terminal N in the amino acid sequence in vii).
  • polypeptides comprising immuno-repeats of VD1 is indicated by SEQ ID NO 9-14 and 45-48.
  • VD2 variable domains 2
  • VD3 variable domains 3
  • VD2 is independently selected from SEQ ID NO. 29-34 or an amino acid sequence which has at least 80% sequence identity herewith
  • zz 1 consists of ix)
  • zz 2 consists of xi)
  • the amino acid sequence WELYTDTTFAWSVGARAALWE SEQ ID NO 36) or xii
  • VD3 is independently selected from SEQ ID NO. 37-42 or an amino acid sequence which has at least 80% sequence identity herewith, and qq 1 consists of xiii) The amino acid sequence ATLGASFQYAQSKPKVEELNVLCNAAEFTINKPKGYVG (SEQ ID NO 43) or xiv) A subsequence of the amino acid sequence in xiii) said subsequence comprising 1-22 amino acid residues, starting with the C-terminal G in the amino acid sequence in xiii) and qq 2 consists of xv) The amino acid sequence TGTKDASIDYHEWQASLALSYRLNMFTPYIGVKWS (SEQ ID NO 44) or xvi) A subsequence of the amino acid sequence in xv) said subsequence comprising 1-35 amino acid residues, starting with the N-terminal T in the amino acid sequence in xv).
  • the immuno-repeats can be heterologous, that is where the variable domain is derived from different serotypes or they can be homologous, that is where the variable domain is derived one serotype.
  • the preferred number of repeats are 2, 3, 4, 5, 6, 7 or 8 repeats.
  • immuno-repeats in the polypeptides can be linearized, that is cysteine residues are replaced with serine.
  • the polypeptides comprising immuno-repeats can additionally comprise a moiety that facilitate export of the polypeptide whens produced recombinantly (e.g. signal peptides), a moiety that facilitate purification of the polypeptide (e.g. his-tags) and/or a moiety which enhance the immunogenicity (e.g. a T cell antigen).
  • the T-cell target can be chosen from a Ct antigen such as CT043, CT004, CT414, CT681 or part hereof. Examples of such fusion proteins are indicated by SEQ ID NO 60-67.
  • a polypeptide according to the invention having the following functional abilities:
  • the present invention also discloses nucleic acids encoding above described polypeptides.
  • the disclosed polypeptides or nucleic acids are used for the preparation of a pharmaceutical composition such as a vaccine.
  • the vaccine can additionally comprise a pharmacologically acceptable carrier (virus like particles), excipient, adjuvant (e.g. DDA/TDB or alum) or immune modulator.
  • the pharmaceutical composition can be used for prophylactic or therapeutic use against Chlamydia sp. Infections, including infections with Chlamydia trachomatis or C. pneumoniae.
  • a method for preventing, treating and/or reducing the incidence of Chlamydia sp. Infections, including infections with Chlamydia trachomatis or C. pneumoniae , by administering this pharmaceutical composition is also disclosed.
  • the preferred outer membrane protein is MOMP but may also include other surface exposed antigens from Chlamydia species that are targets for humoral responses.
  • the immuno-repeat from a surface exposed region can be from the same serotype (homologous immuno-repeats) or represent fragments that contain variable epitopes and are derived from different serotypes (heterologous immuno-repeat).
  • the immuno-repeats contain an extended fragment that contains both a variable and a conserved region known to be rich in T cell epitopes.
  • a preferred surface exposed region of an outer membrane protein is chosen from VD1, VD2, VD3 and VD4 from MOMP.
  • amino acid sequences used for constructing the immuno-repeats described in the examples are chosen from table 1, 2 and 3.
  • variable domain of VD4 of MOMP can be described as an amino acid sequences as defined as:
  • Aa1 consists of the amino acid sequence TTLNPTIAG (SEQ ID NO 76) (which is conserved for all serovars);
  • Aa2 is selected from the group consisting of: SATAIFDT (SEQ ID NO 79) (from serovar D and E), LVTPWDI (SEQ ID NO 80) (from serovar F), LAKPVVDI (SEQ ID NO 81) (from serovar G) and LAEAILDV (SEQ ID NO: 82) (from serovar Ia and J).
  • Aa2 is the sequence from serovar D or E
  • Aa3 is selected from the sequences set forth in AGDVKTGAEGQLG (SEQ ID NO 83) (from serovar D) and AGDVKASAEGQLG (SEQ ID NO 84) (serovar E).
  • Aa2 is the sequence from serovar F
  • Aa3 is the sequence CGSVAGANTEGQIS (SEQ ID NO 85) (from serovar F).
  • Aa2 is the sequence from serovar G
  • Aa3 is the sequence CGSVVAANSEGQIS (SEQ ID NO 86) (from serovar G).
  • Aa3 is selected from KGTVVSSAENELA (SEQ ID NO 87) (from serovar Ia) and KGTVVASGSENDLA (SEQ ID NO 88) (from serovar J)
  • variable domain VD4 of MOMP is depicted in FIG. 2 .
  • the immuno-repeats preferably additionally comprises extensions on either sides which are also depicted in FIG. 2 .
  • the N-terminal side of a VD4 domain can be flanked or extended by one or more amino acids from the more conserved and T-cell epitope rich La1, where La1 is the part of VD4 of MOMP which is embedded in the membrane and has the amino acid sequence EWQASLALSYRLNMFTPYIGVKWSRASFDADTIRIAQPK (SEQ ID NO 21) or an amino acid sequence having 80% sequence identity herewith.
  • the C-terminal side of a VD4 domain can correspondingly be flanked or extended by one or more amino acids from the more conserved and T-cell epitope rich La2, where La2 is the part of VD4 of MOMP which is embedded in the membrane on the C-terminal side and has the amino acid sequence DTMQIVSLQLNKMKSRKSCGIAVGTTIVDA (SEQ ID NO 22) or an amino acid sequence having 80% sequence identity herewith.
  • a similar illustration can describe immuno-repeats comprising the variable domain 1 (VD1) of MOMP with the variable domains (Aa2-Aa1-Aa3) of the various serovars are given by SEQ ID NO 1-6 in table 1.
  • the corresponding N-terminal and C-terminal extensions (La1 and La2) have the respective amino acid sequences SMRVGYYGDFVFDRVLKTDVNKEFQMG (SEQ ID NO 77) (La1) and NPAYGRHMQDAEMFTNAACMALNIWD (SEQ ID NO 78) (La2) which are given in table 2 by SEQ ID NO 7-8.
  • Immuno-repeats comprising VD2 and VD3 can in a similar manner be deduced from FIG. 1 and table 1.
  • La1-Aa2-Aa1-Aa3-La2 defines one of the immune-repeat units. If additionally e.g. VD1 is added to a VD4 unit, this can be described as adding one more sequence to make up a larger immune-repeat unit.
  • the polypeptide of the invention comprises 2, 3, 4, 5, 6, 7 or 8 repeats of immune-repeat units.
  • the outer membrane of Chlamydia sp. can be isolated by treating intact, purified elementary bodies with detergent such as 2% Sarkosyl followed by ultracentrigation (100,000 g for one hour) which will lead to a supernatant with cytosolic components and a pellet containing the outer membrane as previously described 70 .
  • Outer membrane proteins can then be identified by standard protein techniques, e.g. by mass spectrometry after SDS-PAGE.
  • Bacterial surface or membrane proteins comprises trans membrane proteins, secretory and lipoproteins, and anchorless surface proteins. Surface exposed regions on intact bacteria are accessible to antibodies. Methods to identify surface exposed regions of proteins (the ‘surfaceome’ comprise e.g. biotinylation of the membrane proteins in intact bacteria, followed by isolation of the biotin-labelled fraction using streptavidin. The isolated proteins can then be identified by mass spectrometry. Another approach is to treat intact bacteria with a protease, e.g. trypsin (‘shaving’) to cleave surface exposed peptides, followed by collection of the released peptides for identification by mass spectrometry.
  • a protease e.g. trypsin (‘shaving’
  • Variants of outer membrane proteins provided herein describes proteins encoded by the same gene from different serotypes of Chlamydia sp. A variant protein shares significant homology with a reference polypeptide.
  • an “isoform” of protein is under stood as any of several different forms of the same protein e.g. a protein that has the same function but which is encoded by a different gene and may have small differences in its sequence or arises from either single nucleotide polymorphisms, differential splicing of mRNA, or post-translational modifications. Different serotypes of bacteria may have different isoforms of certain proteins.
  • Chlamydia species a bacterium capable of causing the Chlamydia infection in an animal or in a human being. Examples are C. trachomatis, C. pneumoniae and C. muridarum . Also in animals, several infections with Chlamydia sp. are known, e.g. Chlamydia Suis infecting pigs, and Chlamydiaphila abortus which causes abortion in small ruminants (sheep and goats).
  • MOMP variable regions Ct Based on the reactivity of specific mono clonal antibodies against and detailed sequence analysis of the MOMP variable regions Ct can be divided into 15 different serovariants and of these serovariants A, B, Ba and C causes Trachoma, D-K causes sexually transmitted disease (STD), L1-L3 causes Lymphogranuloma venerum, and MoPn ( C. muridarum ) infects mice. Serovariants are sometimes mentioned as serovars or serotypes with the same meaning.
  • immuno-repeats repetitive units of one or more amino acid sequences comprising an immunogenic portion or fragment of an antigen.
  • the units that are repeated can be described as one or more VD regions, that optionally can be extended as described above, that are repeated e.g. 4 examples with three repeats VD4-VD4-VD4, VD4-VD1-VD4-VD1-VD4-VD1, VD4 D -VD4 D -VD4 D , VD4 D -VD4 F -VD4 G , VD4 D -VD3 E -VD4 D -VD3 E -VD4 D -VD3 E .
  • MOMP Major Outer Membrane Protein
  • VD1 of MOMP as defined by Baehr et al (1988) 36 which corresponds to amino acids 91-105 and make up a highly variable region in MOMP from Ct (Seq no 1-6 VD1 from SvD, E, F, G, Ia and J respectively).
  • the extended VD1 region (VD1 ext ) corresponds to amino acids 57-115 and make-up said highly variable region flanked by highly conserved regions in MOMP from Ct (Seq no 9-14 VD1 ext from SvD, E, F, G, Ia and J respectively) ( FIG. 3 ).
  • Variable domain 4 of MOMP as defined by Baehr et al (1988) 36 which corresponds to amino acids 309-338 and make up a highly variable region in MOMP from Ct (Seq no 15-20 VD4 from SvD, E, F, G, Ia and J respectively).
  • the extended VD4 region (VD4 ext ) corresponds to amino acids 282-349 and make-up said highly variable region flanked by highly conserved regions in MOMP from Ct (Seq no 23-28 VD4 ext from SvD, E F, G, Ia and J respectively).
  • linearized in the present invention refers to an amino acid chain of any length, including a full-length protein, oligopeptides, short peptides and fragments thereof, wherein the amino acid cysteine has been substituted with serine in order to hinder the cysteine residues to form disulfide bonds.
  • Neutralizing epitope as used herein is intended an amino acid sequence that defines an antigenic determinant which is bound by an antibody and, in the context of infection, reduces infectivity of a Chlamydial load, e.g. by blocking of the bacterial interaction with host cells, which is important in establishing bacterial infection and disease, facilitating bacterial clearance.
  • Neutralization is to encompass any biological activity of the bacteria, including reduction in the efficiency or ability of the bacterium to establish infection or cause disease or disease symptoms, inhibition of chlamydial EB formation.
  • Antibodies which bind a neutralizing epitope as described above.
  • polypeptide in the present invention should have its usual meaning. That is an amino acid chain of any length, including a full-length protein, oligopeptides, short peptides and fragments thereof, wherein the amino acid residues are linked by covalent peptide bonds.
  • IFN- ⁇ interferon-gamma.
  • the measurement of IFN- ⁇ is used as an indication of an immunological T-cell response.
  • the polypeptide comprises an immunogenic portion or fragment of the polypeptide, such as an epitope for a B-cell or T-cell.
  • the immunogenic portion or fragment of a polypeptide is a part of the polypeptide, which elicits an immune response in an animal or a human being, and/or in a biological sample determined by any of the biological assays described herein.
  • the immunogenic portion or fragment of a polypeptide may be a T-cell epitope or a B-cell epitope.
  • Immunogenic portions or fragments can be related to one or a few relatively small parts of the polypeptide, they can be scattered throughout the polypeptide sequence or be situated in specific parts of the polypeptide. For a few polypeptides epitopes have even been demonstrated to be scattered throughout the polypeptide covering the full sequence.
  • T-cell epitopes are linear, deletion mutants of the polypeptide will, if constructed systematically, reveal what regions of the polypeptide are essential in immune recognition, e.g. by subjecting these deletion mutants e.g. to the IFN- ⁇ assay described herein.
  • Another method utilises overlapping oligopeptides for the detection of MHC class II epitopes, preferably synthetic, having a length of e.g. 20 amino acid residues derived from the polypeptide. These peptides can be tested in biological assays (e.g.
  • the IFN- ⁇ assay as described herein will give a positive response (and thereby be immunogenic) as evidence for the presence of a T cell epitope in the peptide.
  • MHC class I epitopes it is possible to predict peptides that will bind 72 and hereafter produce these peptides synthetic and test them in relevant biological assays e.g. the IFN- ⁇ assay as described herein.
  • the peptides preferably having a length of e.g. 8 to 11 amino acid residues derived from the polypeptide.
  • B-cell epitopes can be determined by analysing the B cell recognition to overlapping peptides covering the polypeptide of interest as e.g. described in Harboe et al 73 .
  • An immunogenic polypeptide is defined as a polypeptide that induces an immune response in a biological sample or an individual currently or previously infected with a chlamydia.
  • a fusion protein two or more polypeptides linked together covalently.
  • the fusion proteins can be produced with superior characteristics of the polypeptide. For instance, fusion partners that facilitate export of the fusion protein when produced recombinantly (e.g. signal peptides), fusion partners that facilitate purification of the fusion protein (e.g. his-tags), and fusion partners which enhance the immunogenicity of the fusion protein are all interesting possibilities.
  • the fusion partner can, in order to enhance immunogenicity, be another polypeptide derived from C. trachomatis , such as a polypeptide, a polypeptide fragment or at least one T-cell epitope or B cell epitope.
  • a pharmaceutical composition is defined as any vaccine (both therapeutic and prophylactic) or any diagnostic reagent.
  • Another part of the invention pertains to a vaccine composition
  • a vaccine composition comprising a fusion protein or a nucleic acid encoding said fusion protein according to the invention.
  • it is preferred that it comprises an immunologically and pharmaceutically acceptable carrier, vehicle or adjuvant.
  • An effective vaccine wherein a fusion protein of the invention is recognized by a mammal including a human being, will decrease bacterial load in target organs, prolong survival times and/or diminish weight loss after challenge with virulent chlamydial bacteria, compared to non-vaccinated individuals.
  • Suitable carriers are selected from the group consisting of a polymer to which the polypeptide(s) is/are bound by hydrophobic non-covalent interaction, such as a plastic, e.g. polystyrene, or a polymer to which the polypeptide(s) is/are covalently bound, such as a polysaccharide, or a polypeptide, e.g. bovine serum albumin, ovalbumin or keyhole limpet haemocyanin.
  • Suitable vehicles are selected from the group consisting of a diluent and a suspending agent.
  • the adjuvant is preferably selected from the group consisting of dimethyl-dioctadecylammonium bromide (DDA), Quil A, poly I:C, aluminium hydroxide, Freund's incomplete adjuvant, IFN ⁇ , IL-2, IL-12, monophosphoryl lipid A (MPL), Trehalose Dimycolate (TDM), Trehalose Dibephenate (TDB) and muramyl dipeptide (MDP), Monomycolyl glycerol (MMG) or a combination hereof.
  • DDA dimethyl-dioctadecylammonium bromide
  • Quil A Quil A
  • poly I:C aluminium hydroxide
  • Freund's incomplete adjuvant IFN ⁇
  • IL-2 monophosphoryl lipid A
  • MPL monophosphoryl lipid A
  • TDM Trehalose Dimycolate
  • TDB Trehalose Dibephenate
  • MDP muramyl dipeptide
  • MMG Monomycolyl
  • the invention also relates to the use of a polypeptide or nucleic acid of the invention for use as therapeutic vaccines as have been described in the literature exemplified by D. Lowry (Lowry et al 1999). Antigens with therapeutic properties may be identified based on their ability to diminish the severity of Ct infection in experimental animals or prevent reactivation of previous infection, when administered as a vaccine.
  • the composition used for therapeutic vaccines can be prepared as described above for vaccines.
  • the present invention describes novel highly immunogenic vaccine antigens with broad antibody based neutralizing capacity that protects against different serovariants of Chlamydia trachomatis .
  • repetitive units of defined fragments from the MOMP antigen provide highly immunogenic molecules which we refer to as immuno-repeats.
  • Vaccination with homologous immuno-repeats containing VD4 extended fragments (covers the VD4 variable domain of MOMP and the adjacent conserved flanking regions) in different adjuvants provides very high antibody titers and we demonstrate that these constructs are much more efficient than immunizing with single units of the VD4 extended fragment.
  • the increased effect can be observed both as markedly increased titer, increased antibody targeting of the surface of the bacteria, increased neutralizing capacity, increased and broadened T cell response and increased protection against a challenge with the homologous strain.
  • the immuno-repeat technology can be utilized also to improve the protection against and neutralization of other serovariants by constructing heterologous immuno-repeats based on VD4 extended fragments from different serovariants such as serovar D, E, F and G ( FIG. 3 ).
  • Heterologous immuno-repeats were highly immunogenic but in addition increased the breadth of the antibody responses which was associated with a broader fine specificity of the antibody response (measured by peptide scans) that targets a more diverse repertoire of linear epitopes within the VD4 region than the homologous immuno-repeats.
  • a strong CMI component e.g.
  • T-cell epitope in an efficient protective immune response against Ct
  • VD4 region N-terminally we can generate immune-repeats that combine the ability to generate high tittered neutralizing antibodies with a strong T cell response clearing residual infection in one construct.
  • immune-repeats can be fused to or mixed with T-cell antigens with vaccine potential and that this combination provide both an early antibody mediated protection against Ct as well as an efficient CMI mediated clearance of residual organisms.
  • MOMP is an important protective antigen with a generally recognized potential in Ct vaccines.
  • the MOMP antigen is however a very complicated antigen to target by vaccines because it has a complex structure with numerous internal disulfide bonds and where important neutralizing epitopes have been exceedingly difficult to expose in recombinant molecules. Adding to this, the MOMP antigen is highly variable and is the basis for the majority of the serovariance found in different strains causing human disease. Any vaccine based on intact MOMP would therefore have to incorporate a number of different versions of the molecule (at least 4-5) to cover the major strains giving rise to disease in humans.
  • the MOMP antigen contains 4 variable regions (VD1-4) of which in particular the VD1 and VD4 contain important neutralizing epitopes but vaccines based on fragments representing these regions have so far failed to induce sufficiently high titers of functional antibodies to have any in vivo effect in animal challenge studies 51 74 .
  • VD1-4 variable regions of which in particular the VD1 and VD4 contain important neutralizing epitopes but vaccines based on fragments representing these regions have so far failed to induce sufficiently high titers of functional antibodies to have any in vivo effect in animal challenge studies 51 74 .
  • the immuno-repeat technology of the present invention solves this problem: By repeating the important variable VD1 and/or VD4 regions flanked by conserved sequences from the MOMP antigen we have obtained immunogens that promote extraordinary levels of functional antibodies. Surprisingly we also demonstrate that the improved immunogenicity can even be achieved in heterologous immuno-repeat constructs that employs variable regions from different serovars interspaced between conserved fragments and that this strategy produces a broadly neutralizing antibody response that protect against different serovariants. Furthermore, do the immuno-repeat technology provide a large number of relevant T cell epitopes that promote T cells with direct effector function as well as the ability to promote accelerated recall responses to the adjacent B cell epitopes.
  • Our invention therefore represents a breakthrough in developing efficient Ct vaccines with a broad response and the ability to neutralize different serovars.
  • BCR B-cell receptor
  • Such antigens are referred to as type 2 T-cell independent B-cell antigens and in artificial systems have been shown to depend on a large number of repeats (typically a minimum of 12-16 75 ), that constitute the minimal epitope and are closely located. This is clearly different from our repeat technology where large fragments (69 amino acids, Mw>7 kDa) are repeated and these fragments contain both B-cell and T-cell epitopes 76 .
  • CT681 amino acid sequences SEQ Amino acid sequences of MOMP ID NO (CT681) from different serovars 68 CT681_SvD 71 CT681_SvE 72 CT681_SvF 73 CT681_SvG 74 CT681_SvIa 75 CT681_SvJ
  • nucleic acid of the invention that is nucleic acid encoding above mentioned fusion proteins, may be used for effecting in vivo expression of immunogenic polypeptides, i.e. the nucleic acid may be used in so-called DNA vaccines as reviewed in Ulmer et al 1993, which is included by reference.
  • Plasmid DNA can then be prepared from overnight cultures of the host strain carrying the plasmid of interest, and purified using e.g. the Qiagen Giga-Plasmid column kit (Qiagen, Santa Clarita, Calif., USA) including an endotoxin removal step. It is essential that plasmid DNA used for DNA vaccination is endotoxin free.
  • the invention also relates to a vaccine comprising a nucleic acid according to the invention, the vaccine effecting in vivo expression of the immunogenic polypeptide by an animal, including a human being, to whom the vaccine has been administered, the amount of expressed polypeptide being effective to confer substantially increased resistance to infections caused by virulent bacteria in an animal, including a human being.
  • the efficacy of such a DNA vaccine can possibly be enhanced by administering the gene encoding the expression product together with a DNA fragment encoding a polypeptide which has the capability of modulating an immune response.
  • One possibility for effectively activating a cellular immune response can be achieved by expressing the relevant immunogenic polypeptide in a non-pathogenic microorganism or virus.
  • a non-pathogenic microorganism or virus are Mycobacterium bovis BCG, Salmonella and Pseudomona and examples of viruses are Vaccinia Virus and Adenovirus.
  • Another important aspect of the present invention is an improvement of the live BCG vaccine presently available, wherein one or more copies of a DNA sequence encoding one or more fusion polypeptides as defined above has been incorporated into the genome of the micro-organism in a manner allowing the micro-organism to express and secrete the fusion polypeptide.
  • the incorporation of more than one copy of a nucleic acid sequence of the invention is contemplated to enhance the immune response.
  • Another possibility is to integrate the DNA encoding the fusion polypeptide according to the invention in an attenuated virus such as the Vaccinia virus or Adenovirus (Rolph et al 1997).
  • the recombinant vaccinia virus is able to enter within the cytoplasma or nucleus of the infected host cell and the fusion polypeptide of interest can therefore induce an immune response, which is envisioned to induce protection against T B.
  • DNA vaccines were developed more than 16 years ago, clinical trials preceding stage I and II in humans are rare. Two veterinary DNA vaccines however, have been licensed; one for West Nile Virus (in horse) and a second for Infectious Hematopoetic Necrosis virus in Salmon. This demonstrates that DNA vaccines can have good protective effects and that new DNA vaccines are not limited by the size of the animal or species. The great success with DNA vaccines observed for the murine model for first generation DNA vaccines did not translate well to humans, nonetheless; researchers have recently demonstrated protective antibodies levels by a single dose of gene gun administrated HA DNA vaccine to humans.
  • DNA vaccines are the inoculation of antigen encoding DNA or RNA as expression cassettes or expression vectors or incorporated into viral vectors with the purpose of inducing immunity to the gene product.
  • DNA vaccines we include all kinds of delivery systems for the antigen encoding DNA or RNA.
  • the vaccine gene can be in form of circular plasmid or a linear expression cassette with just the key features necessary for expression (promotor, the vaccine gene and polyadenylation signal).
  • Delivery systems may most often be naked DNA in buffer with or without adjuvant, DNA coupled to nanoparticles and/or formulated into adjuvant containing compounds or inserted into live viral or bacterial vectors such as Adenovirus, adeno associated virus, alphavirus, poxviruses, herpes virus etc.
  • DNA vaccines hold great promise since they evoke both humoral and cell-mediated immunity, without the same dangers associated with live virus vaccines.
  • DNA vaccines may be delivered to same or different tissue or cells than the live virus that has to bind to specific receptors. The production of antigens in their native forms improves the presentation of the antigens to the host immune system. Unlike live attenuated vaccines, DNA vaccines are not infectious and cannot revert to virulence.
  • DNA vaccines offer many advantages over conventional vaccines. It can be produced in high amounts in short time, abolishing the need for propagation in eggs, it is cost-effective, reproducible and the final product does not require cold storage conditions, because DNA is stable and resistant to the extremes of temperature. All currently licensed inactivated vaccines are efficient at inducing humoral antibody responses but only live attenuated virus vaccines efficiently induce a cytotoxic cellular response as well. DNA vaccines also have this ability and the induced response therefore may better mimic the natural response to viral infection than inactivated vaccines in respect to specificity and antibodies isotypes.
  • DNA vaccines induce an immune response which is comparable to the response acquired by natural virus infection by activating both humoral and cell-mediated immunity.
  • the broad response to DNA vaccines is a result of the encoded genes being expressed by the transfected host cell, inducing both a Th1 and Th2 immune responses.
  • the production of antigens in their native form improves the presentation of the antigens to the host immune system.
  • DNA vaccine administration The two most common types of DNA vaccine administration are saline injection of naked DNA and gene gun DNA inoculations (DNA coated on solid gold beads administrated with helium pressure). Saline intra muscular injections of DNA preferentially generates a Th1 IgG2a response while gene gun delivery tends to initiate a more Th2 IgG1 response. Intramuscular injected plasmids are at risk of being degraded by extracellular deoxyribonucleases, however, the responses induced are often more long-lived than those induced by the gene gun method.
  • Vaccination by gene gun delivery of DNA, to the epidermis, has proven to be the most effective method of immunization, probably because the skin contains all the necessary cells types, including professional antigen presenting cells (APC), for eliciting both humoral and cytotoxic cellular immune responses (Langerhans and dendritic cells). Complete protection from a lethal dose of influenza virus has been obtained with as little as 1 ⁇ g DNA in mice.
  • the standard DNA vaccine vector consists of the gene of interest cloned into a bacterial plasmid engineered for optimal expression in eukaryotic cells.
  • Essential features include; an origin of replication allowing for production in bacteria, a bacterial antibiotic resistance gene allowing for plasmid selection in bacterial culture, a strong constitutive promotor for optimal expression in mammalian cells (promoters derived from cytomegalovirus (CMV) or simian virus provide the highest gene expression), a polyadenylation sequence to stabilise the mRNA transcripts, such as bovine growth hormone (BHG) or simian virus polyadenylation, and a multiple cloning site for insertion of an antigen gene.
  • An intron A sequence improves expression of genes remarkably.
  • DNA vaccine vectors contain unmethylated cytidinephosphate-guanosine (CpG) dinucleotide motifs that may elicit strong innate immune responses in the host.
  • CpG cytidinephosphate-guanosine
  • 2nd generation DNA vaccines 2nd generation DNA vaccines.
  • dicistronic vectors or multiple geneexpressing plasmids have been used to express two genes simultaneously.
  • Specific promoters have been engineered that restrict gene expression to certain tissues, and cytokine/antigen fusion genes have been constructed to enhance the immune response.
  • genes may be codon optimised for optimal gene expression in the host and na ⁇ ve leader sequences may be substituted with optimised leaders increasing translation efficiency.
  • DNA vaccine can be by saline or buffered saline injection of naked DNA or RNA, or injection of DNA plasmid or linear gene expressing DNA fragments coupled to particles, or inoculated by gene gun or delivered by a viral vector (virus like particle) such as Adenovirus, Modified vaccinia virus Ankara (MVA), Vaccinia, Adenoassociated virus (AAV), Alphavirus etc.
  • viral vector virus like particle
  • viruses such as Adenovirus, Modified vaccinia virus Ankara (MVA), Vaccinia, Adenoassociated virus (AAV), Alphavirus etc.
  • an amino acid sequence comprising one or more surface exposed fragments of the same outer membrane protein expressed in a serotype of Chlamydia sp.; and b) two or more additional amino acid sequences which is either the same sequence as defined in a) or is the corresponding surface exposed fragments from a variant of said outer membrane protein expressed in a serotype of Chlamydia sp., which is different from the serotype in a).
  • polypeptide comprising 3 or more different amino acid sequences, where said amino acid sequences each comprises one or more surface exposed fragments from different variants of the same outer membrane protein that varies in different Chlamydia sp. serotypes, said amino acid sequences derived from different Chlamydia sp. serotypes.
  • polypeptide comprising 3 or more repetitions of an amino acid sequence, where said amino acid sequence comprises one or more surface exposed fragments of the same outer membrane protein that varies in different Chlamydia sp. serotypes, said amino acid sequences derived from the same Chlamydia sp. serotype.
  • a polypeptide as described above is provided, wherein the outer membrane protein is MOMP from any serotype.
  • the outer membrane protein may be MOMP from serotype D, E, F, G, Ia or J of Chlamydia trachomatis or C. pneumoniae .
  • a polypeptide may comprise one or more of the variable domains 1, 2, 3, 4 of MOMP. These variable domain sequences may optionally be linearized. These variable domain sequences may comprise the variable domains 4 (VD4) of MOMP, and may be placed next to each other or be spaced with a linker.
  • VD4 variable domains 4
  • a polypeptide comprising an amino acid sequence defined in formula I:
  • sequences may be chosen from SEQ ID NO. 23-28, 49-59.
  • Polypeptides according to any of the above embodiments are also provided additionally comprising a fragment comprising the variable domains 1 (VD1) of MOMP and wherein the amino acid sequences comprising VD1 of MOMP are placed next to each other or are spaced with a linker.
  • VD1 variable domains 1
  • polypeptide comprising an amino acid sequence defined in formula II:
  • sequences may be chosen from SEQ ID NO. 9-14, 45-48.
  • Polypeptides according to any of the above embodiments are also provided comprising a fragment comprising the variable domains 2 (VD2) of MOMP and wherein the amino acid sequences comprising VD2 of MOMP are placed next to each other or are spaced with a linker.
  • VD2 variable domains 2
  • a linker In an embodiment thereof is a polypeptide comprising an amino acid sequence defined in formula III:
  • Polypeptides according to any of the above embodiments are also provided comprising a fragment comprising the variable domains 3 (VD3) of MOMP and wherein the amino acid sequences comprising VD3 of MOMP are placed next to each other or are spaced with a linker.
  • VD3 variable domains 3
  • Polypeptides according to any of the above embodiments are also provided comprising a moiety that facilitate export of the polypeptide when produced recombinantly (e.g. signal peptides), a moiety that facilitate purification of the fusion protein (e.g. his-tags) and/or a moiety which enhance the immunogenicity (e.g. a T cell antigen).
  • the enhancer of immunogenicity is an additional T-cell target which is chosen from a Ct antigen such as CT043, CT004, CT414, CT681 or part hereof.
  • said sequences may be chosen from SEQ ID NO 60-68.
  • polypeptides according to any of the above embodiments, said polypeptide having the ability to
  • nucleic acids encoding a polypeptides according to any of the above embodiments.
  • compositions comprising a polypeptide according to any of the above embodiments or a nucleic acid according to any of the above embodiments.
  • the pharmaceutical compositions may be vaccines.
  • the pharmaceutical compositions may additionally comprise a pharmacologically acceptable carrier, excipient, adjuvant or immune modulator.
  • the pharmaceutical compositions may include an adjuvant selected from DDA/TDB or alum.
  • pharmaceutical compositions may include a carrier that is a virus-like particle.
  • compositions comprising a polypeptide according to any of the above embodiments or a nucleic acid according to any of the above embodiments for prophylactic or therapeutic use against Chlamydia sp. infections, including infections with Chlamydia trachomatis or C. pneumoniae.
  • infections including infections with Chlamydia trachomatis and C. pneumoniae , said method comprising administering a pharmaceutical composition described herein are also provided.
  • Ct serovar D, E and F was propagated in Hela 229 cells (ATCC, Rockville, Md., USA).
  • the cells were cultivated in RPMI 1640 (Gibco BRL, Grand Island, N. Y., USA) media containing 5% fetal calf serum (Gibco BRL; heat inactivated), 1% v/v Hepes, 1% v/v L-glutamine, 1% v/v pyrovate and 10 ⁇ g/ml gentamycine.
  • Semiconfluent monolayers of Hela 229 cells in 6 well-plates were infected with 1.5 inclusion forming unit per cell of Ct serovar E or F in 0.3 ml SPG-buffer/well.
  • the plates were centrifuged 1 hour in a Heraeus Multifuge 3S at 750 g and incubated on a plate rocker for 2 h at 35° C. After 2 h 2 ml cultivation media supplemented with 5% glucose and 1 ⁇ g/ml cycloheximid were added pr. well and the cells were further incubated for 72 h at 37° C. in an atmosphere of 5% CO 2 in humidified air.
  • Chlamydiae were harvested 72 h post infection.
  • the cells were dislodged from the wells with a cell scraper and centrifuged 30 minutes at 35.000 g and 4° C.
  • the pellets were resuspended in HBSS, sonicated on ice and centrifuged at 500 g and 4° C. for 15 minutes.
  • the supernatant was collected and saved on ice and the pellet was resuspended to same volume as before and sonication and centrifugation were repeated.
  • the two supernatants were pooled and centrifuged 30 minutes at 30000 g and 4° C. and the pellet resuspended with a needle and syringe in a SPG buffer (3 ml/Plate).
  • C. trachomatis serovar D, E, F and G are publicly available (NCBI-GenBank). Genes coding for C. trachomatis antigens and fusions where all obtained synthetically for cloning into E. coli bacterial protein expression system (DNA2.0).
  • the pET411 vector was used for expression of the recombinant C. trachomatis protein in E. coli with a Histidine affinity tag.
  • the bacterial host was BL21-STARTTM.
  • E. coli was grown at 37° C. to reach the logarithmic phase OD600 ⁇ 0.5 and protein expression was induced for 4 hours and cells were harvested by centrifugation (6,000 g for 15 min.).
  • coli were lysed using Bugbuster (Novagen) containing Benzonase, rLysozyme and Protease inhibitor Cocktail I (Calbiochem). Inclusion bodies were isolated by centrifugation (10,000 g for 10 min.) The pellet was dissolved in 50 mM NaH2PO4, 0.4M NaCl, 8M Urea, 10 mM Imidazole pH 7.5 and loaded onto HisTrap HP column (Amersham Biosciences) and bound proteins were eluted by applying a gradient of 50 to 500 mM imidazole. Depending on the antigen and fusions isoelectric point they were further purified by ion exchange chromatography. Protein concentrations was determined by BCA protein assay (Pierce).
  • mice Female B6C3F1 mice, 8-12 weeks of age, were obtained from Harlan Laboratories. Animals were housed under standard environmental conditions and provided standard food and water ad libitum. The use of mice is guided by the regulations set forward by the Danish Ministry of Justice (Lov om dyrefors ⁇ g, jvf lovbekendelser nr. 726 of 9. September 1993), and Animal protection committees. A detailed description of the experiments was submitted to and approved by the regional ethical review board (2012-15-2934-00100) held by the applicant.
  • mice were immunized 3 times with 14 days between immunizations.
  • the poly peptides were emulsified in CAF01 and administered simultaneously by the subcutanous (sc) and intranasal (i.n) route.
  • the vaccines given by both routes consisted of 5 ug of peptide (see above) emulsified in 250 ug DDA and 100 ug TDB.
  • DDA/TDB alone, without peptide was injected.
  • FCS fetal calf serum
  • the cells were re-stimulated with individual antigens in 1-10 ⁇ g/ml or VD1 and VD4 peptide pools (2 ⁇ g/ml of each peptide). Stimulation with Concanavalin A (5 ⁇ g/ml) or media as positive control for cell viability and negative control, respectively. After 72 h of incubation at 37° C. in 5% CO 2 , supernatants were harvested and stored at ⁇ 20° C. before use. The amounts of secreted IFN- ⁇ were determined by enzyme-linked immunosorbant assay (ELISA).
  • ELISA enzyme-linked immunosorbant assay
  • mice were bled and serum isolated by centrifugation. Serum was tested by ELISA for reactivity against the Ct surface (SvD, SvE and SvF), against the SvE VD4 monomer, and against peptides (Table 4&5) spanning the VD4 region of SvD, SvE and SvF. Briefly, plates were coated with antigen (1 to 10 ug/ml) at 4° C. in carbonate buffer overnight, blocked with BSA and washed. The plates were then incubated with pre-diluted samples at 4° C. overnight, washed and incubated with a peroxidase conjugated secondary antibody for 1 hr.
  • antigen 1 to 10 ug/ml
  • HaK cells were grown to confluence in 96-well flat-bottom microtiter plates in RPMI 1640 media supplemented with 5% fetal calf serum (Gibco BRL; heat inactivated), 1% v/v Hepes, 1% v/v L-glutamine, 1% v/v pyrovate and 10 ⁇ g/ml gentamycine.
  • Chlamydia stocks were previously titrated and diluted to 3 ⁇ 10 6 IFU/ml for SvE, 2 ⁇ 10 6 IFU/ml for SvD and 5 ⁇ 10 6 IFU/ml for SvF.
  • Serum (pooled) isolated from vaccinated mice was heat inactivated at 56° C. for 1 ⁇ 2 h, diluted 2-4 times and 4-5 fold titrated.
  • 80 ⁇ l of the bacteria suspension was mixed with 80 ⁇ l of serum (+/ ⁇ 20 ⁇ g/ml peptide) and incubated for 30 min. at 3TC on a slowly rocking platform and 50 ⁇ l of the suspension were then inoculated onto the previously prepared HaK cells in duplicates.
  • the media was removed from the HaK monolayers and 100 ⁇ l of the above media supplemented with 0.5% glucose and 10 ⁇ g/ml cyclohexamide was added followed by 50 ⁇ l of the serum/bacteria suspension. Plates were incubated at 35° C. on a slowly rocking platform, then inoculum was removed and 100 ⁇ l of the above media supplemented with 0.5% glucose and 10 ⁇ g/ml cycloheximide was added. The plates were then incubated for 24 h at 3TC in an atmosphere of 5% CO 2 in humidified air. After incubation the medium was removed and the monolayers were fixed with 96% ethanol for 10 min.
  • the plates were centrifuged at 750 ⁇ g for 1 h at RT followed by incubation at 35 C for 2 h. Infection-media was then replaced with fresh media and the cells incubated at 37 C for 30 h. Inclusions were visualised by staining with polyclonal rabbit anti-CT681 serum made in our laboratory, followed by a FITC conjugated swine anti-rabbit Ig (DAKO, Glostrup, Denmark). Background staining was done with propidium iodide (Invitrogen, Taastrup, Denmark). Inclusions were enumerated by fluorescence microscopy observing at least 20 individual fields of vision for each well.
  • Monoclonal anti-mouse CD4 (clone GK1.5) and anti-mouse CD8 (clone YTS156 and YTS169 a gift from Stephen Cobbold) 78, 79 was purified from hybridoma supernatants made in our lab, using HiTrap protein G HP columns (GE-Healthcare Life Sciences, Denmark). The purified IgG was dialyzed against PBS, filtered through 0.22 um filter and protein concentration was determined by OD 280 nm. Mice were depleted of CD4 + or CD8 + T-cells by 4 injections of 250-300 ⁇ g purified anti-CD4 or a mix of anti-CD8 antibodies at day-7, -4, -1 and +2 and +6 relative to the day of infection.
  • CD4 + and CD8 + T cell depletions were verified by FACS analysis on PBMCs at day 1 post infection using a FITC conjugated anti-CD4 antibody (clone RM4-4) and a PE-conjugated anti-CD8 antibody (clone 53-6) (BD Biosciences, Denmark).
  • Chlamydia serovar D stock was previously titrated and diluted to 8 ⁇ 10 4 IFU/ ⁇ l, mixed 1:1 with serum isolated from mice immunized with a heterologous VD4 immuno-repeat SvD-SvE-SvF (CTH89).
  • CTH89 heterologous VD4 immuno-repeat SvD-SvE-SvF
  • mice were challenged i.vag. with 10 ⁇ l of the above mix (4 ⁇ 10 5 IFU of Ct serovar D). Vaginal swabs were obtained at 3, 7 and 10 days after infection.
  • mice/group were immunized 2 times with 14 days between immunizations.
  • the vaccines (2 ⁇ 5 ⁇ g) were emulsified in CAF01 and administered simultaneously by the sc. and i.n routes.
  • blood was collected and antibody levels against the extended VD4 units from SvE and against the bacterial surface of SvE were measured by ELISA.
  • Vaccination with a single VD4 ext unit (monomeric VD4 ext , CTH181) induced lower levels of VD4 ext specific antibodies compared to the level induced after immunization with homologous immuno-repeats composed of 4 VD4 ext repeats of (SvE VD4 ext )*4 ( FIG. 5A ).
  • a construct composed of heterologous immuno-repeats from SvD, E, F and G (CTH518) induced a stronger response to multiple serovars compared to homologous immuno-repeats from SvF
  • Heterologous immuno-repeats promoted an antibody response that recognized the surface of the serovar F strain at the same high level as the response seen with a homologous immuno-repeat from SvF.
  • heterologous immuno-repeat containing extended VD4 regions from the four serotypes SvD, SvE, SvF, SvG
  • we observed a markedly increased titer to the D and E serovariants compared to the homologous immuno-repeat from the serovar F FIG. 6 ).
  • Immunizing with the construct composed of immuno-repeats of heterologous extended VD4's induced a broader response recognizing the surface of multiple serovars (D, E and F) while maintaining the pronounced immunogenicity of the homologous immuno-repeat.
  • Antibodies generated after immunization with the heterologous immuno-repeats recognized a much broader epitope repertoire than serum from animals immunized with the homologous immuno-repeats and the A8-VD4 (7A, B, C and D). This construct was able to cover an epitope repertoire covering both serovar E and F at the level (or better) than achieved by immunizing with homologous immuno-repeats.
  • mice vaccinated with CTH89 were T cell depleted before challenge and the capacity to induce early protection was compared in depleted and non-depleted mice.
  • mice/group were immunized 3 times with 14 days between immunizations.
  • the vaccine (2 ⁇ 5 ⁇ g) was emulsified in CAF01 and administered simultaneously by the sc. and i.n routes.
  • the mice were bleed and antibody responses against chlamydia, the neutralization titer, and in vivo protection with and without T cell depletion were measured.
  • Depletion of the T cell subset eliminated the T cell response to CTH89 ( FIG. 8A ).
  • CTH89 induced a strong antibody response ( FIG. 8B ) that recognized the surface of serovar D ( FIG.
  • Immuno-repeat generates T cell independent early protection against vaginal challenge with Serovar D suggesting an in vivo role of VD4 specific antibodies.
  • mice were mixed with serum isolated from CTH89 immunized mice or serum isolated from naive mice. Depro-provera treated mice were then infected with 4 ⁇ 10 5 bacteria. Mice infected with SvD coated with CTH89 serum efficiently controlled bacterial replication compared to mice challenged with SvD coated with naive serum. Six out of 8 mice were cleared at day 7 and 10 compared to 2 and 3 respectively, in the control group ( FIG. 9 ).
  • MOMP is the target of both humoral and cellular immune-responses but despite the relative success of refolded native MOMP vaccines in generating neutralizing antibodies and protect against infection 54, 56 , experimental vaccines based on recombinant MOMP (rMOMP) have failed.
  • rMOMP recombinant MOMP
  • CTH521 all variable domains
  • CTH521 was fused to CTH518 (CT522) ( FIG. 10 ).
  • mice/group were immunized 3 times with 14 days between immunizations.
  • the vaccines were emulsified in CAF01 and administered simultaneously by the sc. (5 ⁇ g) and i.n. (5 ⁇ g) routes.
  • Post vaccination blood samples were collected and antibodies against the VD4 ext unit, recombinant MOMP and against the bacterial surface were measured.
  • Antibodies generated after immunization with CT522 and CT518 recognized the VD4 region ( FIG. 10A ) and the bacterial surface ( FIG. 10C ) at a much higher level compared to serum isolated after CT521 immunization.
  • Furthermore antibodies form CTH518 and CTH522 were able to neutralize a SvD infection at the same level and much higher than CTH521 ( FIG. 10D ).
  • Vaccination with heterologous immuno-repeats of VD1 ext -VD4 ext 's regions from SvD, SvE and SvF (CTH88) compared to vaccination with a single VD1-VD4 unit from SvD (CTH87).
  • mice/group were immunized 3 times with 14 days between immunizations.
  • the vaccines were emulsified in CAF01 and administered simultaneously by the sc. (5 ⁇ g) and i.n. (5 ⁇ g) routes
  • Antibodies from mice immunized with CTH87 recognized the bacterial surface of both SvD, SvE and SvF ( FIG. 11A ); with the highest titers observed against the homologous SvD strain and the lowest titers against the most distant SvF.
  • Immunizing with immuno-repeats of heterologous VD1 ext -VD4 ext units resulted in significant higher levels of antibodies against the surface of the bacteria compared to the monomeric construct and broadened the response resulting in titers increasing 6-12 times against SvD and SvE and almost 25 times against SvF ( FIG. 11A ).
  • the capacity of these antibodies to neutralize infection in an in vitro neutralizing assay was even more improved as serum from animals immunized with the monomeric VD1 ext -VD4 ext construct from serovar D only had minimal neutralizing capacity compared to the heterologous VD1-VD4 immuno-repeat construct with a neutralization titer of 1:2000 ( FIG. 11B ).
  • vaccination with the heterologous VD1 ext -VD4 ext immuno-repeat construct very efficiently protect against a SvD challenge in a vaginal challenge model ( FIG. 11C ).
  • mice/group were immunized 3 times with 14 days between immunizations.
  • the vaccines (2 ⁇ 5 ⁇ g) were emulsified in CAF01 and administered by the sc. and i.n. routes.
  • the mice were bleed and antibody responses and neutralization titers were measured.
  • Antibodies generated after immunization with CTH91 and CTH88 recognized the VD4 ext region at similar levels ( FIG. 12A ) and serum isolated from both groups were able to neutralize a SvD infection ( FIG. 12B ).
  • FIG. 12C shows that the T cell response to CTH91 was stronger with recognition of both CT414 and CT043
  • mice/group were immunized 3 times with 14 days between immunizations.
  • the vaccine (2 ⁇ 5 ⁇ g) were emulsified in CAF01 and administered simultaneously by the subcutaneous (sc) and intranasal (i.n) route ( FIG. 13 ).
  • Antibodies generated after immunization with CTH89 or the mixture of CTH89 and CTH93 strongly recognized the VD4 regions ( FIG. 13B ) and neutralized the bacteria with similar 50% neutralization titers ( FIG. 13C ).
  • Much reduced levels of VD4 recognition and neutralization was seen after vaccination with the T cell antigen fusion (CTH93, FIG. 13D ) although this molecules also contained MOMP (CT681) and therefore potentially the same neutralizing epitopes.
  • Vaccination with Heterologous Immuno-Repeats Composed of Reduced Length of the VD4 ext regions from SvD, SvE, SvF and SvG
  • mice/group were immunized 3 times with 14 days between immunizations.
  • the vaccines were emulsified in CAF01 and administered simultaneously by the subcutaneous (sc, 5 ⁇ g) and intranasal (i.n, 5 ⁇ g) routes.
  • Splenocytes from 4 mice/group were isolated and the T cell responses to overlapping peptides representing the VD4 ext region ( FIG. 15B ) and the capacity of the serum to neutralize a serovar D and F infection ( FIG. 15C ) were investigated.
  • Much reduced levels of VD4 T cell recognition, and neutralization was seen after vaccination with CTH285 where the VD4 ext regions from the different serovars were reduced with 38 aa.
  • CTH286 on the other hand (each VD4 ext region reduced with 24 aa) induced similar levels of T cell responses and had the same capacity to neutralize a serovar D infection as CTH518.
  • Vaccination with heterologous immuno-repeats composed of extended VD4 ext regions from SvD, SvE, SvF, SvG, SvIa and SvJ.
  • CTH69 SEQ ID NO 47
  • CTH72 SEQ ID NO 48
  • CTH69 was similar to CTH88 but the VD4 ext regions from SvD, SvE and SvF was extended by 12aa N-terminally ( FIG. 16B ).
  • CTH72 also contained VD1 and VD4 ext regions from SvG, SvIa and SvJ.
  • mice were immunized 3 times with 14 days between immunizations.
  • the vaccines were emulsified in CAF01 and administered simultaneously by the subcutaneous (sc, 5 ⁇ g) and intranasal (i.n, 5 ⁇ g) routes.
  • T cell responses to the antigen used for immunization and to peptide pools representing the VD1 and VD4 regions from the different serovars were investigated ( FIG. 16 ). Extending the VD4 ext regions induced a significant higher T cell response (>40.000 ⁇ g/ml) compared to the T cell response obtained with CTH88 ( ⁇ 20.000 pg/ml) ( FIG. 16B ).
  • VD4 ext region enhanced the T cell response compared to CTH88 which led to enhanced protection at day 7 post infection.

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