WO1998042189A1

WO1998042189A1 - POLYPEPTIDES WHICH IMMUNOREACT WITH POLYCLONAL ANTISERA AGAINST $i(H. PYLORI)

Info

Publication number: WO1998042189A1
Application number: PCT/US1998/005823
Authority: WO
Inventors: Kevin P. Killeen; Kimberley Spofford
Original assignee: Avant Immunotherapeutics, Inc.
Priority date: 1997-03-26
Filing date: 1998-03-25
Publication date: 1998-10-01
Also published as: AU6583398A

Abstract

Polypeptides, as well as polynucleotides encoding such polypeptides, are provided which immunoreact with H. Pylori antisera. Such polypeptides are encoded by DNA contained in ATCC Deposit NO. 98372. Such polypeptides are antigenic and are capable of inducing an immune response against H. Pylori.

Description

POLYPEPTIDES WHICH IM UNOREACT WITH POLYCLONAL ANTISERA AGAINST H. pylori

This application claims the priority of United States Provisional Application No. 60/042,404 and 60/044,208, filed on March 26, 1997 and April 23, 1997, respectively.

This invention relates to polypeptides, polynucleotides which encode such polypeptides and the use and production thereof. More particularly, the present invention is directed to polypeptides which irnmunoreact with polyclonal antisera against H. pylori .

Still more particularly, this invention relates to polypeptides and/or polynucleotides which are derived from H. pylori .

Helicobacter pylori (H. pylori) has been implicated as being a cause of peptic ulcer as a result of an infectious disease caused by H. pylori .

As a result, there has been an increasing interest in H. pylori antigens for potential use in the treatment and/or prevention of H. pylori infection.

According to one aspect of the present invention, there is provided polypeptides, as well as polynucleotides encoding such polypeptides, which polypeptides irnmunoreact with H. pylori antisera.

In accordance with another aspect of the present invention, there is provided polypeptides, as well as fragments and analogs thereof, each of which is immunoreactive with H. pylori specific polyclonal antisera. The production of such an antisera is described in the example of this application.

The polypeptides of the present invention are encoded by DNA containing in one of the clones which is part of ATCC Deposit No. 98372.

In accordance with a preferred embodiment of the present invention, the polypeptide is preferably one of the following five polypeptides (or an active fragment or analog thereof) , which polypeptide is immunoreactive with H. pylori polyclonal antisera, and which polypeptide is expressed by DNA contained in one of the clones of ATCC Deposit No. 98372: (1) a polypeptide having a molecular weight of about 18 kDa; (2) a polypeptide having a molecular weight of about 26 kDa; (3) a polypeptide having a molecular weight of about 31 kDa; (4) a polypeptide having a molecular weight of about 220 kDa; and (5) a polypeptide having a molecular weight of about 98 kDa.

The molecular weights, as defined herein, are determined by SDS-PAGE/Western Blotting technique using an 11% gel.

The material deposited as ATCC Deposit No. 98372 on March 26, 1997, with the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Maryland 20852, is a mixture of clones P18, P26/31, P220/98, each of such clones being recombinant E. coli transformed with Super Cos 1 vector (Stratagene) , with DNA obtained from H. pylori inserted at the Bam HI restriction site of such vector.

The clone P26/31 contains DNA which expresses a polypeptide having a molecular weight of 31 kDa and a polypeptide having a molecular weight of 26 kDa which may be a fragment of the 31 kDa polypeptide, each of which is immunoreactive with H. pylori antisera. The P220/98 clone contains DNA which expresses a polypeptide having a molecular weight of 220 kDa and a polypeptide having a molecular weight of 98 kDa which may be a fragment of the 98 kDa polypeptide, each of which is immunoreactive with H. pylori antisera. The deposit (s) have been made under the terms of the Budapest Treaty on the International Recognition of the deposit of micro-organisms for purposes of patent procedure. The strains will be irrevocably and without restriction or condition released to the public upon the issuance of a patent . These deposits are provided merely as convenience to those of skill in the art and are not an admission that a deposit be required under 35 U.S.C. §112. The sequences of the polynucleotides contained in the deposit materials, as well as the amino acid sequences of the polypeptides encoded thereby, are controlling in the event of any conflict with any description of sequences herein. A license may be required to make, use or sell the deposited materials, and no such license is hereby granted.

Thus, in one aspect, the present invention is directed to certain polypeptides , encoded by DNA contained in the clones deposited as ATCC Deposit No. 98372, which polypeptides irnmunoreact with H. pylori specific polyclonal antisera, with such polypeptides preferably being one of the five polypeptides have the hereinabove defined molecular weights, as well as fragments and/or analogs of such polypeptides, as well as the polynucleotides encoding such polypeptides, analogs and fragments, which polynucleotides may be DNA and/or RNA.

The DNA may be double-stranded or single-stranded, and if single stranded, may be the coding strand or non-coding (anti-sense) strand. The coding sequence which encodes the polypeptide may be identical to that of a deposited clone or may be a different coding sequence which coding sequence, as a result of the redundancy or degeneracy of the genetic code, encodes the same, mature polypeptide which immunoreacts with H. pylori antiserum as the DNA of the deposited cDNA, or an immunereactive analog or fragment thereof .

The polynucleotide which encodes for the mature polypeptide which reacts with H. pylori antiserum and which is encoded by the deposited DNA may include: only the coding sequence for the mature polypeptide; the coding sequence for the mature polypeptide and additional coding sequence such as a leader or secretory sequence or a proprotein sequence; the coding sequence for the mature polypeptide (and optionally additional coding sequence) and non-coding sequence, such as sequence 5' and/or 3' of the coding sequence for the mature polypeptide or a fragment or portion of such polynucleotide which encodes an immunoreactive polypeptide.

Thus, the term "polynucleotide encoding a polypeptide" encompasses a polynucleotide which includes only coding sequence for the polypeptide as well as a polynucleotide which includes additional coding and/or non-coding sequence .

The present invention further relates to variants of the hereinabove described polynucleotides which encode for fragments, analogs and derivatives of the polypeptide which reacts with H. pylori antisera encoded by the DNA of one of the deposited clones . The variant of the polynucleotide may be a naturally occurring allelic variant of the polynucleotide or a non-naturally occurring variant of the polynucleotide . The present invention also relates to polynucleotide probes constructed from a portion of the polynucleotide of the invention.

Thus, the present invention includes polynucleotides encoding the same mature polypeptide which reacts with H. pylori antisera encoded by the DNA of the deposited clone as well as variants of such polynucleotides, which variants encode for a fragment, derivative or analog of the polypeptide. Such nucleotide variants include deletion variants, substitution variants and addition or insertion variants .

As hereinabove indicated, the polynucleotide may have a coding sequence which is a naturally occurring allelic variant of the coding sequence. As known in the art, an allelic variant is an alternate form of a polynucleotide sequence which may have a substitution, deletion or addition of one or more nucleotides, which does not substantially alter the function of the encoded polypeptide.

The present invention also includes polynucleotides, wherein the coding sequence for the mature polypeptide may be fused in the same reading frame to a polynucleotide sequence which aids in expression and secretion of a polypeptide from a host cell, for example, a leader sequence which functions as a secretory sequence for controlling transport of a polypeptide from the cell. The polypeptide having a leader sequence is a preprotein and may have the leader sequence cleaved by the host cell to form the mature form of the polypeptide. The polynucleotides may also encode for a proprotein which is the mature protein plus additional 5' amino acid residues. A mature protein having a prosequence is a proprotein and may in some cases be an inactive form of the protein. Once the prosequence is cleaved an active mature protein remains .

Thus, for example, the polynucleotide of the present invention may encode for a mature protein, or for a protein having a prosequence or for a protein having both a presequence (leader sequence) and a prosequence.

Fragments of the polynucleotides of the present invention may be used as a hybridization probe for a library to isolate the full length DNA and to isolate other DNAs which have a high sequence similarity to the gene or similar biological activity. Probes of this type preferably have at least 10, preferably at least 15, and even more preferably at least 30 bases and may contain, for example, at least 50 or more bases. The probe may also be used to identify a DNA clone corresponding to a full length transcript and a genomic clone or clones that contain the complete gene including regulatory and promoter regions . An example of a screen comprises isolating the coding region of the gene by using a DNA sequence of a deposited clone, which DNA encodes a polypeptide which immunoreacts with H. pylori antisera to synthesize an oligonucleotide probe. Labeled oligonucleotides having a sequence complementary to that of a polynucleotide of the present invention are used to screen a library of genomic DNA to determine which members of the library the probe hybridizes to.

The present invention further relates to polynucleotides which hybridize to the hereinabove- described sequences if there is at least 70%, preferably at least 90%, and more preferably at least 95% identity between the sequences in a complementary sense. The present invention particularly relates to polynucleotides which hybridize under stringent conditions to the hereinabove-described polynucleotides . As herein used, the term "stringent conditions" means hybridization will occur only if there is at least 95% and preferably at least 97% identity in a complementary sense between the sequences .

As used herein, "identity" or "identical," when comparing a second sequence to a first sequence, means that the two sequences are properly aligned and then the second sequence is compared with the first sequence over the length of the first sequence. If any base or amino acid of the first sequence does not match an aligned base or amino acid in the second sequence or if the second sequence or the first sequence over the compared aligned length has a base or amino acid which is not aligned with a base or amino acid of the other sequence, then each of such occurrences is counted as a difference. The percent identity is then calculated based on such differences by use of a fraction having as a numerator the difference between the number of bases or amino acids in the first sequence and the number of base or amino acid differences and as a denominator the number of bases or amino acids in the first sequence.

Alternatively, the polynucleotide may have at least 15 bases, preferably at least 30 bases, and more preferably at least 50 bases which hybridize to any part of a polynucleotide of the present invention and which has an identity thereto, as hereinabove described, and which may or may not retain activity. Thus, the present invention is directed to polynucleotides having at least a 70% identity, preferably at least 90% identity and more preferably at least a 95% identity to a polynucleotide which encodes a polypeptide which immunoreacts with H. pylori antisera and which polypeptide is encoded by DNA in one of the deposited clones, as well as fragments thereof, which fragments have at least 15 bases, preferably at least 30 bases and most preferably at least 50 bases, which fragments are at least 90% identical, preferably at least 95% identical and most preferably at least 97% identical to any portion of a polynucleotide of the present invention.

The present invention further relates to a mature polypeptide which immunoreacts with H. pylori antisera and which polypeptide is encoded by DNA in one of the deposited clones, as well as fragments, analogs and derivatives of such polypeptide.

The fragment, derivative or analog of a polypeptide which immunoreacts with H. pylori antiserum and is encoded by DNA of the deposit may be (i) one in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code, or (ii) one in which one or more of the amino acid residues includes a substituent group, or (iii) one in which the mature polypeptide is fused with another compound, such as a compound to increase the half-life of the protein (for example, polyethylene glycol) , or (iv) one in which the additional amino acids are fused to the mature protein, such as a leader or secretory sequence or a sequence which is employed for purification of the mature protein or a proprotein sequence. Such fragments, derivatives and analogs are deemed to be within the scope of those skilled in the art from the teachings herein.

The polypeptides and polynucleotides of the present invention are preferably provided in an isolated form, and preferably are purified to homogeneity. The term "isolated" means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring) . For example, a naturally-occurring polynucleotide or enzyme present in a living animal is not isolated, but the same polynucleotide or protein, separated from some or all of the coexisting materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or proteins could be part of a composition, and still be isolated in that such vector or composition is not part of its natural environment .

The polypeptides of the present invention include the immunoreactive polypeptides encoded by DNA of the deposited clones (in particular the mature polypeptides) as well as polypeptides which have at least 70% similarity (preferably at least 70% identity) to such polypeptides and more preferably at least 90% similarity (more preferably at least 90% identity) to such polypeptides and still more preferably at least 95% similarity (still more preferably at least 95% identity) to such polypeptides and also include portions of such polypeptides with such portion of the polypeptide generally containing at least 30 amino acids and more preferably at least 50 amino acids.

As known in the art "similarity" between two polypeptides is determined by comparing the amino acid sequence and its conserved amino acid substitutes of one polypeptide to the sequence of a second polypeptide.

A variant, i.e. a "fragment", "analog" or "derivative" polypeptide, and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions, fusions and truncations, which may be present in any combination.

Among preferred variants are those that vary from a reference by conservative amino acid substitutions . Such substitutions are those that substitute a given amino acid in a polypeptide by another amino acid of like characteristics. Typically seen as conservative substitutions are the replacements, one for another, among the aliphatic amino acids Ala, Val, Leu and lie; interchange of the hydroxyl residues Ser and Thr, exchange of the acidic residues Asp and Glu, substitution between the amide residues Asn and Gin, exchange of the basic residues Lys and Arg and replacements among the aromatic residues Phe, Tyr.

Most highly preferred are variants which retain the same biological function and activity as the reference polypeptide from which it varies.

Fragments or portions of the polypeptides of the present invention may be employed for producing the corresponding full-length polypeptide by peptide synthesis; therefore, the fragments may be employed as intermediates for producing the full-length polypeptides. Fragments or portions of the polynucleotides of the present invention may be used to synthesize full-length polynucleotides of the present invention.

The present invention also relates to vectors which include polynucleotides of the present invention, host cells which are genetically engineered with polypeptides or vectors of the invention and the production of polypeptides of the invention by recombinant techniques.

Host cells are genetically engineered (transduced or transformed or transfected) with the vectors of this invention which may be, for example, a cloning vector or an expression vector. The vector may be, for example, in the form of a plasmid, a viral particle, a phage, etc. The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the genes of the present invention. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.

The polynucleotides of the present invention may be employed for producing polypeptides by recombinant techniques. Thus, for example, the polynucleotide may be included in any one of a variety of expression vectors for expressing an enzyme. Such vectors include chromosomal, nonchromosomal and synthetic DNA sequences, e.g., derivatives of SV40; bacterial plasmids; phage DNA; baculovirus; yeast plasmids; vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, and pseudorabies . However, any other vector may be used as long as it is replicable and viable in the host.

The appropriate DNA sequence may be inserted into the vector by a variety of procedures . In general , the DNA sequence is inserted into an appropriate restriction endonuclease site(s) by procedures known in the art. Such procedures and others are deemed to be within the scope of those skilled in the art .

The DNA sequence in the expression vector is operatively linked to an appropriate expression control sequence (s) (promoter) to direct mRNA synthesis. As representative examples of such promoters, there may be mentioned: LTR or SV40 promoter, the E. coli. lac or trp, the phage lambda P_L promoter and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses. The expression vector also contains a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression.

In addition, the expression vectors preferably contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli.

The vector containing the appropriate DNA sequence as hereinabove described, as well as an appropriate promoter or control sequence, may be employed to transform an appropriate host to permit the host to express the protein.

As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as E. coli. Streptomyces , Bacillus subtilis; fungal cells, such as yeast; insect cells such as Drosophila S2 and Spodoptera Sf9; animal cells such as CHO, COS or Bowes melanoma; adenoviruses ; plant cells, etc. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein.

More particularly, the present invention also includes recombinant constructs comprising one or more of the sequences as broadly described above. The constructs comprise a vector, such as a plasmid or viral vector, into which a sequence of the invention has been inserted, in a forward or reverse orientation. In a preferred aspect of this embodiment, the construct further comprises regulatory sequences, including, for example, a promoter, operably linked to the sequence. Large numbers of suitable vectors and promoters are known to those of skill in the art, and are commercially available . The following vectors are provided by way of example; Bacterial: pQE70, pQE60, pQE-9 (Qiagen) , pDIO, psiX174, pBluescript II KS, pNH8A, pNH16a, pNH18A, pNH46A (Stratagene) ; ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia); Eukaryotic: pSV2CAT, pOG44 , pXTl, pSG (Stratagene) pSVK3 , pBPV, pMSG, pSVL (Pharmacia) . However, any other plasmid or vector may be used as long as they are replicable and viable in the host .

Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers . Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lad, lacZ, T3 , T7, gpt, lambda P_R/ P and trp. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art .

In a further embodiment, the present invention relates to host cells containing the above-described constructs. The host cell can be a higher eukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell . Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-Dextran mediated transfection, or electroporation (Davis, L., Dibner, M., Battey, I., Basic Methods in Molecular Biology, (1986)).

The constructs in host cells can be used in a conventional manner to produce the gene product encoded by the recombinant sequence. Alternatively, the enzymes of the invention can be synthetically produced by conventional peptide synthesizers.

Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al . , Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989), the disclosure of which is hereby incorporated by reference.

Transcription of the DNA encoding the enzymes of the present invention by higher eukaryotes is increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp that act on a promoter to increase its transcription. Examples include the SV40 enhancer on the late side of the replication origin bp 100 to 270, a cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers .

Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of E. coli and S . cerevisiae TRPl gene, and a promoter derived from a highly-expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3 -phosphoglycerate kinase (PGK) , a-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated enzyme . Optionally, the heterologous sequence can encode a fusion enzyme including an N-terminal identi ication peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product.

Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together with suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host. Suitable prokaryotic hosts for transformation include E. coli. Bacillus subtilis. Salmonella typhimurium and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus , although others may also be employed as a matter of choice.

As a representative but nonlimiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017) . Such commercial vectors include, for example, pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM1 (Promega Biotec, Madison, WI, USA) . These pBR322 "backbone" sections are combined with an appropriate promoter and the structural sequence to be expressed.

Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter is induced by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period. Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification.

Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze- thaw cycling, sonication, mechanical disruption, or use of cell lysing agents, such methods are well known to those skilled in the art .

Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described by Gluzman, Cell, 23:175 (1981), and other cell lines capable of expressing a compatible vector, for example, the C127, 3T3 , CHO, HeLa and BHK cell lines. Mammalian expression vectors will comprise an origin of replication, a suitable promoter and enhancer, and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5' flanking nontranscribed sequences . DNA sequences derived from the SV40 splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements .

The polypeptides can be recovered and purified from recombinant cell cultures by methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps .

The polypeptides of the present invention may be a naturally purified product, or a product of chemical synthetic procedures, or produced by recombinant techniques from a prokaryotic or eukaryotic host (for example, by bacterial, yeast, higher plant, insect and mammalian cells in culture) . Depending upon the host employed in a recombinant production procedure, the polypeptides of the present invention may be glycosylated or may be non- glycosylated. Polypeptides of the invention may or may not also include an initial methionine amino acid residue.

The polypeptides of the present invention, in particular, the polypeptides which irnmunoreact with H. pylori antisera, and which are encoded by DNA of the deposited clones, as well as their fragments, derivatives or analogs, may be used as an immunogen to produce antibodies against H. pylori . These antibodies can be, for example, polyclonal or monoclonal antibodies. The present invention also includes chimeric, humanized, and single- chain antibodies, as well as fragments, thereof. Such antibodies may be produced by procedures generally known in the art .

The polypeptides or antibodies generated against the polypeptides may be employed in immunoassays of the type known in the art for detecting the presence of H. pylori and/or antibodies against H. pylori .

Polypeptides of the present invention are antigens and, therefore, may be employed to induce in a host an immune reaction against H. pylori .

Thus, in accordance with another aspect of the present invention, the polypeptides of the present invention, or polynucleotides encoding such polypeptides, may be employed to induce an immune response, in a host, against H. pylori . The host is a mammal which may be human or non-human. Such polypeptides and polynucleotides are preferably employed to induce a protective immune response against H. pylori infection and, therefore, may be employed for treatment and/or prevention of H. pylori infection.

The polypeptide of the present invention, when used for such a purpose, is generally combined with a pharmaceutically effective carrier and is administered in an amount effective to reduce and/or prevent H. pylori infection. In general, such polypeptide would be administered in an amount from 10 μg to 500 mg, and such administration, for example, may be parenteral, oral or intranasal administration.

In accordance with another aspect of the present invention, a polynucleotide, encoding a polypeptide of the present invention is employed to produce a recombinant, non-toxigenic organism; in particular, a bacterial organism, which expresses a polypeptide of the present invention. As representative examples of such organisms, there may be mentioned V. cholerae and S. typhi . Thus, for example, a wild-type strain of V. cholerae or S. typhi may be attenuated by procedures known in the art to produce a live bacterial strain which has been attenuated to render the bacteria non-toxigenic. Such non-toxigenic recombinant strains may be employed as a live vaccine for expressing, in vivo, a polypeptide of the present invention to induce a protective immune response .

Although the present invention will be further described with respect to the use of V. cholera , it is to be understood that such teachings are equally applicable to other organisms .

The non-toxigenic V. cholerae which is employed for producing a recombinant non-toxigenic V. cholerae in accordance with the present invention is V. cholerae of the type which has been developed for potential use as a vaccine against V. cholerae. As known in the art, such V. cholerae is a live, attenuated V. cholerae which has been attenuated to render such V. cholerae non-toxigenic. The V. cholerae which is employed for producing a recombinant vaccine in accordance with the present invention may be an attenuated 01 strain or a non-01 strain.

As known in the art, wild-type V. cholerae strains are attenuated for example, to render same non-toxigenic by a genetic deletion which removes three toxins (cholerae toxin, zonula occludens toxin, and accessory cholerae enterotoxin) , and which may be further attenuated by removal of a colonization factor (core encoded pilin) , and RSI (a site-specific toxin acquisition cassette) . Such attenuated V. cholerae strains have been designated as Peru-2 and Bengal-2.

In another attenuated strain, the strains hereinabove described were engineered to reintroduce into the recA locus the gene encodings ctxB, which yields the strains referred to as Peru-3 and Bengal-3.

Another non-toxigenic strain of V. cholerae which is a spontaneous non-motile filamentous isolate of Peru-3 has also been isolated as designated as Peru-14. Non-motile isolates of Peru-3 and Bengal-3 have also been identified which have been designated as Peru-15 and Bengal-15.

Non-toxigenic strains of V. cholerae are generally known in the art, and such strains may be employed in the present invention. Such strains include but are not limited to: Bengal -2, Bengal -3 , Bengal -15, Peru-2, Peru-3 , Peru-14 , Peru-15, Bah-2, Bah- 15 , Bang-2, Bang- 3 , and Bang- 15.

In accordance with an aspect of the present invention, a non-toxigenic strain of V. cholerae is transformed with a polynucleotide encoding a polypeptide of the invention which induces an immune response against H. pylori . The polynucleotide encoding such polypeptide is incorporated into a suitable vector for transformation of the V. cholerae. Such vector may be one which integrates the polynucleotide into the chromosome of V. cholerae or may be one which provides for extrachromosomal transformation. Thus, the present invention contemplates a recombinant non- toxigenic V. cholerae in which a polynucleotide encoding a polypeptide which induces an immune response against H. pylori is present either extrachromosomally or integrated into the chromosome of the V. cholorae. The polypeptides which are expressed from the V. cholerae in accordance with the present invention may be one of the polypeptides of the invention which functions as an antigen or immunogen to induce an immune response in a host and in particular in a human host.

Thus, in accordance with the present invention, a polynucleotide encoding such antigens or immunogens is placed in an appropriate vector, and such vector is employed for transforming a non-toxigenic strain of V. cholerae to provide a vaccine for use in the treatment and/or prevention of H. pylori infection.

The vector is provided with an appropriate promoter for expression of the polypeptide in V. cholerae. The vector which is employed is one which functions in V. cholerae to provide for expression of the polypeptide which induces an immune response against H. pylori . The promoter, in a preferred embodiment, is derived from V. cholerae. A preferred promoter is a V. cholerae heat shock promoter known as htpGp. The vector or plasmid generally also includes a suitable marker to permit selection of recombinant strains .

Non-toxigenic V. cholerae which has been transformed to express a polypeptide which provides an immune response against H. pylori and in particular a protective immune response may be employed as an oral vaccine for treatment and/or prevention of H. pylori infection. The vaccine is employed in an amount effective to treat or prevent H. pylori infection. In general, the recombinant V. cholerae is administered in a dosage of from about 10⁷ to 10⁸ colonry forming units. The vaccine may be administered in a single dose or in multiple doses; e.g., biweekly.

The recombinant V. cholerae in accordance with the present invention may be incorporated into an appropriate pharmaceutically acceptable carrier and in particular for oral delivery. The carrier may be a liquid; e.g., and mixture of bicarbonate and ascorbate or a solid such as an enteric coated capsule.

As hereinabove indicated, the non-toxigenic V. cholerae is transformed by use of an appropriate vector, which in one embodiment integrates the polynucleotide expressing the appropriate antigen or immunogen into the chromosome of the V. cholerae. Such vector or plasmid may be employed to facilitate site specific integration onto the chromosome; for example, at either the lacZ, recA or irgA loci (Published PCt Application WO 94/01780) . In accordance with a preferred embodiment, when integration is desired, the vector is capable of inserting the polynucleotide encoding the polypeptide which provides an immune response against H. pylori into the V. cholerae chromosome at the lacZ locus .

Integrating vectors may also be employed for providing transformation in which the appropriate polypeptide is expressed from extrachromosomal DNA. Thus, after the transformation, an appropriate selection procedure is employed to select V. cholerae in which the polynucleotide has been integrated into the chromosome or V. cholerae in which the DNA is maintained as an extrachromosomal plasmid.

Thus, for example, in one embodiment, an attenuated V. cholerae in which the recA gene is deleted is used for preparation of a recombinant V. cholerae in which the polypeptide is expressed from an extrachromosomal plasmid.

In another embodiment, an attenuated V. cholerae which includes the recA gene is used for preparation of a recombinant V. cholerae in which the polypeptide is expressed from DNA integrated into the V. cholerae chromosome .

In both cases, the same vector may be employed, e.g., a plasmid which includes a lacZ sequence. In the case where the recA gene is deleted, the polynucleotide is not integrated into the chromosome; however, when such vector is used for transformation of attenuated V. cholerae which includes recA gene, integration can occur at the lacZ locus and a recombinant V^". cholerae in which the DNA is integrated at the lacZ locus can be selected.

Thus in accordance with an aspect of the present invention, there is provided a product and a process for treatment and/or prevention of H. pylori infection wherein a non-toxigenic V. cholerae strain is transformed with a polynucleotide which encodes a polypeptide of the invention which provides an immune response against H. pylori . Such recombinant non-toxigenic V. cholerae strain may be employed as a live oral vaccine for the treatment and/or prevention of H. pylori infection. In accordance with the present invention, more than one copy of a polynucleotide encoding a polypeptide which induces an immune response may be integrated into the chromosome of V. cholerae. Thus, for example, such polynucleotide may be integrated into more than one locus in the chromosome; e.g., lacZ, recA, and irgA.

The invention will be further described with respect to the following examples; however, the scope of the invention is not to be limited thereby:

EXAMPLE Characterization of H. pylori Claudio.

H. pylori Claudio strain was streaked on Trypticase Soy agar with 5% defibrinated sheep blood and incubated at 37°C for 48 to 72 hours in an anaerobic chamber. Cells were collected from plates with a sterile swab stick and suspended in 1 ml Brucella broth. The broth culture was deemed pure by: i) colonial morphology, ii) wet mount microscopy, iii) Gram stain, iv) urease⁺, and, v) agglutination of cells with anti-whole-cell helicobacter polyclonal rabbit sera. The characterized Claudio strain was cell-banked in 10% glycerol and stored in Cryovials in liquid nitrogen.

Harvesting DNA from Claudio .

Two hundred ml Brucella broth supplemented with 5% fetal calf serum, TVP antibiotics (Trimethoprim, Vancomycin and Polymixin-B) and anti-fungal Amphotericin, was inoculated with the characterized Claudio cell suspension to OD₆₀₀= 0.05-0.1. The air in the flask was replaced with a gas mixture containing 6% 0₂, 10% C0₂, and 84% N₂. The flask was incubated for 18-24 hours at 37°C with shaking (150 rpm) . Cells from this preparation were used to harvest chromosomal DNA (11) . Chromosomal DNA was digested with Sau3A and BamHI and electrophoresed on 0.7% agarose gel . Southern blot analysis of chromosomal DNA probed with a H. pylori ureAB gene exhibited a strong hybridization signal indicating that the chromosomal DNA was H. pylori in origin. Cosmid cloning of Claudio chromosomal DNA.

A DNA cosmid library of H. pylori Claudio chromosomal DNA was made using the SuperCosl cosmid vector (Stratagene) . Chromosomal DNA was partially digested with Sau3A for 3 minutes and phosphatased. Vector SuperCosl cosmid DNA was prepared by digestion with Xbal , phosphatase treatment, and digestion with BamHI . Insert and vector DNA were ligated at 4°C overnight and packaged into Gigapacklll Gold packaging extract per manufacturer's instructions. Titration of the unamplified cosmid library in E. coli XL1B- MR was 3.4xl0⁴cfu/ml . Amplification of the cosmid library generated clones at 5xl0⁷cfu/ml. The efficiency of packaging was calculated and in accord with the value indicated in the manufacturer's manual.

Rabbit Immunization with H. pylori Claudio whole-cells.

A rabbit was immunized six times intramuscularly over a 32-day period with 7xl0⁶, Ixl0⁷,2xl0⁷, 3xl0⁷, and twice with 5xl0⁷ cfu of H. pylori cells fixed with 2% formalin. On days 26 and 40, the rabbit was bled and sera was adsorbed with an E. coli XL1B-MR cell lysate.

Screening the H. pylori cosmid library using H. pylori - specific polyclonal anti-sera.

The adsorbed anti-H. pylori Claudio whole-cell polyclonal sera (1:1000 dilution) was used to screen the cosmid library by colony immunoblot. Approximately 50,000 cfu were lysed with 3% BSA/400 ug/mL lysozyme/1 U/mL DNase in 50 mM Tris-HCl/150 mM NaCl/5 mM MgCl₂ before the immunological screen. An anti-rabbit IgG-alkaline phosphatase (1:1000) was used as the secondary antibody/conjugate. Initially, a total of twenty immunoreactive colonies were identified. Eight of the twenty clones maintained cross-reactivity with the polyclonal rabbit sera during enrichment and purification. Those clones were re-streaked for individual colonies, picked, amplified in LB broth containing ampicillin and frozen in 10% glycerol at -80°C. Characterization of H. pylori recombinant protein clones

P_1&J P_26/3ij__and__P₂₂o_/98 by Western blot analysis .

Whole-cell lysates were isolated from each cosmid clone and Western blotted using the polyclonal anti-whole- cell rabbit sera. Three of the eight clones that were immunopositive by colony immunoblot exhibited specific molecular mass bands which were cross-reactive with the anti sera. Clone P₁₈ produced an 18 kDa antigen, P_26/31 26 and 31 kDa antigens, and P₂₂o_/98 produced 220 and 98 kDa antigens. Western blots of whole-cell lysates digested with Proteinase-K (0.1 mg/mL) overnight at 37°C did not detect any immunoreactive antigens which indicates the proteinaceous nature of the immunoreactive bands .

The specific regions of the H. pylori DNA contained in the clones and which encode the antigens are determined by subcloning of the cosmid DNA from recombinant clones Pι₈, P_26/3ι, and P₂₂₀₉₈. Cosmid DNA is purified by Qiagen midi-prep columns and subsequently digested with restriction endonucleases (e.g., EcoRI, Bgll, Hindlll, etc.). DNA fragments resulting from such digestions are ligated into a cloning vector (e.g., pBluescript II KS, pKK223-3, pUC19, etc.) and digested with the corresponding restriction endonuclease . The products of the ligations are transformed into E. coli XL1B-MR. Recombinant sub-clones are evaluated for expression of the antigen by colony immunoblot as described previously. The immunoreactive clones are isolated, purified, and screened for cross- reactivity with the polyclonal anti-whole-cell sera by Western blot . This subcloning process determines the minimum size of H. pylori DNA contained in a deposited clone which is needed for expression of an antigen which is immunoreactive with H. pylori anti sera and which encodes an antigen having the noted molecular weights . In addition, such sub-cloning identifies fragments of such antigens which irnmunoreact with the polysera. Following sub-cloning, the H. pylori DNA producing an immunoreactive polypeptide is sequenced.

The gene(s) encoding the protein (s) detected by Western immunoblot with the polyclonal anti-whole-cell are also identified by sequencing the amino terminus of the antigen. Whole-cell lysates of the recombinant cosmid clones are separated by SDS-PAGE and blotted to polyvinylidene difluoride (PVDF) membrane. Proteins are stained with Coomassie blue and the bands corresponding to those reactive by immunoblot are excised and sequenced using an automatic protein sequencer. Degenerate oligonucleotides are created from the amino acid sequence and used to probe E. coli recombinant cosmids by DNA hybridization and Southern blot analyses. The DNA of the positive clones is then sequenced.

Identification of P, g_. P_26/3, , and P-,-,_n/Q« recombinant protein clones.

The deposit made to American Type Culture Collection is a mixture of 3 recombinant clones of Escherichia coli XL1B-MR (P₁₈, P₂₆₃i, and P_220/98) which harbor cosmids expressing Helicobacter pylori protein antigens. Cells were grown in Luria Bertani (LB) broth supplemented with ampicillin (50 μg/ml) with glycerol added to final concentration of 15%. In order to isolate each clone, a sample of the frozen vial should be streak plated for individual colonies on LB agar supplemented with ampicillin (50 μg/ml) and incubated at 37°C for 18 hr. Ten to twenty colonies should be picked aseptically, amplified in LB broth, collected by centrifugation, lysed and Western blotted using the anti-H. pylori whole-cell sera originally used to identify the clones . The identity of the three different strains can be discerned by immunoreactive protein band molecular weights. P₁₈ lysates will contain an 18 kDa immunoreactive band, P_26/31 will contain bands of 26 and 31 kDa and P_220/98 will contain two bands of 220 and 98 kDa. Numerous modifications and variations of the present invention are possible in light of the above teachings and, therefore, within the scope of the impending claims, the invention may be practiced otherwise than as particularly described.

Claims

WHAT IS CLAIMED IS:

1. An isolated polynucleotide comprising: a polynucleotide which is at least 90% identical to a polynucleotide sequence encoding a polypeptide which is immunoreactive with H. pylori antisera wherein said polypeptide is produced by a member selected from the group consisting of DNA of clone P18, DNA of clone P26/31 and DNA of clone P220/98, said clones being contained in ATCC Deposit No. 98372.

2. The isolated polynucleotide of claim 1 comprising a polynucleotide which is at least 95% identical to said polynucleotide sequence.

3. The isolated polynucleotide of claim 2 wherein said member is DNA of clone P18.

4. The isolated polynucleotide of claim 2 wherein said member is DNA of clone P26/31.

5. The isolated polynucleotide of claim 2 wherein said member is DNA of clone P220/98.

6. The isolated polynucleotide of claim 1 comprising said polynucleotide sequence.

7. A recombinant cell containing the polynucleotide of claim 1.

8. A recombinant cell containing the polynucleotide sequence of claim 6.

9. A recombinant vector containing the polynucleotide of claim 1.

10. A recombinant vector containing the polynucleotide of claim 6.

11. A process for producing a polypeptide comprising expressing a polypeptide from the cell of claim 7.

12. A process for producing a polypeptide comprising expressing a polypeptide from the cell of claim 8.

13. An isolated polypeptide comprising a polypeptide which immunoreacts with H. pylori antisera and which is at least 95% identical to a polypeptide encoded by a member selected from the group consisting of DNA of clone P18, DNA of clone P26/31 and DNA of clone P220/98, said clones being contained in ATCC Deposit No. 98372.

14. The polypeptide of claim 13 wherein said member is DNA of clone P18.

15. The polypeptide of claim 13 wherein said member is DNA of clone P26/31.

16. The polypeptide of claim 13 wherein said member is DNA of clone P220/98.

17. The isolated polypeptide of claim 13 comprising a polypeptide encoded by said member.

18. A fragment of the polypeptide of claim 1 comprising at least 30 consecutive bases thereof.

19. A process for inducing an immune response in a mammal against H. pylori comprising: administering to a mammal at least one polypeptide of Claim 1 in an amount effective to produce an immune response .