The present invention relates to the field of medicine, in particular to the fields of immunology, medical microbiology and vaccinology. The invention pertains to modified LPS molecules that can be obtained from bioengineered meningococcal LPS mutants and that are useful as part of a whole cell vaccine, OMV vaccine or as purified LPS or lipid A molecules.

Background of the invention

Lipopolysaccharides (LPS), also known as bacterial endotoxin, are an abundant component of the outer membrane of gram-negative bacteria. During infection with gram-negative bacteria, LPS or more precisely the lipid A part of LPS activates the host's innate immune system (1-3). This activation occurs through binding of LPS to the pattern recognition receptor Toll-like receptor 4/myeloid differentiation factor 2 (TLR4/MD-2) complex, which starts a signalling cascade leading to cytokine production necessary to clear the infection (3,4). However, overstimulation of this signalling cascade and overproduction of the inflammatory cytokines is detrimental to the host and can lead to life-threatening conditions such as septic shock (5, 6).

For complete activation of the TLR4/MD-2 complex, a lipid A structure with six acyl chains and two phosphate groups is critical (7). However, many bacterial species carry enzymes that can modify their lipid A structure either by changing the number of acyl chains or phosphate groups resulting in altered activation of the TLR4/MD-2 complex (8), even to the point of being an antagonist instead of an agonist as is observed for the tetra-acylated E. coli lipid IVa structure (7,9).

The TLR4/MD-2 complex is unique among the TLR family of receptors because it can signal through both the MyD88 as well as the TRIF pathway. Modified lipid A structures can induce select signalling by preferential recruitment of the MyD88 or TRIF adaptor molecules. Preferential signalling through the TRIF pathway, which triggers production of type I interferons, is thought to be important for vaccine adjuvants (10, 11). Monophosphoryl lipid A (MPLA) is an example of a modified lipid A that triggers a TRIF-biased signalling (11). MPLA is a heterogeneous lipid A mixture from Salmonella Minnesota, which has been chemically detoxified and is approved for the use as adjuvant in some vaccines (12). The main component of MPLA consists of a hexa- acylated 4'-monophosphoryl lipid A. Use of MPLA has the disadvantage that for its production a chemical treatment is needed in addition to LPS isolation from the bacteria and it only consists of the lipid A portion of LPS, making it water insoluble.

Neisseria meningitidis typically produces hexa-acylated LPS with phosphate and phosphoethanolamine groups appended to the 1 and 4' position of the lipid A (13, 14). Heterologous expression of LPS modifying enzymes such as PagL or deletion of lipid A biosynthesis enzymes such as LpxLl and LpxL2 has been used to detoxify the highly active meningococcal LPS (13, 15). Deletion of LpxLl was shown to be an advantageous method for detoxifying meningococcal LPS when making meningococcal outer membrane vesicle vaccines, without the need to use a detergent to reduce excess LPS- related reactogenicity (16). However, the activity of this modified LPS has been reduced to the point that it barely induces any activation of the TLR4/MD-2 complex on human cells, making it less applicable as a stand-alone vaccine adjuvant (17). Heterologous expression of pagL inN meningitidis results in a different attenuated penta-acylated LPS structure, which is still capable of inducing TLR4 activation and induces a TRIF-biased cytokine production on a human monocytic cell line (13).

Pupo et al. (2014, J. Biol. Chem. 289: 8668-8680) describe the structural analysis and modified agonist properties of penta-acylated mutant lipid A from either a AlpxLl or a pagL ⁺ single mutant in Neisseria meningitidis.

It is an object of the invention of providing modified LPS molecules useful as adjuvants, which have the optimal balance between retaining a sufficient amount of immune activation while limiting toxic side effects. The present invention addresses this problem by heterologous expression of LPS modifying enzymes in combination with targeted deletion of lipid A biosynthesis genes to provide a diverse set of meningococcal LPS structures with a broad range of TLR4/MD-2 activation capacities that are useful in a variety of prophylactic and therapeutic applications. Summary of the invention

In a first aspect, the invention relates to a neisserial LPS having a tetra-acylated lipid A moiety, wherein the tetra-acylated lipid A moiety is modified as compared to the lipid A moiety of a wild-type neisserial LPS in that it lacks one of the secondary acyl chains and lacks a primary acyl chain on the 3-position of the glucosamine on the reducing end of the lipid A moiety. Preferably, the LPS, except for the tetra-acylated lipid A moiety, has the structure of LPS of Neisseria meningitidis, Neisseria gonorrhoeae or Neisseria lactamica, whereby more preferably, the Neisseria meningitidis, Neisseria gonorrhoeae or Neisseria lactamica is at least one of IgtB ^' and galE ^~ and whereby most preferably, the Neisseria meningitidis is at least one of serogroup B and immunotype L3.

In a preferred neisserial LPS according to the invention, the tetra-acylated lipid A moiety has the structure of formula (I) or (II) (see below), wherein Ri and R ₂ , independently, are either -P(0)(OH) ₂ , -[P(0)(OH)-0] ₂ -H, -[P(0)(OH)-0] ₂ - CH ₂ CH ₂ NH ₂ , -[P(0)(OH)-0] ₃ -CH ₂ CH ₂ NH ₂ , -[P(0)(OH)-0] ₃ -H or -P(0)(OH)-0- CH ₂ CH ₂ NH ₂ , and wherein, preferably Rl and R2, independently, are either -P(0)(OH) ₂ , -[P(0)(OH)-0] ₂ -H, -[P(0)(OH)-0] ₂ -CH ₂ CH ₂ NH ₂ or -[P(0)(OH)-0] ₃ -CH ₂ CH ₂ NH ₂ .

A particularly preferred neisserial LPS according to the invention is an LPS wherein the lipid A moiety lacks the secondary acyl chain bound to the primary acyl chain attached to the glucosamine on the non-reducing end of the lipid A moiety and lacks a primary acyl chain on the 3-position of the glucosamine on the reducing end of the lipid A moiety, or wherein the lipid A moiety has the structure of formula (I).

In a second aspect, the invention relates to a genetically modified bacterium of the genus Neisseria, wherein the bacterium comprises: a) a genetic modification that reduces or eliminates the activity of a lipid A biosynthesis lauroyl acyltransferase encoded by an endogenous IpxLl gene or an endogenous lpxL2 gene; and, b) a genetic modification that confers to the bacterium lipid A 3-O-deacylase activity. Preferably, the bacterium is a genetically modified Neisseria meningitidis, Neisseria gonorrhoeae or Neisseria lactamica. Preferably, in the genetically modified bacterium, the endogenous IpxLl gene is a gene encoding an LpxLl protein having an amino acid sequence with at least 90% sequence identity with at least one of SEQ ID NO's: 1 - 3, or the endogenous lpxL2 gene is a gene encoding an LpxL2 protein having an amino acid sequence with at least 90% sequence identity with at least one of SEQ ID NO's: 4 - 7, and the genetic modification that confers to the bacterium lipid A 3-O-deacylase activity is a genetic modification that introduces the expression of a heterologous pagL gene having a nucleotide sequence that encodes a PagL lipid A 3-O-deacylase that has at least 30 % amino acid sequence identity with at least one of SEQ ID NO's: 8 - 17. The genetically modified bacterium of the invention, further preferably is genetically modified to express a heterologous antigen, whereby preferably, the heterologous antigen is expressed on the extracellular outer membrane surface of the bacterium. In a preferred embodiment, the genetically modified bacterium has a genetic modification that reduces or eliminates the expression of at least one of an endogenous IgtB gene and an endogenous galE gene.

Preferably a genetically modified bacterium according to the invention is a Neisseria meningitidis serogroup B, immunotype L3. More preferably, the bacterium is Neisseria meningitidis strain H44/76 or a derivative thereof.

In a third aspect, the invention pertains to a neisserial LPS according to the invention, wherein the LPS is obtainable or obtained from a genetically modified bacterium according to the invention.

In a fourth aspect, the invention relates to an OMV comprising a neisserial LPS of the invention. The OMV preferably is obtainable or obtained from a genetically modified bacterium according to the invention.

In a fifth aspect, the invention pertains to a composition comprising at least one of a neisserial LPS of the invention, a genetically modified bacterium of the invention and an OMV of the invention. Preferably, the composition is a pharmaceutical composition further comprising a pharmaceutically accepted excipient. A preferred composition is an acellular vaccine comprising a neisserial LPS of the invention, or an OMV of the invention. Another preferred composition is a whole cell vaccine comprising a bacterium of the invention. Preferably the compositions of the invention further comprises at least one non-neisserial antigen.

In a sixth aspect, the invention relates to a process for producing a neisserial LPS according to the invention. The process preferably comprises the steps of: a) cultivating a bacterium of the invention; and, b) optionally, at least one of extraction and purification of the LPS.

In a seventh aspect, the invention relates to a process for producing an OMV according to the invention. The process preferably comprises the steps of: a) cultivating a genetically modified bacterium of the invention; b) optionally, extracting the OMV; and, c) recovering the OMV, wherein the recovery at least comprises removal of the bacteria from the OMV. A preferred process for producing OMV is a detergent-free process. In an eighth aspect, the invention relates to a process for producing an acellular vaccine of the invention. The process preferably comprises the steps of: a) producing at least one of: i) a neisserial LPS according to the invention, preferably in a process as defined hereinabove; and, ii) an OMV according to the invention, preferably in a process as defined hereinabove; and, b) formulating at least one of the neisserial LPS and the OMV, optionally with further vaccine components, into a vaccine formulation.

In a ninth aspect, the invention relates to a process for producing a whole cell vaccine of the invention, wherein the process comprises the steps of: i) cultivating a bacterium of the invention; and, ii) optionally, at least one of inactivation of the bacterium and formulation into a vaccine.

In a tenth aspect, the invention relates to a neisserial LPS of the invention, a bacterium of the invention, an OMV of the invention, or a composition of the invention, for use as a medicament.

In an eleventh aspect, the invention relates to a neisserial LPS of the invention, for use in a treatment comprising inducing or stimulating an immune response in a subject. Preferably, the neisserial LPS is for a use as adjuvant.

In a preferred embodiment, the neisserial LPS is used in a treatment further comprising the administration of an antigen together with the neisserial LPS and wherein the treatment is for preventing or treating an infectious disease or tumour associated with the antigen.

In another preferred embodiment, the neisserial LPS of the invention is for a use as a Toll-like receptor 4 (TLR4) agonist in an immunotherapy, wherein preferably, the immunotherapy is an immunotherapy of a cancer or of a neurodegenerative disease. In an alternative embodiment, the immunotherapy comprises a generalized immune stimulation for preventing and/or reducing the spread of diverse microbial infections and/or to suppress bacterial growth.

Description of the invention

Definitions

The terms "homology", "sequence identity" and the like are used interchangeably herein. Sequence identity is herein defined as a relationship between two or more amino acid (polypeptide or protein) sequences or two or more nucleic acid (polynucleotide) sequences, as determined by comparing the sequences. In the art, "identity" also means the degree of sequence relatedness between amino acid or nucleic acid sequences, as the case may be, as determined by the match between strings of such sequences. "Similarity" between two amino acid sequences is determined by comparing the amino acid sequence and its conserved amino acid substitutes of one polypeptide to the sequence of a second polypeptide. "Identity" and "similarity" can be readily calculated by known methods.

"Sequence identity" and "sequence similarity" can be determined by alignment of two peptide or two nucleotide sequences using global or local alignment algorithms, depending on the length of the two sequences. Sequences of similar lengths are preferably aligned using a global alignment algorithms (e.g. Needleman Wunsch) which aligns the sequences optimally over the entire length, while sequences of substantially different lengths are preferably aligned using a local alignment algorithm (e.g. Smith Waterman). Sequences may then be referred to as "substantially identical" or "essentially similar" when they (when optimally aligned by for example the programs GAP or BESTFIT using default parameters) share at least a certain minimal percentage of sequence identity (as defined below). GAP uses the Needleman and Wunsch global alignment algorithm to align two sequences over their entire length (full length), maximizing the number of matches and minimizing the number of gaps. A global alignment is suitably used to determine sequence identity when the two sequences have similar lengths. Generally, the GAP default parameters are used, with a gap creation penalty = 50 (nucleotides) / 8 (proteins) and gap extension penalty = 3 (nucleotides) / 2 (proteins). For nucleotides the default scoring matrix used is nwsgapdna and for proteins the default scoring matrix is Blosum62 (Henikoff & Henikoff, 1992, PNAS 89, 915-919). Sequence alignments and scores for percentage sequence identity may be determined using computer programs, such as the GCG Wisconsin Package, Version 10.3, available from Accelrys Inc., 9685 Scranton Road, San Diego, CA 92121-3752 USA, or using open source software, such as the program "needle" (using the global Needleman Wunsch algorithm) or "water" (using the local Smith Waterman algorithm) in Emboss WIN version 2.10.0, using the same parameters as for GAP above, or using the default settings (both for 'needle' and for 'water' and both for protein and for DNA alignments, the default Gap opening penalty is 10.0 and the default gap extension penalty is 0.5; default scoring matrices are Blossum62 for proteins and DNAFull for DNA). When sequences have a substantially different overall lengths, local alignments, such as those using the Smith Waterman algorithm, are preferred. Alternatively percentage similarity or identity may be determined by searching against public databases, using algorithms such as FASTA, BLAST, etc. Thus, the nucleic acid and protein sequences of the present invention can further be used as a "query sequence" to perform a search against public databases to, for example, identify other family members or related sequences. Such searches can be performed using the BLASTn and BLASTx programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215 :403— 10. BLAST nucleotide searches can be performed with the NBLAST program, score = 100, wordlength = 12 to obtain nucleotide sequences homologous to oxidoreductase nucleic acid molecules of the invention. BLAST protein searches can be performed with the BLASTx program, score = 50, wordlength = 3 to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al, (1997) Nucleic Acids Res. 25(17): 3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., BLASTx and BLASTn) can be used. See the homepage of the National Center for Biotechnology Information at htt ://www.ncbi.nlm.nih. gov/.

Optionally, in determining the degree of amino acid similarity, the skilled person may also take into account so-called "conservative" amino acid substitutions, as will be clear to the skilled person. Conservative amino acid substitutions refer to the interchangeability of residues having similar side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and iso leucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagines and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulphur-containing side chains is cysteine and methionine. Preferred conservative amino acids substitution groups are: valine- leucine-iso leucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, and asparagine-glutamine. Substitutional variants of the amino acid sequence disclosed herein are those in which at least one residue in the disclosed sequences has been removed and a different residue inserted in its place. Preferably, the amino acid change is conservative. Preferred conservative substitutions for each of the naturally occurring amino acids are as follows: Ala to ser; Arg to lys; Asn to gin or his; Asp to glu; Cys to ser or ala; Gin to asn; Glu to asp; Gly to pro; His to asn or gin; He to leu or val; Leu to ile or val; Lys to arg; gin or glu; Met to leu or ile; Phe to met, leu or tyr; Ser to thr; Thr to ser; Trp to tyr; Tyr to trp or phe; and, Val to ile or leu.

As used herein, the term "selectively hybridizing", "hybridizes selectively" and similar terms are intended to describe conditions for hybridization and washing under which nucleotide sequences at least 66%, at least 70%, at least 75%, at least 80%, more preferably at least 85%, even more preferably at least 90%, preferably at least 95%, more preferably at least 98% or more preferably at least 99% homologous to each other typically remain hybridized to each other. That is to say, such hybridizing sequences may share at least 45%, at least 50%, at least 55%, at least 60%, at least 65, at least 70%, at least 75%), at least 80%>, more preferably at least 85%, even more preferably at least 90%>, more preferably at least 95%, more preferably at least 98% or more preferably at least 99% sequence identity.

A preferred, non-limiting example of such hybridization conditions is hybridization in 6 x sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 1 X SSC, 0.1 % SDS at about 50°C, preferably at about 55°C, preferably at about 60°C and even more preferably at about 65°C.

Highly stringent conditions include, for example, hybridization at about 68°C in 5 x SSC/5 x Denhardfs solution / 1.0% SDS and washing in 0.2 x SSC/0.1% SDS at room temperature. Alternatively, washing may be performed at 42°C.

The skilled artisan will know which conditions to apply for stringent and highly stringent hybridization conditions. Additional guidance regarding such conditions is readily available in the art, for example, in Sambrook et al, 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; and Ausubel et al. (eds.), Sambrook and Russell (2001) "Molecular Cloning: A Laboratory Manual (3 ^rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, New York 1995, Current Protocols in Molecular Biology, (John Wiley & Sons, N.Y.).

Of course, a polynucleotide which hybridizes only to a poly A sequence (such as the 3' terminal poly(A) tract of mRNAs), or to a complementary stretch of T (or U) resides, would not be included in a polynucleotide of the invention used to specifically hybridize to a portion of a nucleic acid of the invention, since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly (A) stretch or the complement thereof (e.g., practically any double-stranded cDNA clone). A "nucleic acid construct" or "nucleic acid vector" is herein understood to mean a man-made nucleic acid molecule resulting from the use of recombinant DNA technology. The term "nucleic acid construct" therefore does not include naturally occurring nucleic acid molecules although a nucleic acid construct may comprise (parts of) naturally occurring nucleic acid molecules. The terms "expression vector" or "expression construct" refer to nucleotide sequences that are capable of effecting expression of a gene in host cells or host organisms compatible with such sequences. These expression vectors typically include at least suitable transcription regulatory sequences and optionally, 3' transcription termination signals. Additional factors necessary or helpful in effecting expression may also be present, such as expression enhancer elements. The expression vector will be introduced into a suitable host cell and be able to effect expression of the coding sequence in an in vitro cell culture of the host cell. The expression vector will be suitable for replication in the host cell or organism of the invention.

As used herein, the term "promoter" or "transcription regulatory sequence" refers to a nucleic acid fragment that functions to control the transcription of one or more coding sequences, and is located upstream with respect to the direction of transcription of the transcription initiation site of the coding sequence, and is structurally identified by the presence of a binding site for DNA-dependent RNA polymerase, transcription initiation sites and any other DNA sequences, including, but not limited to transcription factor binding sites, repressor and activator protein binding sites, and any other sequences of nucleotides known to one of skill in the art to act directly or indirectly to regulate the amount of transcription from the promoter. A "constitutive" promoter is a promoter that is active in most tissues under most physiological and developmental conditions. An "inducible" promoter is a promoter that is physiologically or developmentally regulated, e.g. by the application of a chemical inducer.

The term "selectable marker" is a term familiar to one of ordinary skill in the art and is used herein to describe any genetic entity which, when expressed, can be used to select for a cell or cells containing the selectable marker. The term "reporter" may be used interchangeably with marker, although it is mainly used to refer to visible markers, such as green fluorescent protein (GFP). Selectable markers may be dominant or recessive or bidirectional.

As used herein, the term "operably linked" refers to a linkage of polynucleotide elements in a functional relationship. A nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence. For instance, a transcription regulatory sequence is operably linked to a coding sequence if it affects the transcription of the coding sequence. Operably linked means that the DNA sequences being linked are typically contiguous and, where necessary to join two protein encoding regions, contiguous and in reading frame.

The term "peptide" as used herein is defined as a chain of amino acid residues, usually having a defined sequence. As used herein the term peptide is interchangeable with the terms "polypeptide" and "protein". In the context of the present invention, the term "peptide" is defined as being any peptide or protein comprising at least two amino acids linked by a modified or unmodified peptide bond. The term "peptide" refers to short-chain molecules such as oligopeptides or oligomers or to long-chain molecules such as proteins. A protein/peptide can be linear, branched or cyclic. The peptide can include D amino acids, L amino acids, or a combination thereof. A peptide according to the present invention can comprise modified amino acids. Thus, the peptide of the present invention can also be modified by natural processes such as post-transcriptional modifications or by a chemical process. Some examples of these modifications are: acetylation, acylation, ADP-ribosylation, amidation, covalent bonding with flavine, covalent bonding with a heme, covalent bonding with a nucleotide or a nucleotide derivative, covalent bonding to a modified or unmodified carbohydrate moiety, bonding with a lipid or a lipid derivative, covalent bonding with a phosphotidylinositol, cross- linking, cyclization, disulfide bond formation, demethylation, cysteine molecule formation, pyroglutamate formation, formylation, gamma-carboxylation, hydroxylation, iodination, methylation, oxidation, phosphorylation, racemization, hydroxylation, etc. Thus, any modification of the peptide which does not have the effect of eliminating the immunogenicity of the peptide, is covered within the scope of the present invention.

The term "gene" means a DNA fragment comprising a region (transcribed region), which is transcribed into an RNA molecule (e.g. an mRNA) in a cell, operably linked to suitable regulatory regions (e.g. a promoter). A gene will usually comprise several operably linked fragments, such as a promoter, a 5' leader sequence, a coding region and a 3'-nontranslated sequence (3'-end) comprising a polyadenylation site. "Expression of a gene" refers to the process wherein a DNA region which is operably linked to appropriate regulatory regions, particularly a promoter, is transcribed into an RNA, which is biologically active, i.e. which is capable of being translated into a biologically active protein or peptide. The term "homologous" when used to indicate the relation between a given (recombinant) nucleic acid or polypeptide molecule and a given host organism or host cell, is understood to mean that in nature the nucleic acid or polypeptide molecule is produced by a host cell or organisms of the same species, preferably of the same variety or strain. If homologous to a host cell, a nucleic acid sequence encoding a polypeptide will typically (but not necessarily) be operably linked to another (heterologous) promoter sequence and, if applicable, another (heterologous) secretory signal sequence and/or terminator sequence than in its natural environment. It is understood that the regulatory sequences, signal sequences, terminator sequences, etc. may also be homologous to the host cell.

The terms "heterologous" and "exogenous" when used with respect to a nucleic acid (DNA or R A) or protein refers to a nucleic acid or protein that does not occur naturally as part of the organism, cell, genome or DNA or RNA sequence in which it is present, or that is found in a cell or location or locations in the genome or DNA or RNA sequence that differ from that in which it is found in nature. Heterologous and exogenous nucleic acids or proteins are not endogenous to the cell into which it is introduced, but have been obtained from another cell or synthetically or recombinantly produced. Generally, though not necessarily, such nucleic acids encode proteins, i.e. exogenous proteins, that are not normally produced by the cell in which the DNA is transcribed or expressed. Similarly exogenous RNA encodes for proteins not normally expressed in the cell in which the exogenous RNA is present. Heterologous/exogenous nucleic acids and proteins may also be referred to as foreign nucleic acids or proteins. Any nucleic acid or protein that one of skill in the art would recognize as foreign to the cell in which it is expressed is herein encompassed by the term heterologous or exogenous nucleic acid or protein. The terms heterologous and exogenous also apply to non-natural combinations of nucleic acid or amino acid sequences, i.e. combinations where at least two of the combined sequences are foreign with respect to each other.

The term "immune response" as used herein refers to the production of antibodies and/or cells (such as T lymphocytes) that are directed against, and/or assist in the decomposition and/or inhibition of, a particular antigenic entity, carrying and/or expressing or presenting antigens and/or antigenic epitopes at its surface. The phrases "an effective immunoprotective response", "immunoprotection", and like terms, for purposes of the present invention, mean an immune response that is directed against one or more antigenic epitopes of a pathogen, a pathogen-infected cell or a cancer cell so as to protect against infection by the pathogen or against cancer in a vaccinated subject. For purposes of the present invention, protection against infection by a pathogen or protection against cancer includes not only the absolute prevention of infection or cancer, but also any detectable reduction in the degree or rate of infection by a pathogen or of the cancer, or any detectable reduction in the severity of the disease or any symptom or condition resulting from infection by the pathogen or cancer in the vaccinated subject, for example as compared to an unvaccinated infected subject. An effective immunoprotective response in the case of cancer also includes clearing up the cancer cells, thereby reducing the size of cancer or even abolishing the cancer. Vaccination in order to achieve this is also called therapeutic vaccination. Alternatively, an effective immunoprotective response can be induced in subjects that have not previously been infected with the pathogen and/or are not infected with the pathogen or do not yet suffer from cancer at the time of vaccination, such vaccination can be referred to as prophylactic vaccination.

According to the present invention, the general use herein of the term "antigen" refers to any molecule that binds specifically to an antibody. The term also refers to any molecule or molecular fragment that can be bound by an MHC molecule and presented to a T-cell receptor. Antigens can be e.g. proteinaceous molecules, i.e. polyaminoacid sequences, optionally comprising non-protein groups such as carbohydrate moieties and/or lipid moieties or antigens can be e.g. molecules that are not proteinaceous such as carbohydrates. An antigen can be e.g. any portion of a protein (peptide, partial protein, full-length protein), wherein the protein is naturally occurring or synthetically derived, a cellular composition (whole cell, cell lysate or disrupted cells), an organism (whole organism, lysate or disrupted cells) or a carbohydrate or other molecule, or a portion thereof, that is able to elicit an antigen-specific immune response (humoral and/or cellular immune response) in a particular subject, which immune response preferably is measurable via an assay or method.

The term "antigen" is herein understood as a structural substance which serves as a target for the receptors of an adaptive immune response. An antigen thus serves as target for a TCR (T-cell receptor) or a BCR (B-cell receptor) or the secreted form of a BCR, i.e. an antibody. The antigen can thus be a protein, peptide, carbohydrate or other hapten that is usually part of a larger structure, such as e.g. a cell or a virion. The antigen may originate from within the body ("self) or from the external environment ("non- self). The immune system is usually non-reactive against "self antigens under normal conditions due to negative selection of T cells in the thymus and is supposed to identify and attack only "non-self invaders from the outside world or modified/harmful substances present in the body under e.g. disease conditions. Antigens structures that are the target of a cellular immune response are presented by antigen presenting cells (APC) in the form of processed antigenic peptides to the T cells of the adaptive immune system via a histocompatibility molecule. Depending on the antigen presented and the type of the histocompatibility molecule, several types of T cells can become activated. For T- Cell Receptor (TCR) recognition, the antigen is processed into small peptide fragments inside the cell and presented to a T-cell receptor by major histocompatibility complex (MHC).

The term "immunogen" is used herein to describe an entity that comprises or encodes at least one epitope of an antigen such that when administered to a subject, preferably together with an appropriate adjuvant, elicits a specific humoral and/or cellular immune response in the subject against the epitope and antigen comprising the epitope. An immunogen can be identical to the antigen or at least comprises a part of the antigen, e.g. a part comprising an epitope of the antigen. Therefore, to vaccinate a subject against a particular antigen means, in one embodiment, that an immune response is elicited against the antigen or immunogenic portion thereof, as a result of administration of an immunogen comprising at least one epitope of the antigen. Vaccination preferably results in a protective or therapeutic effect, wherein subsequent exposure to the antigen (or a source of the antigen) elicits an immune response against the antigen (or source) that reduces or prevents a disease or condition in the subject. The concept of vaccination is well-known in the art. The immune response that is elicited by administration of a prophylactic or therapeutic composition of the present invention can be any detectable change in any facet of the immune status (e.g., cellular response, humoral response, cytokine production), as compared to in the absence of the administration of the vaccine.

An "epitope" is defined herein as a single immunogenic site within a given antigen that is sufficient to elicit an immune response in a subject. Those of skill in the art will recognize that T cell epitopes are different in size and composition from B cell epitopes, and that T cell epitopes presented through the Class I MHC pathway differ from epitopes presented through the Class II MHC pathway. Epitopes can be linear sequences or conformational epitopes (conserved binding regions) depending on the type of immune response. An antigen can be as small as a single epitope, or larger, and can include multiple epitopes. As such, the size of an antigen can be as small as about 5-12 amino acids (e.g., a peptide) and as large as: a full length protein, including multimeric proteins, protein complexes, virions, particles, whole cells, whole microorganisms, or portions thereof (e.g., lysates of whole cells or extracts of microorganisms).

An adjuvant is herein understood to be an entity, that, when administered in combination with an antigen to a human or an animal subject to raise an immune response against the antigen in the subject, stimulates the immune system, thereby provoking, enhancing or facilitating the immune response against the antigen, preferably without necessarily generating a specific immune response to the adjuvant itself. A preferred adjuvant enhances the immune response against a given antigen by at least a factor of 1.5, 2, 2.5, 5, 10 or 20, as compared to the immune response generated against the antigen under the same conditions but in the absence of the adjuvant. Tests for determining the statistical average enhancement of the immune response against a given antigen as produced by an adjuvant in a group of animal or human subjects over a corresponding control group are available in the art. The adjuvant preferably is capable of enhancing the immune response against at least two different antigens.

OMV (also referred to as "blebs") are bi-layered membrane structures, usually spherical, with a diameter in the range of 20-250 nm (sometimes 10 - 500 nm), that are pinched off from the outer membrane of Gram-negative bacteria. The OMV membrane contains phospholipids (PL) on the inside and lipopolysaccharides (LPS) and PL on the outside, mixed with membrane proteins in various positions, largely reflecting the structure of the bacterial outer membrane from which they pinched off. The lumen of the OMV may contain various compounds from the periplasm or cytoplasm, such as proteins, R A/DNA, and peptidoglycan (PG), however, unlike bacterial cells, OMV lack the ability to self-replicate. In the context of the present invention three type of OMV can be distinguished depending on the method of their production. sOMV are spontaneous or natural OMV that are purified and concentrated from culture supernatant, by separating intact cells from the already formed OMVs. Detergent OMV, dOMV, are extracted from cells with detergent, such as deoxycholate, which also reduces the content of reactogenic LPS. After detergent extraction dOMV are separated from cells and cellular debris and further purified and concentrated. Finally, the term native nOMV is used herein for OMV that are generated from concentrated dead cells with non-detergent cell disruption techniques, or that are extracted from cells with other (non-disruptive) detergent-free methods, to be able to clearly distinguish them from the wild-type spontaneous OMVs and from the detergent-extracted dOMV.

Any reference to nucleotide or amino acid sequences accessible in public sequence databases herein refers to the version of the sequence entry as available on the filing date of this document.

Detailed description of the invention

The present invention relates to a novel neisserial LPS having a tetra-acylated lipid

A moiety and which is useful in generating and/or stimulating immune responses. Penta- acylated LPS molecules obtained from IpxLl, lpxL2 and pagL single mutant neisserial strains all have reduced TLR4 activity as compared to the corresponding hexa-acylated LPS from the parent strain (13,15). Tetra-acylated LPS is expected to always be less active than penta-acylated LPS. Indeed, tetra-acylated lipid IVa of E. coli is even known to be an antagonist of the human TLR4/MD-2 complex (7,9,28). Surprisingly, the inventors have found that meningococcal tetra-acylated AlpxLl-pagL LPS is more active than the penta-acylated AlpxLl LPS, whereas tetra-acylated AlpxLl-AlpxL2 LPS did not yield detectable activity (data not shown). Also stimulation with AlpxL2-pagL whole bacteria that also carry a tetra-acylated LPS again increased TLR4/MD-2 activity compared to its penta-acylated AlpxLl parent strain. Together these findings indicate that removal of C120H from the 3'position by PagL in combination with deletion of a secondary acyl chain resulting in tetra-acylated lipid A unexpectedly yields a higher TLR4 activity compared to sole removal of the secondary acyl chain or both secondary acyl chains.

In a first aspect therefore, the invention pertains to a neisserial LPS having a tetra- acylated lipid A moiety, or to the tetra-acylated lipid A moiety itself. Preferably the tetra- acylated lipid A moiety is modified as compared to the lipid A moiety of a wild-type neisserial LPS in that it lacks one of the secondary acyl chains and in that it lacks a primary acyl chain on the 3 -position of the glucosamine on the reducing end of the lipid A moiety. Thus, compared to the hexa-acylated lipid A moiety of a wild-type neisserial LPS, the tetra-acylated lipid A moiety of the invention has two modifications that reduce the total number of acyl chains on the lipid A moiety from six to four: 1) the lipid A moiety lacks either one of the two secondary acyl chains, i.e. either the secondary acyl chain bound to the primary acyl chain attached to the glucosamine on the non-reducing end of the lipid A moiety, or the secondary acyl chain bound to the primary acyl chain attached to the glucosamine on the reducing end of the lipid A moiety; and, 2) the lipid A moiety lacks a primary acyl chain on the 3-position of the glucosamine on the reducing end of the lipid A moiety. Preferably, the neisserial LPS or the tetra-acylated lipid A moiety are isolated

In a preferred neisserial LPS of the invention, the tetra-acylated lipid A moiety has the structure of formulas (I) or (II):

(I)

(Π)

wherein Ri and R ₂ , independently, are either -P(0)(OH) ₂ , -[P(0)(OH)-0] ₂ -H, - [P(0)(OH)-0]2-CH ₂ CH ₂ NH2, -[P(0)(OH)-0]3-CH ₂ CH ₂ NH2, -[P(0)(OH)-0] ₃ -H or - P(0)(OH)-0-CH ₂ CH ₂ NH ₂ , and wherein, preferably Rl and R2, independently, are either -P(0)(OH) ₂ , -[P(0)(OH)-0] ₂ -H, -[P(0)(OH)-0] ₂ -CH ₂ CH ₂ NH ₂ or -[P(0)(OH)-0] ₃ - CH ₂ CH ₂ NH ₂ .

In a preferred embodiment, the neisserial LPS of the invention has a tetra-acylated lipid A moiety that lacks the secondary acyl chain bound to the primary acyl chain attached to the glucosamine on the non-reducing end of the lipid A moiety. Preferably in this embodiment, the tetra-acylated lipid A moiety has the structure of formula (I) above.

Except for the tetra-acylated lipid A moiety, the neisserial LPS of the invention otherwise has the structure of a lipopolysaccharide that is obtained or obtainable from a bacterium of the genus Neisseria. The neisserial LPS are sometimes also referred to as lipooligosaccharides (LOS) due to the fact that they differ from the LPS of the Enterobacteriaceae by lacking the O side chains. In the context of the invention the terms "LPS" and "LOS" are however interchangeable. For reasons of consistency we shall further refer to LPS. The bacterium of the genus Neisseria from which the LPS of the invention is obtained or obtainable can be a wild type Neisseria, or a Neisseria having one or more of the genetic modifications described herein below. The bacterium of the genus Neisseria preferably is of a species selected from Neisseria meningitidis, Neisseria gonorrhoeae and Neisseria lactamica, whereby more preferably the Neisseria meningitidis that is at least one of serogroup B and immunotype L3.

Preferably therefore, except for the tetra-acylated lipid A moiety, the remainder of the neisserial LPS of the invention has the structure of LPS of Neisseria meningitidis, Neisseria gonorrhoeae or Neisseria lactamica or a strain of these species having a genetic modification as described herein below. More preferably, except for the tetra- acylated lipid A moiety, the remainder of the neisserial LPS of the invention has the structure of LPS of Neisseria meningitidis that is at least one of serogroup B and immunotype L3 or a strain of this serogroup and/or immunotype having a genetic modification as described herein below.

In a preferred embodiment the neisserial LPS of the invention has a modified oligosaccharide structure so as to remove possible epitopes that are suspected to provoke autoimmune responses, and/or to increase binding to dendritic cells and adjuvant activity. Preferably therefore, the neisserial LPS of the invention is obtained or obtainable from a bacterium of the genus Neisseria that has a genetic modification that reduces or eliminates the expression of at least one of an endogenous IgtB gene and an endogenous galE gene. Neisserial IgtB genes encode enzymes having lacto-N-neotetraose biosynthesis glycosyl transferase activity and are described e.g. by Jennings et al. (Mol Microbiol, 1995, 18:729-740) and by Arkin et al. (J Bacteriol. 2001, 183: 934-941). LPS from neisserial strains with IgtB disruptions has been shown to target the DC-SIGN lectin receptor on dendritic cells (DC), thereby skewing T-cell responses driven by DC towards T helper type 1 activity (Steeghs et al. Cell Microbiol. 2006, 8:316-25). Neisserial galE genes encode enzymes having UDP-glucose 4-epimerase activity and are described by Jennings et al. (Mol Microbiol, 1993, 10:361-369) and by Lee et al. (Infect Immun. 1995, 63: 2508-2515). In a second aspect, the invention relates to a genetically modified bacterium of the genus Neisseria. The bacterium preferably is a bacterium comprising a neisserial LPS having a tetra-acylated lipid A moiety according to the first aspect of the invention. The bacterium is preferably genetically modified in that it comprises: a) a genetic modification that reduces or eliminates the activity of a lipid A biosynthesis lauroyl acyltransferase encoded by an endogenous IpxLl gene or an endogenous lpxL2 gene; and, b) a genetic modification that confers to the bacterium lipid A 3-O-deacylase activity. A genetic modification that reduces or eliminates the activity of the lauroyl acyltransferase can e.g. be a missense mutation such as described in Fransen et al. (2009, PLoS Pathogens 5(4): el000396). Preferably, the genetic modification that reduces or eliminates the activity of the lipid A biosynthesis lauroyl acyltransferase is a modification that reduces or eliminates the expression of an endogenous IpxLl gene or an endogenous lpxL2 gene. The genetically modified bacterium preferably is bacterium of a species selected from Neisseria meningitidis, Neisseria gonorrhoeae and Neisseria lactamica. More preferably, the genetically modified Neisseria meningitidis is at least one of serogroup B and immunotype L3, most preferably, the genetically modified Neisseria meningitidis is the Neisseria meningitidis H44/76 strain or a derivative thereof.

The endogenous IpxLl gene to be modified preferably is a gene that encodes a lipid A biosynthesis lauroyl acyltransferase. IpxLl genes have also been referred to as htrBl or msbB genes. The IpxLl gene of which the expression is to be reduced or eliminated in the bacterium of the invention, preferably is a gene that encodes a LpxLl (lipid A biosynthesis lauroyl acyltransferase) comprising an amino acid sequence with at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity with at least one of SEQ ID NO: 1 (LpxLl of Neisseria meningitidis H44/76), SEQ ID NO: 2 (LpxLl of Neisseria gonorrhoeae, Genbank WP_050158792) and SEQ ID NO: 3 (LpxLl of Neisseria lactamica, Genbank CBN86767). In a preferred embodiment, the expression of the IpxLl gene is eliminated by inactivation of the gene, e.g. by disruption or deletion of the gene by methods known in the art per se.

The endogenous lpxL2 gene to be modified preferably is a gene that encodes a lipid A biosynthesis lauroyl acyltransferase. lpxL2 genes have also been referred to as htrB2 genes. Preferably, the lpxL2 gene of which the expression is to be reduced or eliminated preferably is a gene that encodes a LpxL2 (lipid A biosynthesis lauroyl acyltransferase) comprising an amino acid sequence with at least 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity with at least one of SEQ ID NO: 4 (LpxL2 of Neisseria meningitidis 1144116, Genbank WP_055391354), SEQ ID NO: 5 (LpxL2 of Neisseria gonorrhoeae, Genbank WP 020996767) and SEQ ID NO: 6 (LpxL2 of Neisseria lactamica, Genbank WP_042508043). In a preferred embodiment, the expression of the lpxL2 gene is eliminated by inactivation of the gene, e.g. by disruption or deletion of the gene by methods known in the art per se.

The genetic modification that confers to the bacterium lipid A 3-O-deacylase activity preferably is a genetic modification that introduces the expression of a heterologous pagL gene having a nucleotide sequence that encodes a PagL lipid A 3-0- deacylase. The outer membrane PagL 3-O-deacylase hydro lyses the ester bond at the 3 position of lipid A, thereby releasing the primary 3-OH acyl moiety, whereby the enzyme lacks fatty acyl chain-length specificity (Geurtsen et al. supra). The overall sequence conservation between the various PagL homologs was found to be rather low, with e.g. only 32%o sequence identity between the PagL amino acid sequences of Bordetella bronchiseptica and Pseudomonas aeruginosa. Outer membrane PagL 3-O-deacylases have been reported in a number of Gram-negative pathogens including Salmonella typhimurium, Salmonella enterica, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas syringae, Pseudomonas putida, Ralstonia metallidurans, Ralstonia solanacearum, Burkholderia mallei, Burkholderia pseudomallei, Burkholderia fungorum, Azotobacter vinelandii, Bordetella bronchiseptica, Bordetella parapertussis and Bordetella pertussis (Geurtsen et al, 2005, J Biol Chem, 280: 8248-8259). More recently also PagL 3-O-deacylase was shown to be active in the nitrogen-fixing endosymbiont Rhizobium etli (Brown et al., 2013, J Biol Chem, 288: 12004-12013). Nucleotide sequences for expression of PagL lipid A 3-O-deacylase activity can thus be nucleotide sequences encoding PagL lipid A 3-O-deacylases that are obtainable from these bacteria.

However, preferably, the nucleotide sequence for expression of PagL lipid A 3-O- deacylase activity in a genetically modified bacterium of the invention is a nucleotide sequence that encodes a PagL lipid A 3-O-deacylase comprising an amino acid sequence with at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42. 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity with at least one of SEQ ID NO: 7 (Bordetella bronchiseptica, Genbank WP 003813842, identical to PagL of B. parapertussis), SEQ ID NO: 8 {Salmonella enterica subsp. enterica serovar Typhimurium, Genbank AAL21147), SEQ ID NO: 9 (Pseudomonas aeruginosa, Genbank NP_253350), SEQ ID NO: 10 (Pseudomonas fluorescens, Genbank AFJ58359), SEQ ID NO: 11 (Pseudomonas putida, Genbank BAN56395), SEQ ID NO: 12 (Pseudomonas syringae, Genbank KFE57666), SEQ ID NO: 13 (Burkholderia sp., Genbank WP 028199068), SEQ ID NO: 14 (Ralstonia solanacearum, Genbank CEJ17533), SEQ ID NO: 15 (Azotobacter vinelandii, Genbank AC076453) and SEQ ID NO: 16 (Rhizobium etli, Genbank WP 039619975).

In one embodiment the nucleotide sequence encodes a polypeptide with PagL lipid

A 3-O-deacylase activity as it occurs in nature, e.g. as it can be isolated from a wild type source bacterium. Alternatively, the nucleotide sequence can encode engineered forms of any of the PagL lipid A 3-O-deacylases defined above and that comprise one or more amino acid substitutions, insertions and/or deletions as compared to the corresponding naturally occurring PagL lipid A 3-O-deacylase but that are within the ranges of identity or similarity as defined herein.

Preferably, a nucleotide sequence for expression of PagL lipid A 3-O-deacylase activity in a genetically modified bacterium of the invention is a nucleotide sequence that encodes a PagL lipid A 3-O-deacylase comprising an amino acid sequence that at least comprises the active site residues His-154 and Ser-156 (Rutten et al, 2006, PNAS 103 : 7071-7076) in positions corresponding to positions 154 and 156, respectively, in the Bordetella bronchiseptica PagL amino acid sequence (SEQ ID NO: 8), in a ClustalW (1.83) to sequence alignment using default settings. It is further preferred that the PagL lipid A 3-O-deacylase amino acid sequence comprises in each of the other invariable positions (that are indicated with a "*", i.e. an asteriks in the sequence alignment of Figure 2 of Geurtsen et al, 2005, J Biol Chem, 280: 8248-8259), the amino acid present in that invariable position. More preferably, the PagL lipid A 3-O-deacylase amino acid sequence also comprises in the strongly conserved positions (that are indicated with a ":", i.e. a colon in Figure 2 of Geurtsen et al, 2005, supra) one of the amino acids that is present in the respective strongly conserved positions. Most preferably, the amino acid sequence further also comprises in the weakly conserved positions (that are indicated in Figure 2 of Geurtsen et al, 2005, supra with a i.e. a dot) one of the amino acids that is present in the respective weakly conserved positions. Amino acid substitutions outside of these invariable and conserved positions are less likely to have a negative effect on the PagL lipid A 3-O-deacylase enzymatic activity.

The genetically modified bacterium of the invention further preferably has one or more genetic modifications selected from the group consisting of: (i) a genetic modification that alters the LPS biosynthesis pathway, preferably in order to further modify the endotoxicity and/or reactogenicity of the LPS; (ii) a genetic modification that causes outer membrane retention of normally secreted antigens; (iii) a genetic modification that increases OMV production by removing outer membrane anchor proteins; (iv) a genetic modification that removes immune-modulating components which may trigger an undesired type of immune response; and, (v) a genetic modification that introduces expression of heterologous antigens.

An LPS that is modified to have reduced endotoxicity is herein understood as an LPS that is modified to have less toxicity than the toxicity of a corresponding wild-type LPS. Preferably, the modified LPS has less than about 90, 80, 60, 40, 20, 10, 5, 2, 1, 0.5, or 0.2% of the toxicity of the corresponding wild-type LPS. The toxicities of wild-type and various modified LPS's with reduced toxicity may be determined in any suitable assay known in the art. A preferred assay for determining the toxicity, i.e. the biological activity of the LPS is IL-6 induction in the MM6 macrophage cell line (see par. 1.4 below).

A preferred genetic modification that alters the LPS biosynthesis pathway is a genetic modification that is selected from the group consisting of: a) a genetic modification that reduces or eliminates expression of at least one of an IptA gene, an IpxK gene and homologues of these genes; and b) a genetic modification that introduces or increases the expression of at least one of an IpxE gene, an IpxF gene and homologues of these genes.

A preferred genetic modification that increases OMV production is a genetic modification that reduces or eliminates expression of a gene encoding an anchor protein between outer membrane and peptidoglycan in order to increase vesicle formation and thereby increase OMV yield. A suitable genetic modification for this purpose e.g. reduces or eliminates expression of an OmpA homologue, which are commonly found in Gram-negative bacteria, e.g. the RmpM protein in Neisseria (Steeghs et al., 2002 Cell Microbiol, 4:599-611; van de Waterbeemd et al, 2010 Vaccine, 28:4810 - 4816). Thus, preferably, the genetically modified bacterium has a genetic modification reduces or eliminates expression of an rmpM gene or a homologue thereof.

Preferred genetic modifications that removes immune-modulating components which may trigger an undesired type of immune response are genetic modifications that reduces or eliminates the expression of at least one of an endogenous IgtB gene and an endogenous galE gene as described above. Further preferred genetic modifications reduce or eliminate the expression of at least one gene selected from the group consisting of cps, ctrA, ctrB, ctrC, ctrD, exbB, exbD,frpB, IpbB, nmb0033, opA, opC, phoP, pilC, pmrE, pmrF, porA, porB, siaA, siaB, siaC, siaD, synA, synB, synC, tbpA, tbpB, and homologues of any of these genes. Many of these mutations are reviewed in WO02/09746.

In a further embodiment, the genetically modified bacterium of the invention, is further genetically modified to express a heterologous antigen. Preferably, the heterologous antigen is expressed on the extracellular outer membrane surface of the bacterium. The heterologous antigen can e.g. be an outer membrane protein from another bacterium, preferably from another Gram negative bacterium. Alternatively, the heterologous antigen can be fused to a protein that is expressed on the extracellular outer membrane surface of the bacterium, e.g. a neisserial outer membrane protein as are well known in the art per se.

Preferably, the heterologous antigen expressed by the genetically modified bacterium of the invention, comprises at least one epitope for inducing and/or enhancing an immune response against an antigen comprising the epitope. Preferably, a B-cell, humoral or antibody response is elicited by the epitope in the heterologous antigen. Preferably the epitope in the heterologous antigen elicits a protective and/or neutralizing antibody response. Alternatively and/or additionally, the heterologous antigen comprises epitopes that elicit a T cell response. A preferred T-cell response induced and/or enhanced by an immunogenic peptide comprises at least one of an HLA class I restricted CTL response and an HLA class II restricted Th response. More preferably the T-cell response consists of both an HLA class I restricted CTL response and simultaneously an HLA class II restricted Th response, and may be advantageously accompanied by a B- cell response.

The heterologous antigen can comprise one or more epitopes from a wide range of antigens of pathogens (infectious agents) and/or tumours. For example, the heterologous antigen may comprise one or more epitopes from antigens from pathogens and infectious agents such as viruses, bacteria, fungi and protozoa. Some examples of pathogenic viruses causing infections or tumours from which epitopes from antigens may be derived include: hepatitis (A, B, or C), herpes virus (e.g., VZV, HSV-I, HAV-6, HSV-II, and CMV, Epstein Barr virus), adenovirus, SV40 virus (causing mesothelioma), influenza virus, flaviviruses, ebola virus, echovirus, rhinovirus, coxsackie virus, coronavirus, respiratory syncytial virus (RSV), mumps virus, rotavirus, measles virus, rubella virus, parvovirus, vaccinia virus, HTLV virus, dengue virus, molluscum virus, poliovirus, rabies virus, JC virus, arboviral encephalitis virus, and human immunodeficiency virus (HIV virus; e.g., type I and II), human papilloma virus (HPV). Some examples of pathogenic bacteria causing infections from which epitopes from antigens may be derived include: Borrelia, Listeria, Escherichia, Chlamydia, Coxiella, Rickettsial bacteria, Mycobacteria, Staphylococci, Streptocci, Pneumonococci, Meningococci, Gonococci, Klebsiella, Proteus, Serratia, Pseudomonas, Legionella, Diphtheria, Salmonella, Bacilli, Bordetella, bacteria causing Cholera, Tetanus, Botulism, Anthrax, Plague, Leptospirosis, Whooping cough and Lymes disease. Some examples of pathogenic fungi causing infections from which epitopes from antigens may be derived include: Candida (e.g., albicans, krusei, glabrata and tropicalis), Cryptococcus neoformans, Aspergillus (e.g., fumigatus, niger), fungi of the genus Mucorales (Mucor, Absidia and Rhizopus), Sporothrix schenkii, Blastomyces dermatitidis, Paracoccidioides brasiliensis, Coccidioides immitis and Histoplasma capsulatum. Some examples of pathogenic parasites causing infections from which epitopes from antigens may be derived include: Entamoeba histolytica, Balantidium coli, Naegleria, Fowleri, Acanthamoeba sp., Giardia lambia, Cryptosporidium sp., Pneumocystis carinii, Plasmodium vivax, Babesia microti, Trypanosoma brucei, Trypanosoma cruzi, Leishmania donovani, Toxoplasma gondii and Plasmodium falciparis.

In addition, the C-terminal fusion can comprise one or more epitopes from a wide range of tumour antigens, including e.g. MAGE, BAGE, RAGE, GAGE, SSX-2, NY- ESO-1, CT-antigen, CEA, PSA, p53, XAGE and PRAME but also virally induced malignancies, comprising Human papilloma virus (HPV), Kaposi sarcoma herpes virus (KSHV), Epstein Bar virus induced lymphoma's (EBV). Other examples of tumour antigens from which epitopes for use in the present invention may be derived are various ubiquitously expressed self-antigens that are known to be associated with cancer, which include e.g. p53, MDM-2, HDM2 and other proteins playing a role in p53 pathway, molecules such as surviving, telomerase, cytochrome P450 isoform 1B1, Her-2/neu, and CD 19 and all so-called house hold proteins. Cancers that may be treated in accordance with the present invention are selected among the following list: lung, colon, esophagus, ovary, pancreas, skin, gastric, head and neck, bladder, sarcoma, prostate, hepatocellular, brain, adrenal, breast, endometrial, mesothelioma, renal, thyroid, hematological, carcinoid, melanoma, parathyroid, cervix, neuroblastoma, Wilms, testes, pituitary and pheochromocytoma cancers. In one embodiment, the heterologous antigen comprises or consists of one or more surface exposed epitopes from a proteinaceous antigen of an infectious agent or tumour. The heterologous antigen can e.g. comprises or consists of an extracellular and/or surface exposed domain of the proteinaceous antigen of an infectious agent or tumour.

In a third aspect, the invention relates to a neisserial LPS as herein defined above, wherein the LPS is obtained or obtainable from a genetically modified bacterium as herein defined above.

In a fourth aspect, the invention pertains to an OMV comprising a neisserial LPS as herein defined above. OMV (also known as "blebs") for use in vaccines have traditionally been prepared by detergent extraction (a dOMV purification process), wherein detergents such deoxycholate are used to remove LPS and increase vesicle release. The LPS of most Gram-negative bacteria, such as N. meningitidis is highly toxic, yet residual amounts (approx. 1%) are needed in OMV to maintain vesicle structure and for adjuvant activity. However, the neisserial LPS of the invention combines reduced toxicity with useful adjuvant activity and therefore preferably remains present in the OMV to a much larger degree than the toxic wild type LPS. The detergent extraction process is therefore less suitable for producing OMV comprising the neisserial LPS of the present invention. An OMV comprising a neisserial LPS according to the invention therefore preferably is not a detergent-extracted OMV. It is understood however, that a process for preparing an OMV that is not a detergent-extracted OMV does not exclude the use of any detergents. The use of low concentration of detergent and/or the use of mild detergents are not excluded as long as most of the neisserial LPS according to the invention, i.e. at least 5, 10, 20, 50, 60, 70, 80, 90, 95 or 99% of the neisserial LPS, is maintained, e.g. as compared the amount of neisserial LPS present in spontaneous or supernatant OMV from an equal amount of the same culture. A preferred OMV comprising a neisserial LPS of the invention is a supernatant or spontaneous OMV, i.e. sOMV as herein defined above, or a native OMV, i.e. nOMV as herein defined above. Methods for preparing nOMV are e.g. described in Saunders et al. (1999, Infect Immun, 67, 113-119), van de Waterbeemd et al. (2012, Vaccine, 30: 3683- 3690) and in WO2013006055 and methods for preparing sOMV are e.g. described in van de Waterbeemd et al. (2013, PLoS ONE, 8(1): e54314. doi: 10.1371/journal.pone.0054314) and in Lee et al. (2007, Proteomics, 7: 3143-3153), all of which are incorporated herein by reference. The OMV comprising a neisserial LPS of the invention are preferably obtained or obtainable from a genetically modified neisserial bacterium as herein defined above.

In a fifth aspect, the invention relates to a composition comprising at least one of a neisserial LPS, a genetically modified bacterium and an OMV as herein defined above.

In a preferred embodiment, the composition as defined herein comprises at least about 0.01, 0.05, 0.10, 1, 5, 10, 20, 30, 40, 50, 100 or 500 μg/ml of the neisserial LPS, genetically modified bacterium or OMV.

Preferably, the composition is a pharmaceutical composition further comprises a pharmaceutically acceptable excipient, carrier, medium or delivery vehicle as are conventionally known in the art (see e.g. "Handbook of Pharmaceutical Excipients", Rovve et al eds. 7 ^th edition, 2012, www.pharmpress.com). Pharmaceutically acceptable stabilizing agents, osmotic agents, buffering agents, dispersing agents, and the like may also be incorporated into the pharmaceutical compositions. The preferred form depends on the intended mode of administration and therapeutic application. The pharmaceutical carrier can be any compatible, non-toxic substance suitable to deliver to the patient. The "active ingredients of the invention" are herein understood to be one or more of a neisserial LPS, a genetically modified bacterium or an OMV as defined herein above.

Pharmaceutically acceptable carriers for parenteral delivery are exemplified by sterile buffered 0.9% NaCl or 5% glucose optionally supplemented with a 20% albumin. Alternatively, the active ingredients of the invention can be suspended in Phosphate buffer saline (PBS). Preparations for parental administration must be sterile. The parental route for administration of the active ingredients of the invention is in accord with known methods, e.g. injection or infusion by intravenous, intraperitoneal, intramuscular, intraarterial or intralesional routes. A typical pharmaceutical composition for intramuscular injection would be made up to contain, for example, 1 - 10 ml of phosphate buffered saline comprising the effective dosages of the active ingredients of the invention. Methods for preparing parenterally administrable compositions are well known in the art and described in more detail in various sources, including, for example, "Remington: The Science and Practice of Pharmacy" (Ed. Allen, L. V. 22nd edition, 2012, www.pharmpress.com).

In a preferred embodiment, the pharmaceutical composition of the invention is a vaccine. The vaccine can be an acellular vaccine preferably comprising at least one a neisserial LPS and an OMV as defined herein above. Alternatively, the vaccine can be a whole cell vaccine comprising at least a bacterium as herein defined above, wherein preferably the bacterium is inactivated or killed using means known in the art per se.

In a sixth aspect, the invention pertains to a process for producing a neisserial LPS of the invention. The process preferably comprises the steps of a) cultivating a genetically modified bacterium as herein defined above, preferably under condition conducive to the production of the LPS; and b) optionally, at least one of extraction and purification of the LPS. Methods for extraction of LPS are well known in the art (see e.g. 19). Methods for purification of LPS are described in the Examples herein and can e.g. include solid phase extraction (SPE) on reverse phase cartridges.

In a seventh aspect, the invention relates to a process for producing an OMV of the invention. The process preferably comprises the steps of a) cultivating a genetically modified bacterium as herein defined above, preferably under condition conducive to the production of the OMV; b) optionally, extracting the OMV; and recovering the OMV, wherein the recovery at least comprises removal of the bacteria from the OMV. Methods for preparing OMV, preferably detergent-free methods for preparing OMV, are described herein above. A preferred process for preparing OMV of the invention is thus a detergent- free process, e.g. a process for preparing nOMV or sOMV.

In an eighth aspect, the invention pertains to a process for producing an acellular vaccine as herein defined above. The process preferably comprises the steps of: a) producing at least one of: i) a neisserial LPS as herein defined above, preferably in a process for producing a neisserial LPS as herein defined above; and, ii) an OMV as herein defined above, preferably, in a process for producing an OMV as herein defined above; and, b) formulating at least one of the neisserial LPS and the OMV, optionally with further vaccine components, into a vaccine formulation. In a ninth aspect, the invention relates to a process for producing a whole cell vaccine as herein defined above. The process preferably comprises the steps of: i) cultivating a genetically modified bacterium as herein defined; and, ii) optionally, at least one of inactivation of the bacterium and formulation into a vaccine.

In a tenth aspect, the invention pertains to the use as medicament of at least one of a neisserial LPS of the invention, a genetically modified bacterium of the invention, an OMV of the invention, and a pharmaceutical composition of the invention.

In an eleventh aspect, the invention relates to a neisserial LPS of the invention for use in a treatment comprising inducing or stimulating an immune response in a subject. Preferably, in the treatment, the neisserial LPS is used as adjuvant. A neisserial LPS of the invention can e.g. be included as adjuvant in a vaccine composition, preferably together with an antigen against which it is desirable to induce or stimulate an immune response. Preferably therefore, a neisserial LPS of the invention is used in a treatment comprising inducing or stimulating an immune response in a subject, wherein the treatment further comprises the administration of an antigen together with the neisserial LPS and wherein the treatment is for preventing or treating an infectious disease or tumour associated with the antigen, wherein the antigen preferably is an antigen as herein defined above.

In this aspect, the invention thus relates to a method for vaccination against, or for prophylaxis or therapy of an infectious disease or tumour, or for inducing or stimulating an immune response against an infectious disease or tumour. The method preferably at least comprises the step of administration of a therapeutically or prophylactically effective amount of an neisserial LPS of the invention or a pharmaceutical composition comprising said LPS, to a subject in need of said prophylaxis, therapy or immune response. The pharmaceutical composition comprising preferably also an antigen associated with the infectious disease or tumour, wherein the antigen preferably is an antigen as herein defined above.

In a twelfth aspect, the invention relates to a neisserial LPS of the invention for use as a Toll-like receptor 4 (TLR4) agonist. Preferably, the neisserial LPS is used as TLR4 agonist in an immunotherapy. Preferably, the immunotherapy is an immunotherapy of a cancer (see e.g. 37) or of a neurodegenerative disease (see e.g. 35), including e.g. Alzheimer's disease or Parkinson's disease. Alternatively, the neisserial LPS is used as TLR4 agonist in a generalized immune stimulation for preventing and/or reducing the spread of (diverse) microbial infections and/or to suppress bacterial growth (see e.g. 36).

In this document and in its claims, the verb "to comprise" and its conjugations is used in its non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded. In addition, reference to an element by the indefinite article "a" or "an" does not exclude the possibility that more than one of the element is present, unless the context clearly requires that there be one and only one of the elements. The indefinite article "a" or "an" thus usually means "at least one".

All patent and literature references cited in the present specification are hereby incorporated by reference in their entirety.

The following examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way.

Description of the figures

Figure 1. Charge deconvo luted ESI-FT mass spectra of LPS. The charge deconvoluted ESI-FT mass spectra of the LPS isolated from twelve different strains of Neisseria meningitidis are shown as follows: parent HB-1 strain (A), AlpxLl (B), AlpxL2 (C),pagL (D), AlpxLl-pagL (E), AlpxL2-pagL (F), AlpxLl-lpxP cultured at 30°C for 5 h (G) or at 25°C overnight (H), AlptA (I), AlptA-AlpxLl (J), AlptA-pagL (K) and AlptA-lpxE (L). A simplified representation of the LPS structure assigned to the ion of 3408.507 u is included in mass spectrum (A). The vertical line at a mass of 3408.514 u, which corresponds to the calculated molecular mass of this latter LPS species, is used as a reference to indicate LPS composition assigned to other ion signals. See Supplemental Table 1 for detailed LPS composition proposals. All annotations refer to monoisotopic masses of the neutral molecules. Figure 2. TLR4 activation by N. meningitidis strains as indicated. HEK-blue hTLR4 cells were stimulated with 5-fold serial dilutions of heat-inactivated N. meningitidis for 20 h. TLR4 activation was measured by detection of secreted alkaline phosphatase. Results of serial dilutions are depicted in a line graph (A) and for a single ODeoonm of 0.0004 in a bar graph (B). Data are expressed as mean values or mean ± SD of three independent experiments. Statistical significance was determined with an ANOVA test comparing against HB-1. *, p < 0.05; p < 0.0001. Data are also presented in Table 4.

Figure 3. TLR4 activation by purified LPS structures. HEK-blue hTLR4 cells were stimulated with 10-fold serial dilutions of 12 different LPS structures. TLR4 activation was measured by detection of secreted alkaline phosphatase. Data are representative results from three independent experiments and are depicted as the mean values of triplicates.

Figure 4. Cytokine release of MM 6 cells stimulated with purified LPS structures. MM6 cells were incubated with 10-fold serial dilution of different LPS structures for 20 h. IL- 6 (A), IP- 10 (B), IL-Ιβ (C), MCP-1 (D) production was measured by ELISA. IL-6 and IL-Ιβ are considered MyD88 dependent cytokines and IP- 10 and MCP-1 are more TRIF dependent. Cytokine levels of MM6 cells stimulated with 5 ng/ml LPS are also presented as percentages of the HB-1 strain (E) and cytokine ratios in concentration (F) and percentages (G). For the cytokine ratios (F+G) the background without LPS stimulation was subtracted. Data shown are depicted as the mean values of two independent experiments. Statistical significance was determined with a 2-way ANOVA test comparing against HB-1. *, p < 0.05. Data are also presented in Tables 5 and 6.

Examples

1. Methods and Materials

1.1 Bacterial strains and plasmids

All mutants were created in a N. meningitidis H44/76 strain (HB-1) strain using plasmid pMF121, resulting in deletion of the capsular biosynthesis locus including the galE gene. N. meningitidis strains were grown on GC medium base (Difco) plates supplemented with IsoVitaleX, in a humid atmosphere containing 5% C02 at 37 °C. For liquid culture, strains were grown in 36 mg/mL tryptic soy broth medium (Difco) in a conical flask at 37 °C, shaken at 140 RPM. Required antibiotics were added to plate and liquid cultures (kanamycine 100μg/ml, chlooramphenicol 3μg/ml). The IpxLl and lpxL2 mutants were obtained by transformation with a linearized PCRII plasmid (Invitrogen) carrying the genes with a kanamycine resistance cassette described by van der Ley et al. (15) or a pGem T easy plasmid (Promega) with the IpxLl gene that has a deleted section replaced with a chloramphenicol (CAM) cassette. For the IptA mutant the gene was amplified by PCR from the H44/76 strain, cloned into a pGem T easy plasmid (Promega) and a kanamycine cassette was placed in the gene at the Muni restriction site. The plasmid was linearized by digestion with a restriction enzyme cleaving outside the gene and transformed into the N. meningitidis H44/76 (HB-1) strain. N. meningitidis derivatives carrying the genes pagL, lpxP and lpxE were created using a pENl 1 plasmid previously described for the expression of the Bordetella bronchiseptica pagL gene (13,18). To obtain lpxP and lpxE derivatives the pagL gene in the pENl l plasmid was replaced with the lpxP or lpxE gene amplified by PCR fromE. coli and B. bronchiseptica, respectively. Expression of the genes on the penl 1 plasmid was induced by addition of lmM isopropyl-P-D-thioglactopyranoside (IPTG) and CAM (3μ /ιη1) to the liquid culture medium. Primers are listed in Table 1.

Table 1. PCR primers used in the construction of the the mutant strains

1.2 LPS isolation

LPS from bacterial mutants was extracted with hot phenol- water (19) and purified further by solid phase extraction (SPE) on reverse phase cartridges. In short, cells from 50 ml of bacterial culture with an ODeoonm of 1.4 (or 100 ml of the AlpxLl-lpxP mutant grown at 30 °C) were collected by centrifugation at 2,739 x g for 1 h at 20°C. Then, bacteria were suspended in 20 ml of water and centrifuged at 2,739 x g for 25 min at 20°C. For hot phenol-water extraction, bacterial pellets were suspended with 4 ml of water, heated to 70°C, mixed with 3.2 ml of phenol at the same temperature and kept under agitation for 10 min at 70°C. The aqueous phase was separated from the phenolic phase by centrifugation at 2,739 x g for 15 min at 20°C. After transferring the aqueous phase to a new vial, the phenolic phase was extracted again by adding 3 ml of water at 70°C and repeating the extraction procedure. The aqueous phases from two consecutive extractions were pooled (~6.5 ml) and prepared for SPE by adding 5 ml of 0.356 M triethylammonium acetate (TEAA) pH 7 (solvent A) and 3.8 ml of 2- propanol:water:triethylamine:acetic acid (70:30:0.03:0.01, v/v) pH 8.7 (solvent B). In total, ten LPS extracts each from a different bacterial mutant could be purified simultaneously by SPE on reverse phase Sep-Pak CI 8 cartridges (1 ml syringe-barrel- type Vac cartridge, 50 mg of CI 8 resin, Waters) using a 20-position vacuum manifold (Waters). Cartridges were conditioned for SPE by applying consecutively 1 ml of 2- propanol:water:triethylamine:acetic acid (85: 15:0.015:0.005, v/v) pH 8.7 (solvent C), 0.07 mM TEAA pH 7 (solvent D) and solvent A under vacuum. Then, samples were split into two aliquots of equal volume and each aliquot was applied into a different cartridge. Next, cartridges were washed once with 1 ml of solvent A and twice with 1 ml of 20% (v/v) solvent B in solvent D. LPS was eluted from the columns by applying 0.6 ml of solvent C. Eluates from the same sample were combined (1.2 ml per sample in total) and dried in a centrifugal vacuum concentrator (Concentrator plus, Eppendorf) at room temperature. LPS concentration in isolated samples was determined by the 3-deoxy-D- man/70-oct-2-ulosonic acid (Kdo) assay (20). In addition, the purity and integrity of purified samples were judged by Tricine-SDS-PAGE using 1 mm-thick, 16% precast Novex ^® mini-gels (Thermo Fisher Scientific Inc.), LPS silver staining (21) and protein visualization with Imperial™ Protein Stain (Thermo Scientific).

1.3 Mass spectrometry

Electrospray ionization Fourier transform mass spectrometry (ESI-FT-MS) was performed on an LTQ Orbitrap XL instrument (Thermo Scientific) in negative ion mode. LPS samples were dissolved in a mixture of water, 2-propanol and triethylamine (50:50:0.001, by volume) pH 8.5 and infused into the mass spectrometer by static nano- ESI (22,23). The MS instrument was calibrated with a Pierce Negative Ion Calibration Solution (Thermo Scientific) and internally with taurocholic acid following standard procedures provided by the manufacturer (Thermo Scientific). Fragmentation analysis of intact LPS was carried out by in-source collision-induced fragmentation (SID). Y- and B-type fragment ions, corresponding to the lipid A and oligosaccharide moieties of LPS, respectively, were generated by SID at a potential difference of 100 V. Fragment ions are annotated according to the nomenclature of Domon and Costello (24). Mass spectra were charge-deconvoluted using the Xtract tool of Thermo Xcalibur 3.0 software (Thermo Scientific). All mass values given refer to monoisotopic molecular masses. Proposed LPS compositions are based on the general chemical structure of the L3 immunotype LPS from N. meningitidis reported previously (25,26). 1.4 Cell stimulation

Mono Mac 6 cells were seeded at lxl 0 ⁵ cells per well in 96 well microtiter plates in 100 μΐ Iscove's modified Dulbecco's medium (IMDM) (Invitrogen) medium supplemented with 100 units/ml penicillin, 100 μg/ml streptomycin, 292 μg/ml 1- glutamine (Invitrogen), and 10% fetal calf serum (Invitrogen). Hek blue-hTLR4 cells (Invivogen), a HEK293 cell line stably expressing human TLR4, MD-2 and CD 14, were seeded at 3.5x10 ⁴ cells per well in 96-well microtiter plates in 100 μΐ DMEM (Invitrogen) medium supplemented with 100 units/ml penicillin, 100 μg/ml streptomycin, 292 μg/ml 1-glutamine (Invitrogen), and 10% fetal calf serum (Invitrogen). Cells were stimulated with 10-fold serial dilutions of LPS in IMDM (MM6 cells) or DMEM (HEK blue-hTLPv4 cells) for 18-20h at 37°C in a humid atmosphere containing 5% C0 ₂ . HEK- blue-hTLPv4 cells were also stimulated with serial dilution of whole bacterial cells. Cytokine concentration in the supernatants of MM6 cells was determined by enzyme- linked immunosorbent assay (ELISA). All cytokine (IL-6, IL-Ιβ, IP- 10, MCP-1) concentrations were determined using a DUOset ELISA development kit (R&D systems) following the manufacturer's instructions. To quantify alkaline phosphatase secreted by HEK-blue-hTLR4 cells, 20 μΐ of the supernatant from each well was added to 200 μΐ Quanti-blue (Invivogen) and incubated at 37°C for 2-3 hours. Read out was done on a spectrophotometer at 649nm. Statistically significant differences were determined by the one-way (alkaline phosphatase secretion) or two-way (Cyokine release) ANOVA test by using GraphPad Prism 6.04 statistical software (GraphPad Software, Inc.).

2. Results

2.1 Bioengineering of modified LPS structures

LPS mutants in N. meningitidis were constructed in the HB-1 derivative of strain H44/76.The HB-1 strain is capsule deficient and has a galE deletion that results in truncation of the LPS oligosaccharide. Mass spectrometric analysis demonstrated that the HB-1 strain expresses a hexa-acylated, tri-phosphate, bis-phosphoethanolamine lipid A structure (see below). To construct a diverse set of LPS mutants in strain HB-1, we inactivated the autologous genes encoding for the LPS enzymes LptA, LpxLl and LpxL2 and heterologously expressed the LpxE, LpxP and PagL LPS enzymes (see Table 2) by cloning the genes on the penl 1 plasmid behind a lac promotor. Table 2. Overview of the inactivated the autologous genes encoding for the LPS enzymes LptA, LpxLl and LpxL2 and heterologously expressed the LpxE, LpxP and PagL LPS enzymes.

In addition, combinations of deletion of autologous genes and expression of heterologous enzymes were constructed. This approach resulted in 11 LPS mutant strains as listed in Table 3.

For the expression of LpxE (Protein ID: CAE41138.1) we initially cloned an IpxE homologue from Bordetella pertussis. However, expression of the gene in HB-1 or its IptA mutant derivative did not result in any LPS structural changes as determined by mass spectrometry. As an altenative the IpxE (Genbank accession number: WP 003809405.1) homologue from Bordetella bronchiseptica, which exists as a pseudogene in B. pertussis, was cloned and expressed in a AlptA mutant strain. This resulted in the loss of a phosphate group in the lipid A and was included in our panel of LPS mutant strains (Fig 1L).

LpxP (Genbank accession number: U49787.1), an enzyme known to add a secondary 9-hexadecenoic acid (C16:l) to the 2' acyl chain m E.coli (27), was expressed in the N. meningitidis AlpxLl mutant strain, because the LpxLl enzyme also adds a secondary acyl chain on the same position. This modification was done to create a hexa- acylated lipid A structure different from the original by carrying a longer C 16 secondary acyl chain in the 2' position instead of C12. When LpxP was expressed in the AlpxLl mutant strain at 37°C this resulted in a very faint addition of CI 6: 1. However, the CI 6: 1 is added onto E.coli LPS only at 12°C, so for this reason we grew the bacteria at lower temperatures. Cultivation of meningococci below 25°C is, unlike in E. coli, not possible, but at 25°C and 30°C we already found a much higher relative abundance of the LpxP hexa-acylated lipid A structure carrying the additional C 16: 1 , with 25°C resulting in the highest efficiency (at least 50 % relative abundance) (Fig 1H).

Table 3. Overview of the constructed LPS mutants in the N. meningitidis HB-1 strain

2.2 Mass spectrometric characterization of modified LPS

The charge-deconvo luted ESI-FT mass spectra of intact LPS isolated from the constructed N. meningitidis mutants are shown in Figure 1. The mass spectrum of LPS of the HB-1 (galE ^~ ) parent strain (Fig. 1A), displayed an ion signal of 3408.507 u consistent with LPS comprised of wild-type hexa-acyl lipid A carrying three phosphate (P) and two phosphoethanolamine (PEA) groups and an L3-immunotype oligosaccharide structure substituted with a glycine (Gly) residue and truncated at the proximal galactose (Gal) of its alpha chain due to inactivation of the galE gene (Mcalc.=3408.514 u, see Supplemental Table 1 for LPS composition proposals). Accompanying ion peaks of 3351.488, 3285.501 and 3228.480 u (Fig. 1A) corresponded to LPS species which lack Gly (Ameas.=-57.019 u), carry one less PEA group in the lipid A (Ameas.=-123.006 u) or both (Ameas.=- 180.027 u), respectively. This chemical heterogeneity of the LPS from HB-1 (galE-) strain is likely caused by variation in lipid A phosphorylation and oligosaccharide non-stoichiometric substitution with glycine. Composition proposals based on mass spectra of intact LPS were additionally supported by FT-MS analysis of LPS fragment ions corresponding to lipid A and oligosaccharide moieties, which were generated by in-source collision induced dissociation (SID) of intact LPS. For instance, SID FT mass spectra of LPS from HB-1 (galE ^~ ) strain displayed fragment ions of 1916.098 and 2039.106 u corresponding to hexa-acyl lipid A species with 2 and 3 PEA groups (Mcalc.= 1916.100 and 2039.109 u, respectively) and a fragment ion of 1369.404 u corresponding to the dehydrated derivative of the oligosaccharide moiety described above (Mcalc.= 1369.406 u). Fragmentation analyses of LPS derived from other strains of N. meningitidis described here showed that different types of LPS carry the same oligosaccharide moieties (PEAi.Hexi.Hep2-HexNAci.Kdo2-Glyi), with the exception of some LPS species, which lack a glycine or carry a second hexose residue (Hex) (Supplemental Table 2). Consequently, other differences observed between the LPS species, such as in the number of PEA and P groups, may be attributed to changes in the composition of the lipid A (Supplemental Table 2).

Analysis of the intact LPS from the AlpxLl mutant revealed that he main ion peaks of the mass spectrum (3046.315, 3103.336, 3169.324 and 3226.342 u, Fig. IB) had shifted compared to the 4 main ion signals of the LPS from the parent HB-1 (galE-) strain (Fig. 1A) by -182.165 u. This is in agreement with the lack of a dodecanoic acid (C12) (Acalc.=-182.167 u) in the lipid A after deletion of the Ipxll gene.

Comparative analysis of the mass spectrum of the LPS from the AlpxLl mutant displayed ion peaks of 3023.367, 2966.348, 3185.419 and 3128.398 u (Fig. 1C), which are consistent with the loss of a C 12 fatty acyl chain together with PPEA from the lipid A (Acalc.=-385.142 u) in combination with non-stoichiometric substitution of the oligosaccharide with Gly (Acalc.=57.021 u) or a second hexose (Acalc.=162.053 u). This is in agreement with effective deletion of the lpxL2 gene. It is worthy to note that deletion of the lpxL2 gene not only led to the loss a C12 fatty acyl chain, as observed earlier upon deletion of the IpxLl gene, but also resulted in the loss of a P and a PEA group from the lipid A.

The ion peaks in the mass spectrum of the LPS from the pagL mutant (3210.345, 3153.325, 3087.338 and 3030.318 u, Fig. ID) were found to be shifted by -198.163 u from the 4 main ion peaks of the LPS from the parent HB-1 strain. This is in agreement with efficient removal of a 3-hydroxy-dodecanoic acid (C120H) (Acalc.=-198.162 u) from the lipid A by the PagL enzyme. Nonetheless, display of minor ion peaks of 3408.505 and 3351.485 u (Fig. ID) corresponding to unmodified hexa-acyl LPS species indicated that LPS 3-O-deacylation activity of the PagL enzyme could not fully exhaust the hexa-acyl lipid A substrate.

The 4 main ion signals in the mass spectrum of the LPS from the AlpxLl-pagL mutant (3028.180, 2971.160, 2905.173 and 2848.152 u, Fig IE) differed by -380.328 u from the 4 main ion signals of the LPS from the HB-1 strain, which is accordance with lack of a C 12 and a C120H in the lipid A of the AlpxLl-pagL mutant (Acalc.=-380.329 u). The absence of ion signals corresponding to LPS carrying two C12 acyl chains indicates that the deletion of the IpxLl gene resulted in complete removal of a single C12 from the lipid A (see Supplemental Table 1 for detailed LPS composition proposals). In contrast, minor ion signals of 3226.339 and 3169.319 u were present in the mass spectrum of the LPS from the AlpxLl-pagL mutant, which correspond to penta-acyl LPS species carrying two C120H acyl chains. This indicates that a low level of LPS molecules was not 3-O-deacylated by the PagL enzyme.

The mass spectrum of the LPS from the AlpxL2-pagL mutant showed an ion peak of 2825.206 u (Fig. IF) that was shifted by -583.301 u from the ion signal of 3408.507 u of the mass spectrum of the LPS from the parent HB-1 strain (Fig. 1A). This fits the expected loss of a C120H, a C12 and PPEA from the lipid A (Acalc.=-583.304 u). Other ion signals of 2768.187, 2930.236 and 2987.257 u (Fig. IF) are consistent with non- stoichiometric substitution of the oligosaccharide with Gly or a second Hex.

Comparison of the mass spectrum of the LPS from the AlpxLl-lpxP mutant grown at 30°C (Fig. 1G) with that of the LPS from the AlpxLl mutant (Fig. IB) revealed that the LPS from the AlpxLl-lpxP mutant contained not only the main LPS species that were present in the LPS from the AlpxLl mutant (3046.315, 3103.333, 3169.322 and 3226.340 u, Fig. 1G), corresponding to penta-acyl LPS lacking a CI 2, but also LPS species (3282.524, 3339.543, 3405.533 and 3462.553 u, Fig. 1G) that shifted in the spectrum to higher mass values by 236.211 u. This is in agreement with incorporation of a 9- hexadecenoic acid (C 16 : 1 ) to the lipid A. Therefore, this preparation comprised a mixture of penta-acyl LPS that lacks a C12 and hexa-acyl LPS that lacks a C12 and additionally carry a C16: l .

The mass spectrum of the LPS from the AlpxLl-lpxP mutant cultured at 25°C (Fig.

1H) showed ion signals corresponding to hexa-acyl LPS lacking a C12 and carrying additionally a C16: l (3282.526, 3339.546, 3405.535 and 3462.554 u,Fig. 1H), which were of a higher relative abundance as compared to the same signals in the spectrum of the LPS from the AlpxLl-lpxP mutant grown at 30°C. Furthermore, other ion peaks corresponding to hexa-acyl LPS carrying a CI 6: 1 were displayed which arose from elongation of the oligosaccharide with a second Hex (3624.608 u) or the latter in combination with the loss of Gly substitution (3567.586 u) and the loss of a PEA group from the lipid A (3501.596 u) (Fig. 1H).

The ion peak of 3162.489 u in the mass spectrum of the LPS from the AlptA mutant (Fig. II) differed by -246.018 u from the ion signal of 3408.507 u of the mass spectrum of the LPS from the parent HB-1 strain (Fig. 1A). This points to the loss of two PEA groups from the lipid A (Acalc.=-246.017u). Other ion signals corresponded to LPS species that in addition to lacking PEA in the lipid A either lacked Gly in the oligosaccharide (3105.471), contained a second Hex in the oligosaccharide (3324.541) or contained a second Hex and lacked Gly in the oligosaccharide (3267.521 u) (Fig. II).

The mass spectrum of the LPS from the ΔΙρΐΑ-AlpxLl mutant displayed ion peaks of 2980.324, 2923.307, 3142.375 and 3085.354 u indicating the loss of 2PEA and a C12 from the lipid A (Acalc.=-428.184 u) combined with non-stoichiometric substitution of the oligosaccharide with Gly or a second Hex (Fig. 1 J). In addition, MS/MS spectra of the main lipid A fragment ion produced by in-source collision-induced dissociation of LPS were consistent with the presence of a P group at both the 1 and 4 'positions of the lipid A (data not shown). Therefore, the activity of the LpxE enzyme consisted in removal of one of the three P groups present in lipid A producing bisphosphorylated lipid A species with a P group on each side of the diglucosamine backbone.

The main ion signals of the mass spectrum of the LPS from the AlptA-pagL mutant

(2964.328 and 2907.31 1 u, Fig. IK) are consistent with the loss of 2PEA and a C120H from the lipid A (Acalc.=-444.179 u) together with non-stoichiometric substitution of the oligosaccharide with Gly (Acalc.=57.021 u). Minor ion peaks of 3105.468 and 3162.488 u were observed corresponding to hexa-acyl LPS species which lost only 2PEA from the lipid A, indicating a low level of incomplete LPS 3-O-deacylation by the PagL enzyme.

Finally, the mass spectrum of the LPS from the ΔΙρΐΑ-lpxE mutant showed 2 main ion peaks of 3082.525 and 3025.508 u consistent with loss of 2PEA and P from the lipid A (Acalc.=-325.983 u) in combination with non-stoichiometric substitution of the oligosaccharide with Gly (Fig. 1L).

2.3 TLR4 stimulation by the LPS mutant strains

To determine the scope of TLR4 activation by the entire set of lipid A mutant structures, an initial screening was done using HEK-Blue humanTLR4 cells. These cells express human TLR4, MD-2, and CD 14 and contain a nuclear factor kappa- light-chain- enhancer of activated B cells (NF-κΒ) and activator protein 1 (AP-1) dependent secreted embryonic alkaline phosphatase (SEAP) reporter gene. Stimulation of cells with serial dilutions of the different LPS mutants yielded a wide range of TLR4 activities (Fig. 2 and Table 4), with HB-1 inducing strongest TLR4 activation and ALpxL2 bacteria yielding lowest levels of activation. The other LPS mutants showed intermediate TLR4 stimulating activity (Fig. 2). A particularly notable result was that the absence of phosphoethanolamine in the AlptA strain resulted in reduced TLR4 activation both in the hexa-acylated wild type strain and the penta-acylated AlpxLl and pagL backgrounds. Induction of LpxE in the AlptA strain showed similar TLR4 activation as AlptA strain, which was slightly less than the HB-1 wild type strain. This indicates that the reduction of three phosphates to two in the lipid A structure with one phosphate on each side of the diglucosamine backbone did not affect TLR4 signalling.

Expression of LpxP at 25°C in combination with deletion of LpxLl resulted in a heterogeneous hexa- and penta-acylated structure-LPS expressing strain with a slightly reduced TLR4 activating potential compared to the wild type bacteria. Cultivation of this strain at 30°C resulted in less hexa-acylated lipid A and even slightly less TLR4 activity.

Surprisingly, when the AlpxLl strain was combined with expression of PagL, reducing the penta-acylted lipid A structure to a tetra-acylated lipid A structure, an increase of TLR4 activity was obtained. This was unexpected as tetra-acylated lipid A structures typically acts as a TLR4 antagonists as reported for E.coli lipid Iva (7,9,28).

2.4 Human TLR4 stimulation using purified mutant LPS We also purified LPS from all strains and used them to stimulate HEK-Blue TLR4 cells to confirm our initial findings with whole bacteria. Purified LPS generally yielded similar results as those obtained with intact bacteria although purified LPS, AlpxLI, AlptA- AlpxLl, AlpxL2 and A IpxL 2 -pagL showed almost no induction of TLR4 activity and were barely distinguishable from each other (Fig 3), whereas the bacteria these variants displayed low but distinct TLR4 activities above the background. In addition, a higher concentration of purified penta-acylated pagL LPS was needed for activation of TLR4 than with all the hexa-acylated LPS derivatives, but with whole bacteria stimulation, a lower absorption density was necessary for the pagL strain to induce TLR4 activity than the other hexa-acylated mutant strain (Fig 2+3). However, the maximum amount of alkaline phosphatase secretion was still lower for the pagL mutant strain compared to the hexa-acylated mutant strains. Of note, the three LPS mutants AlpxLl-pagL, pagL and AlptA-pagL had substantially reduced activating capabilities when compared to the wild type LPS, but still induced activation above the background level of unstimulated cells (Fig 3).

2.5 Cytokine induction by the purified mutant LPS

The cytokine induction profile of the modified LPS structures was investigated in the human monocytic cell line Mono Mac 6 (MM6). The concentration of secreted MyD88 dependent cytokines IL-6 (Fig 4A and Table 5 A) and IL-Ιβ (Fig 4B and Table 5B) and TRIF dependent cytokines interferon gamma- induced protein 10 (IP- 10) (Fig 4C and Table 5C) and monocyte chemotactic protein-1 (MCP-1) (Fig 4D and Table 5D) were determined after 20 h of stimulation with purified LPS (Fig 4 E, F and G and Table 6). The possible contribution of minor protein contamination in LPS samples to the observed responses was excluded as activation of a HEK-hTLR2 cell line by the LPS samples was negligible in the range of LPS concentrations tested (data not shown).

A wide variety of cytokine levels was determined from the different LPS structures, with the highest levels being produced by the HB-1 wild type hexa-acylated LPS and all other LPS ranging from close to wild type until virtually zero cytokine induction as seen for AlpxL2 LPS. Besides quantitative differences in cytokine induction, we also observed qualitative differences with LPS structures causing reduced levels of certain cytokines, but still capable of producing others. Some examples are pagL and AlptA-pagL LPS, which displayed a reduced capacity to induce the production of MyD88 dependent pro- inflammatory cytokines IL-6 and IL- 1 β only inducing 10% and 25% of the levels induced by wild-type LPS, respectively, but retained most of the ability to induce the secretion of TRIF dependent IP- 10 (50%) and MCP-1 (90%). Interestingly, differences were observed between AlpxLl-lpxP grown at 30°C and 25°C, with AlpxLl-lpxP grown at 30°C producing 30-40 % IL-6 and IL-Ιβ and 60-85% ofthose cytokines at 25°C, whereas IP- 10 and MCP-1 induction were similar. These results emphasize how LPS bioengineering can provide a wide range of agonists to fine-tune cytokine release.

3. Discussion

Although LPS has great potential as an adjuvant, adverse effects keep being a concern. Finding the optimal balance between adjuvant activity and minimal toxic effects requires the development of new LPS derivatives. Here we report a collection of novel meningococcal LPS structures inducing a broad range of TLR4 responses and differential cytokine patterns. These combinatorial bioengineered LPS mutants can be used as part of a whole cell vaccine, OMV vaccine or as purified LPS or lipid A molecule. OMVs of N. meningitidis are being actively investigated as potential vaccines and have been already approved for use in humans as a component of the Bexsero vaccine against serogroup B meningococcal disease (29,30). Attenuated AlpxLl LPS is under investigation as constituent of meningococcal OMV vaccines and is a safe method to detoxify OMVs (16,31). In addition, in an immunization study purified AlpxLl LPS retained similar adjuvant activity compared to wild type meningococcal LPS, but with reduced toxicity (15).

The modified LPS molecules LpxLl, LpxL2 and PagL all result in a reduced TLR4 activity compared to the parent strain (13,15). This was expected because they reduce the number of acyl chains in LPS from hexa to penta. Surprisingly, the expectation that tetra-acylated LPS is always less active than penta-acylated LPS is challenged by our results. Tetra-acylated lipid IVa of E. coli is a known antagonist of the human TLR4/MD-2 complex (7,9,28). Yet, we show that meningococcal tetra-acylated AlpxLl- pagL LPS is more active than the penta-acylated AlpxLl LPS, whereas tetra-acylated AlpxLl-AlpxL2 LPS did not yield detectable activity (data not shown). Stimulation with AlpxL2-pagL whole bacteria that also carry a tetra-acylated LPS again increased TLR4/MD-2 activity compared to its penta-acylated AlpxLl parent strain, although purified LPS from both the AlpxL2-pagL and AlpxLl were inactive. Together these findings indicate that removal of C120H from the 3'position by PagL in combination with deletion of a secondary acyl chain resulting in tetra-acylated lipid A yields a higher TLR4 activity compared to sole removal of the secondary acyl chain or both secondary acyl chains. LPS structures engineered in E. coli by Needham et al. (32), included a tetra- acylated LPS resulting through expression of PagL and deletion of LpxM, in removal of C120H from the 3'position by PagL and deletion of a secondary acyl chain from the glucosamine on the reducing end of the lipid A. This tetra-acylated LPS produced in E. coli thus has a different acyl chain distribution and chain length than the tetra-acylated structure of the AlpxLl-pagL mutant lipid A of the present invention, even though it is also more active than the penta-acylated LPS from its parent strain.

Interestingly, introduction of LpxP from E. coli into N. meningitidis conferred temperature-sensitive lipid A modification to N. meningitidis. Since conservation of temperature-sensitive gene expression signals is unlikely, this means that the enzyme itself is most active at lower temperatures. Selection of a temperature of 25 or 30°C for culture of the AlpxLl-lpxP strain influenced the amount of hexa-acylated LPS species present in the mixture of penta- and hexa-acylated LPS produced by this mutant, with the lower temperature leading to the highest degree of substitution. The temperature sensitivity of the LpxP enzyme thus enables to prepare penta- and hexa-acylated LPS mixtures in a controlled manner. By selecting the time and/or temperature that the mutant strain is grown, it is feasible to increase or decrease the amount of hexa-acylated lipid A structure and thereby the TLR4 activity and cytokine profile. This provides a new approach of fine-tuning the immunological properties of meningococcal OMV vaccines.

In addition, we have obtained new insight in the specificity of the LpxE enzyme. Previously, the IpxE gene from Francisella tularensis or Francisella novicida expressed in E. coli was shown to be specific for the removal of the P group in the 1 'position (32,33). We have found that the IpxE homologue from B. bronchiseptica removed only one P group from the total of three present in the lipid A of N. meningitidis. MS/MS spectra of the lipid A from AlptA-lpxE mutants were consistent with the presence of a P group at both the 1 and 4'positions of the lipid A. In addition, removal of the P group was only seen in double AlptA-lpxE mutants, therefore only in the absence of PEA substitution of the lipid A. Thus, it is likely that the presence of PEA prevents IpxE from removing the P group. Most likely, the newly described LpxE enzyme is a pyrophosphatase, only catalyzing hydrolysis between two phosphate groups. The absence of PEA in the lipid A through deletion of the IptA gene resulted in a reduced TLR4/MD-2 activity. This concurs with earlier observations by John et al. (34) that show a significant reduction of TNFa release by THP-1 cells upon stimulation with LptA lacking strains. Here we showed that reduction of the activity is even more apparent when stimulated with penta- acylated AlptA-pagL LPS or whole bacteria.

Interestingly, our results indicate that the absence of 2' C12 fatty acyl chain by deletion of LpxL2 is accompanied by removal of a single P group and PEA group. This was previously not observed due to isolation of lipid A by an acid hydrolysis method before mass spectrometric analysis, which can result in the loss of P groups from the lipid A(15). In the present study, we used complete LPS molecules without introducing any deleterious chemical modifications for mass spectrometric analysis, giving us the possibility to observe new phosphorylation changes of the lipid A.

Several of the constructed attenuated LPS structures did not only need a higher concentration to induce TLR4 stimulation, but also did not yield the level of activation observed for the parent strain. This was most apparent for pagL LPS. The reason for this phenomenon is unclear, but could be due to instable dimerization of the LPS-TLR4-MD2 receptor complex at the cell surface but stable dimerization inside the cell, and/or to a less stable dimerization with high concentrations of the particular LPS. In addition, certain LPS species showed no activation at all and could potentially have antagonistic features, and might therefore serve as a TLR4 blocking drug. Indeed, meningococcal AlpxLl and pagL penta-acylated LPS can block the TLR4 response when administered together with hexa-acylated wild type meningococcal LPS (13).

In the present study, we have used combinatorial bio engineering in meningococci to produce a range of LPS species with a broad array of TLR4 activity and cytokine profile. The application of these structures can be very broad, from inclusion into vaccines as adjuvants to their use in various forms of immunotherapy which have been described or suggested for LPS, such as cancer therapy, Alzheimer's disease or generalized immune stimulation to prevent diverse infections (3,35-37). Table 4. TLR4 activation by N. meningitidis strains (the same data are graphically presented in Fig. 2A). HEK-blue hTLR4 cells were stimulated with 5-fold serial dilutions at A600nm (y-axis) of heat-inactivated N. meningitidis for 20 h. TLR4 activation was measured by detection of secreted alkaline phosphatase at A649nm. Data are expressed as mean values of three independent experiments.

Table 5. Cytokine release of MM 6 cells stimulated with purified LPS (the same data are graphically presented in Fig. 4). MM6 cells were incubate with 10-fold serial dilution of different LPS mutants for 20 h. IL-6, IP- 10, IL-Ιβ, MCP-1 production was measured by ELISA. Data shown are depicted as the mean values in pg/mL of two independent experiments.

Table 6. Cytokine release in percentages of MM 6 cells stimulated with purified LPS (the same data are graphically presented in Fig. 4). MM6 cells were stimulated with 5 ng/ml LPS. Data are expressed as mean values of two independent experiments.

Supplemental Table 1 . Composition of the main ion peaks observed in charge-deconvo luted ESI-FT mass spectra of intact LOS from twelve mutants of N. meningitidis (see Fig. 1).

Measured Proposed LOS composition Calculated Deviation

Bacteria

mass (u) Oligosaccharide Lipid A mass (u) (ppm)

HB-1 3408.507 PEAi .Hexi .Hep2-HexNAci .Kdo2-Glyi P3-PEA2-HexN2-C122-C120H2-C140H2 3408.514 2.2

3351.488 PEAi -Hexi .Hep2-HexNAci -Kdo2 P3-PEA2-HexN2-C122-C120H2-C140H2 3351.493 1.5

3285.501 PEAi -Hexi .Hep2-HexNAci .Kdo2-Glyi P3-PEAi.HexN2-C122-C120H2-C140H2 3285.506 1.5

3228.480 PEAi -Hexi .Hep2-HexNAci -Kdo2 P3-PEAi.HexN2-C122-C120H2-C140H2 3228.484 1.4

AlpxU 3226.342 PEAi -Hexi .Hep2-HexNAci .Kdo2-Glyi P3-PEA2-HexN2-C12i.C120H2-C140H2 3226.347 1.7

3169.324 PEAi -Hexi .Hep2-HexNAci -Kdo2 P3-PEA2-HexN2-C12i.C120H2-C140H2 3169.326 0.6

3103.336 PEAi -Hexi .Hep2-HexNAci .Kdo2-Glyi P3-PEAi.HexN2-C12i.C120H2-C140H2 3103.339 0.9

3046.315 PEAi -Hexi .Hep2-HexNAci -Kdo2 P3-PEAi.HexN2-C12i.C120H2-C140H2 3046.317 0.8

3388.394 PEAi .Hex2'Hep2'HexNAci .Kdo2-Glyi P3-PEA2-HexN2-C12i.C120H2-C140H2 3388.400 1.8

3331.373 PEAi .Hex2'Hep2'HexNAci -Kdo2 P3-PEA2-HexN2-C12i.C120H2-C140H2 3331.379 1.7

AlpxL2 3023.367 PEAi -Hexi .Hep2-HexNAci .Kdo2-Glyi P2-PEAi.HexN2-C12i.C120H2-C140H2 3023.373 1.8

2966.348 PEAi -Hexi .Hep2-HexNAci -Kdo2 P2-PEAi.HexN2-C12i.C120H2-C140H2 2966.351 1.0

3185.419 PEAi .Hex2'Hep2'HexNAci .Kdo2-Glyi P2-PEAi.HexN2-C12i.C120H2-C140H2 3185.425 2.0

3128.398 PEAi .Hex2'Hep2'HexNAci -Kdo2 P2-PEAi.HexN2-C12i.C120H2-C140H2 3128.404 1.9

Measured Proposed LOS composition Calculated Deviation

Bacteria

mass (u) Oligosaccharide Lipid A mass (u) (ppm)

2687.254 PEAi .Hexi .Hep2-HexNAci -Kdoi P3-HexN2-C122-C120Hi-C140H2 2687.256 0.6

AlptA-lpxE 3082.525 PEAi -Hexi .Hep2-HexNAci .Kdo2-Glyi P2-HexN2-C122-C120H2-C140H2 3082.531 2.0

3104.507* PEAi -Hexi .Hep2-HexNAci .Kdo2-Glyi P2-HexN2-C122-C120H2-C140H2 3104.514 2.1

3025.508 PEAi -Hexi .Hep2-HexNAci -Kdo2 P2-HexN2-C122-C120H2-C140H2 3025.510 0.5

3047.488* PEAi -Hexi .Hep2-HexNAci -Kdo2 P2-HexN2-C122-C120H2-C140H2 3047.492 1.3

3069.468** PEAi -Hexi .Hep2-HexNAci -Kdo2 P2-HexN2-C122-C120H2-C140H2 3069.475 2.1

3244.576 PEAi .Hex2'Hep2'HexNAci .Kdo2-Glyi P2-HexN2-C122-C120H2-C140H2 3244.584 2.4

3187.556 PEAi .Hex2'Hep2'HexNAci -Kdo2 P2-HexN2-C122-C120H2-C140H2 3187.562 2.0

2805.449 PEAi -Hexi .Hep2-HexNAci -Kdoi P2-HexN2-C122-C120H2-C140H2 2805.451 0.8

(*) Monosodium adduct. (**) Disodium adduct. Abbreviations: Kdo, 3-deoxy-D-wa««o-oct-2-ulosonic acid; Hep, L-glycero-O-manno- eptose; Hex, hexose; HexNAc, N- acetylhexosamine; Gly, glycine; PEA, phosphoethanolamine; P, phosphate; C120H, 3-hydroxy-dodecanoic acid; C140H, 3 -hydro xy-tetradecanoic acid; C12, dodecanoic acid; CI 6: 1, 9-hexadecenoic acid

Supplemental Table 2. Proposed compositions for charge-deconvo luted fragment ion peaks obtained by in-source collision-induced dissociatio ESI-FT MS of LOS.

Fragment Proposed LOS composition

Measured Calculated Deviation

Bacteria ion

mass (u) Oligosaccharide Lipid A mass (u) (ppm) type ³ '

HB-1 B 1369.404 PEi ·ΗΘΧΙ .Hep2 _' HexNAci .Kdo2 _' Glyi 1369.406 1.1

B-Kdo-C02 1105.355 PEi .Hexi .Hep2 _' HexNAci .Kdo2 _' Glyi 1105.357 2.2

B-Kdo-C02 1048.334 PEi -Hexi ·ΗΘΡ2·ΗΘΧΝΑΟΙ - do2 1048.336 1.9

Y 1916.098 P3-PEi.HexN2-C122-C120H2-C140H2 1916.100 1.2

Y 2039.106 P3-PE2-HexN2-C122-C120H2-C140H2 2039.109 1.4

AlpxU B 1369.405 PEi -Hexi .Hep2 _' HexNAci .Kdo2 _' Glyi 1369.406 0.4

B-Kdo-C02 1105.356 PEi -Hexi ·Ηβρ2·ΗΘχΝΑοι .Kdo2>Glyi 1105.357 1.3

B-Kdo-C02 1048.335 PEi -Hexi ·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1048.336 0.9

Y 1733.933 P3-PEi.HexN2-C12i.C120H2-C140H2 1733.933 0.2

Y 1856.942 P3-PE2-HexN2-C12i.C120H2-C140H2 1856.942 0.1

AlpxL2 B 1369.404 PEi -Hexi .Hep2 _' HexNAci .Kdo2'Glyi 1369.406 1.1

B-Kdo-C02 1105.356 PEvHexi-Hep2-HexNAci.Kdo2'Glyi 1105.357 1.3

B-Kdo-C02 1048.335 PEi -Hexi ·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1048.336 0.9

B-Kdo-C02 1267.409 PEi .Hex2 _' Hep2 _' HexNAci .Kdo2-Glyi 1267.410 1.0

Fragment Proposed LOS composition

Measured Calculated Deviation

Bacteria ion

mass (u) Oligosaccharide Lipid A mass (u) (ppm) type ³ '

Y 1733.932 P3-PEi.HexN2-C12i.C120H2-C140H2 1733.933 0.7

Y-P 1653.965 P3-PEi.HexN2-C12i.C120H2-C140H2 1653.967 1.2

Y-2P-H20 1555.988 P3-PEi.HexN2-C12i.C120H2-C140H2 1555.990 1.3

Y 2093.153 P3-PE2-HexN2-C12i.C120H2-C140H2.C16:1 i 2093.156 1.4

Y 1970.147 P3-PEi.HexN2-C12i.C120H2-C140H2.C16:1 i 1970.147 0.2

Y-P 1890.182 P3-PEi.HexN2-C12i.C120H2-C140H2.C16:1 i 1890.181 0.5

Y-2P-H20 1792.202 P3-PEi.HexN2-C12i.C120H2-C140H2.C16:1 i 1792.204 1.2

AlpxL1-LpxP

25°C B 1369.404 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ•Kdo2-Glyi 1369.406 1.1

B 1312.379 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1312.384 3.9

B-Kdo-C02 1105.356 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ•Kdo2-Glyi 1105.357 1.3

B-Kdo-C02 1048.335 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1048.336 0.9

B-Kdo-C02 1267.409 PEi ·ΗΘΧ2·ΗΘΡ2·ΗΘΧΝΑΟΙ•Kdo2-Glyi 1267.410 1.0

B-Kdo-C02 1210.387 PEi ·ΗΘΧ2·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1210.389 1.5

Y 1856.941 P3-PE2-HexN2-C12i.C120H2-C140H2 1856.942 0.4

Y 1733.932 P3-PEi.HexN2-C12i.C120H2-C140H2 1733.933 0.7

Y-P 1653.965 P3-PEi.HexN2-C12i.C120H2-C140H2 1653.967 1.2

Fragment Proposed LOS composition

Measured Calculated Deviation

Bacteria ion

mass (u) Oligosaccharide Lipid A mass (u) (ppm) type ³ '

Y-2P-H20 1555.988 P3-PEi.HexN2-C12i.C120H2-C140H2 1555.990 1.3

Y 2093.152 P3-PE2-HexN2-C12i.C120H2-C140H2.C16:1 i 2093.156 1.8

Y 1970.147 P3-PEi.HexN2-C12i.C120H2-C140H2.C16:1 i 1970.147 0.2

Y-P 1890.18 P3-PEi.HexN2-C12i.C120H2-C140H2.C16:1 i 1890.181 0.5

Y-2P-H20 1792.203 P3-PEi.HexN2-C12i.C120H2-C140H2.C16:1 i 1792.204 0.6

Δ/ptA B 1369.404 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ•Kdo2-Glyi 1369.406 1.1

B 1312.38 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1312.384 3.1

B-Kdo-C02 1105.356 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ•Kdo2-Glyi 1105.357 1.3

B-Kdo-C02 1048.335 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1048.336 0.9

B-Kdo-C02 1267.408 PEi ·ΗΘΧ2·ΗΘΡ2·ΗΘΧΝΑΟΙ•Kdo2-Glyi 1267.410 1.8

B-Kdo-C02 1210.387 PEi ·ΗΘΧ2·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1210.389 1.5

Y 1793.09 P3-HexN2-C122-C120H2-C140H2 1793.092 1.0

Y 1713.123 P2-HexN2-C122-C120H2-C140H2 1713.125 1.5

AlptA-AlpxL1 B 1369.405 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ•Kdo2-Glyi 1369.406 0.4

B 1312.38 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1312.384 3.1

B-Kdo-C02 1105.356 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ•Kdo2-Glyi 1105.357 1.3

Fragment Proposed LOS composition

Measured Calculated Deviation Bacteria ion

mass (u) Oligosaccharide Lipid A mass (u) (ppm) type ³ '

B 1474.436 PEi ·ΗΘΧ2·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1474.437 0.6

B-Kdo-C02 1 1 05.355 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ .Kdc^-GIyi 1 1 05.357 2.2

B-Kdo-C02 1 048.335 PEi ·ΗΘΧΙ ·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 1 048.336 0.9

B-Kdo-C02 121 0.387 PEi ·ΗΘΧ2·ΗΘΡ2·ΗΘΧΝΑΟΙ -Kdo2 121 0.389 1 .5

Y 1 71 3. 124 P2-HexN2-C122-C120H2-C140H2 1 71 3. 125 0.9

In-source collision- induced dissociation of LOS produced B- and Y-type fragment ions corresponding to oligosaccharide and lipid A domains due to the rupture of the glycosidic bond between Kdo and lipid A. Fragment ions are assigned according to the nomenclature of Domon and Costello (24). Mass numbers given refer to monoisotopic masses of the neutral molecules. Abbreviations: Kdo, 3-deoxy-D-ma/?/?o-oct-2-ulosonic acid; Hep, L-glycero-O-manno-heptose; Hex, hexose; HexNAc, N-acetylhexosamine; Gly, glycine; PEA, phosphoethanolamine; P, phosphate; C120H, 3- 5 hydroxy-dodecanoic acid; C140H, 3-hydroxy-tetradecanoic acid; C12, dodecanoic acid; C16: l, 9-hexadece

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