Patent Grant
11236127
This patent application is the U.S. national phase of International Application No. PCT/EP2011/070907, filed on Nov. 24, 2011, which claims the benefit of European Patent Application No. 10192564.2, filed Nov. 25, 2010, the disclosures of which are incorporated by reference.
Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: 021,532 Byte ASCII (Text) file named “5510803REV1 ST25,” created on Aug. 19, 2016.
The present invention relates to peptides or polypeptides with capacity to recruit and activate NKT cells and their use in treating infections with intracellular organisms or tumors, and preventing diseases by vaccination strategies.
Chronic infectious diseases due to intracellular pathogens are difficult to treat because infected cells reduce surface expression of a number of molecules which would normally allow the immune system to specifically recognize said infected cells. Examples are Mycobacterium infections in which infected cells inhibit expression of molecules of the major histocompatibility (MHC) complexes thereby preventing recognition by T lymphocytes of the CD8 lineage (via MHC class I recognition) and by lymphocytes of the CD4 lineage (via class II MHC recognition). In fact, many bacteria and viruses have elaborated methods to escape recognition of infected cells.
To some extent, the same mechanisms allow tumors to escape detection. A few of such tumors express MHC class II determinants at least under inflammatory conditions. Recent experiments have shown that even when increased CD8 recognition of MHC class I-presented tumor derived peptides by for instance vaccination, the overall effect on tumor growth remains limited.
Both in chronic infection with intracellular pathogens and in tumors, there is an urgent need to elaborate new methods by which infected, or tumor cells, respectively, would be recognized and eliminated.
Vaccination for infectious diseases is current practice. Yet, in a significant number of conditions, the efficacy of vaccination is limited by the preferential induction of specific antibodies to the pathogens and no or little elicitation of immune cells which would recognize infected cells. Thus, prevention of viral and bacterial diseases by vaccination is often of limited efficacy. Examples are to be found in the efficacy of several vaccines for viral diseases, such as influenza virus, rotavirus or even poliovirus at least in some world areas. In some instances, the antigens considered for vaccination are weak immunogens and, due to the large diversity of MHC determinants, a significant variation in efficacy is observed from one subject to the other.
Vaccination for allergic diseases also suffers from limitations related to either the weak immunogenicity of allergens or to the lack of control of risks related to the administration of an allergen to a subject precisely prone to react with allergic symptoms.
In both vaccinations against infectious agents and against allergens there is a need for more efficient and more secure methods.
Natural killer T (NKT) cells constitute a distinct lineage of non-conventional T lymphocytes that recognize antigens presented by the non-classical MHC complex molecule CD1d. Two subsets of NKT cells are presently described. Type 1 NKT cells, also called invariant NKT cells (iNKT), are the most abundant. They are characterized by the presence of an alpha-beta T cell receptor (TCR) made of an invariant alpha chain, Valpha14 in the mouse and Valpha24 in humans. This alpha chain is associated to a variable though limited number of beta chains. Type 2 NKT cells have an alpha-beta TCR but with a polymorphic alpha chain. However, it is apparent that other subsets of NKT cells exist, the phenotype of which is still incompletely defined, but which share the characteristics of being activated by glycolipids presented in the context of the CD1d molecule.
NKT cells typically express a combination of natural killer (NK) cell receptor, including NKG2D and NK1.1. NKT cells are part of the innate immune system, which can be distinguished from the adaptive immune system by the fact that they do not require expansion before acquiring full effector capacity. Activation of NKT cells results in various effects. Such cells release preformed mediators, including a large array of cytokines (including IL-4, IFN-gamma, IL-21 and IFN-alpha) which provide help to B cells for the production of antibodies and it has been suggested that the release of cytokines could also influence CD4+ T cells (Burrows et al Nature Immunology 2009, 10: 669-671). In the context of the present invention, increasing B cell activation and major histocompatibility (MHC) class II-restricted CD4+ T cells activation would be beneficial.
The recognition unit for NKT cells, the CD1d molecule, has a structure closely resembling that of the MHC class I molecule, including the presence of beta-2 microglobulin. It is characterized by a deep cleft bordered by two alpha chains and containing highly hydrophobic residues, which accepts lipid chains. The cleft is open at both extremities, allowing to accommodate longer chains. The canonical ligand for CD1d is the synthetic alpha galactosylceramide (alpha GalCer). However, many natural alternative ligands have been described, including glyco- and phospholipids, the natural lipid sulfatide found in myelin, microbial phosphoinositol mannoside and alpha-glucuronosylceramide. The present consensus (see reviews, such as Matsuda et al, Current Opinion in Immunology 2008, 20:358-368 and Godfrey et al, Nature reviews Immunology 2010, 11: 197-206) is that CD1d binds only ligands containing lipid chains, or in general a common structure made of a lipid tail which is buried into CD1d and a sugar residue head group that protrudes out of CD1d.
Peptides are not deemed to be able to activate NKT cells through presentation by CD1d. It was, however, suggested that long hydrophobic peptides containing bulky aminoacid residues could bind to CD1d (Castano et al, Science 1995, 269: 223-226). Observations carried out using phage display libraries expressing random sequence peptides with no defined physiological relevance, allowed establishing a theoretical consensus motif (Castano et al, Science 1995, 269: 223-226 and see below).
In fact, Castano et al show that the cells which are activated are CD8+ T cells, namely MHC class I restricted cells, and not NKT cells. These findings teach the one skilled in the art that there is no evidence that hydrophobic peptides are presented by CD1d molecules. The physiological relevance of the claims made by Castano et al was further questioned due to the inability to elicit NKT cells under conventional immunization protocols (Matsuda et al, Current Opinion in Immunology 2008, 20:358-368 and Brutkiewicz Journal of Immunology 2006, 177: 769-775). Artificial systems such as immunization with cells transfected to overexpress CD1d and loaded in vitro with an ovalbumin-derived peptide were able to elicit NKT cells. Likewise, intradermal immunization with plasmid DNA together with murine CD1d and costimulatory molecules induce cytolytic CD1d-restricted T cells (Lee et al, Journal of Experimental Medicine 1998, 187: 433-438). Hydrophobic peptides containing a structural motif made of an aromatic residue in position P1 and P7, and an aliphatic chain in position P4 were claimed by Castano et al (Science 269: 223, 1995) to contain a core motif for CD1d binding epitopes. As described above, the conclusions reached by Castano et al are not supported by data.
We made the unexpected finding that peptides encompassing a hydrophobic aminoacid sequence are in fact capable of eliciting activation of NKT cells.
Additionally, activation of NKT cells provides a way to increase the efficiency of vaccines against infectious diseases and against allergens, due to the large amounts of cytokines secreted by NKT cells which help in eliciting B cell and class II restricted T cell activation (Burrows et al Nature Immunology 2009, 10: 669-671) and thereby the production of antibodies.
If epitopes from proteins could bind to CD1d, then addition of a CD1d binding motif to a protein could increase activation of NKT cells, which could result in either induction of antigen-presenting cell killing, as it would be appropriate for the treatment of infections with intracellular pathogens or of tumors, or increase the immunogenicity of antigens, as would be appropriate in vaccination strategies for infectious diseases or allergy.
Examples of infection with intracellular pathogens include Mycobacterium infections, intracellular bacterial infection, viral diseases and parasitic infections. Examples of tumors are any tumor expressing CD1d. Examples of antigens used for vaccination are virus proteins used in influenza vaccination, oral rotavirus or oral poliovirus vaccination and allergen vaccination.
More specifically, addition of a CD1d-binding motif would be of use when it is desirable to increase the killing activity of NKT cells towards antigen-presenting cells, or to increase the production of cytokines made by NKT cells and thereby increase immunogenicity.
Generating new CD1d binding motif(s) within the natural sequence of peptides or polypeptides, or adding CD1d binding motif(s) to such peptides or polypeptides to recruit and activate NKT cells forms the basis of the present invention.
The present invention relates to the use of peptides or polypeptides for the treatment of infections with intracellular pathogens in a subject by increasing the elimination of cells carrying such pathogens.
The present invention also relates to the use of peptides or polypeptides for the therapy of tumors in a subject by increasing recognition and killing of tumor cells.
The present invention also relates to the use of peptides or polypeptides for vaccination purposes in a subject with antigens from infectious agents or allergens.
We made the unexpected observation that peptides can be presented by CD1d molecules and activate NKT cells. Activation of such cells results in acquisition of cytolytic properties against the cell presenting the peptide bound to CD1d and in the release of cytokines.
The present invention relates in one aspect to the use of at least one isolated immunogenic peptide or polypeptide derived from an intracellular pathogen, which is modified by generating at least one CD1d binding motif within the natural sequence of said peptide or polypeptide, or by adding at least one CD1d binding motif to said peptide or polypeptide as a medicament for treating in a subject infection with said intracellular pathogen.
The present invention also relates in one aspect to the use of at least one isolated immunogenic peptide or polypeptide derived from a tumor, which is modified by generating at least one new CD1d binding motif within the natural sequence of said peptide or polypeptide, or by adding at least one CD1d binding motif to said peptide or polypeptide as a medicament for treating in a subject said tumor.
The present invention also relates in one aspect to the use of at least one isolated immunogenic peptide or polypeptide derived from an extracellular infectious agent, which is modified by generating at least one new CD1d binding motif within the natural sequence of said peptide or polypeptide, or by adding at least one CD1d binding motif to said peptide or polypeptide as a medicament for preventing in a subject said infection.
The present invention also relates in one aspect to the use of at least one isolated immunogenic peptide or polypeptide derived from an allergen, which is modified by generating at least one new CD1d binding motif within the natural sequence of said peptide or polypeptide, or by adding at least one CD1d binding motif to said peptide or polypeptide as a medicament for preventing in a subject allergic reactions.
It should be clear for the one skilled in the art that the generation of a CD1d binding motif, in any of the indications listed above, implies that said motif, when presented by the CD1d molecule expressed by an antigen-presenting cell, is recognized by NKT cells and activate said NKT cells.
In a further aspect, the invention also covers the use of at least one isolated peptide or polypeptide derived from an intracellular pathogen, a tumor, an infectious agent or an allergen, which is modified by generating at least one new CD1d binding motif within the natural sequence of said peptide or polypeptide, or by adding at least one CD1d binding motif to said peptide or polypeptide to recruit and activate NKT cells, as a medicament for activating in a subject cytolytic activity and cytokine production by CD4+ NKT cells in said subject.
In any of the above uses said peptide or polypeptide derived from an intracellular pathogen may be any peptide or polypeptide derived from viruses, bacteria, mycobacteria or parasites with an intracellular life cycle. Viruses include ssDNA, dsDNA and RNA viruses, with as examples Herpesviridae, Flaviviridae and Picornaviridae, influenza, measles and immunodeficiency viruses. Bacteria and mycobacteria include Mycobacterium tuberculosis, other mycobacteria pathogenic for humans or animals, Yersiniosis, Brucella, Chlamydiae, Mycoplasma, Rickettsiae, Salmonellae and Shigellae. Parasites include Plasmodiums, Leishmanias, Trypanosomas, Toxoplasma gondii, Listeria, Histoplasma.
In any of the above uses said peptide or polypeptide derived from a tumor may be any peptide or polypeptide derived from: (1) oncogenes, such as the MAGE identified in some melanomas; (2) proto-oncogenes, such as cyclin D1 expressed on soft tissues carcinomas such as those of the kidney or parathyroid, as well as in multiple myeloma; (3) virus-derived proteins, such as those from the Epstein-Barr virus in some carcinomas and in some Hodgkin-type lymphomas; (4) surviving factors, which are anti-apoptotic factors such as survivin or bcl2; (5) clonotypic determinants, such as idiotypic determinants derived from B cell receptor in follicular lymphomas or multiple myelomas or T cell receptor determinants in T cell malignancies
In any of the above uses said peptide or polypeptide derived from an infectious agent, including viruses, bacteria and parasites.
In any of the above uses said peptide or polypeptide derived from an allergen may be any peptide or polypeptide derived from
The invention further encompasses isolated viral vectors characterized in that they comprise at least one peptide or polypeptide derived from an intracellular pathogen, from a tumor, from an infectious agent or from an allergen wherein at least one new CD1d binding motif is generated within the natural sequence of said peptide or polypeptide, or wherein at least one CD1d binding motif is added.
The term “peptide” when used herein refers to a molecule comprising an amino acid sequence of between 2 and 200 amino acids, connected by peptide bonds, but which can in a particular embodiment comprise non-amino acid structures (like for example a linking organic compound). Peptides according to the invention can contain any of the conventional 20 amino acids or modified versions thereof, or can contain non-naturally occurring amino acids incorporated by chemical peptide synthesis or by chemical or enzymatic modification. The term “polypeptide” when used herein refers to generally longer peptides or proteins.
The term “epitope” when used herein refers to one or several portions (which may define a conformational epitope) of a protein which is/are specifically recognized and bound by an antibody or a portion thereof (Fab′, Fab2′, etc.) or a receptor presented at the cell surface of a B or T cell lymphocyte, and which is able, by said binding, to induce an immune response.
The term “antigen” when used herein refers to a structure of a macromolecule comprising one or more hapten(s) and/or comprising one or more T cell epitopes. Typically, said macromolecule is a protein or peptide (with or without polysaccharides) or made of proteic composition and comprises one or more epitopes; said macromolecule can herein alternatively be referred to as “antigenic protein” or “antigenic peptide”.
The term “allergen” refers to a specific subset of antigen characterized by its capacity to elicit antibodies of the IgE isotype in predisposed individuals.
The term “T cell epitope” or “T-cell epitope” in the context of the present invention refers to a dominant, sub-dominant or minor T cell epitope, i.e., a part of an antigenic protein that is specifically recognized and bound by a receptor at the cell surface of a T lymphocyte. Whether an epitope is dominant, sub-dominant or minor depends on the immune reaction elicited against the epitope. Dominance depends on the frequency at which such epitopes are recognized by T cells and able to activate them, among all the possible T cell epitopes of a protein. In particular, a T cell epitope is an epitope bound by MHC class I or MHC class II molecules.
The term “NKT cell epitope” refers to a part of an antigenic protein that is specifically recognized and bound by a receptor at the cell surface of a T lymphocyte. In particular, a NKT cell epitope is an epitope bound by CD1d molecules.
The term “CD4+ effector cells” refers to cells belonging to the CD4-positive subset of T-cells whose function is to provide help to other cells, such as, for example B-cells. These effector cells are conventionally reported as Th cells (for T helper cells), with different subsets such as Th0, Th1, Th2, and Th17 cells.
The term “NKT cells” refers to cells of the innate immune system characterized by the fact that they carry receptors such as NK1.1 and NKG2D, and recognize epitopes presented by the CD1d molecule. In the context of the present invention, NKT cells can belong to either the type 1 (invariant) or the type 2 subset.
The “CD1d molecule” refers to a non-MHC derived molecule made of 3 alpha chains and an anti-parallel set of beta chains arranged into a deep hydrophobic groove opened on both sides and capable of presenting lipids, glycolipids or hydrophobic peptides to NKT cells.
The term “CD1d binding motif” refers to an aminoacid sequence which corresponds to the general aminoacid motif [FW]-XX-[ILMV]-XX-[FW], in which F stands for phenylalanine, W for tryptophan, I for isoleucine, L for leucine, M for methionine and V for valine. X represents any aminoacid. In some cases, [FW] in position 7 is replaced by T (for threonine) or H (for histidine).
The term “putative CD1d binding motif” when used herein refers to an aminoacid sequence which corresponds to the general aminoacid motif [FWHY]-X2X3-[ILMV] or [ILMV]-X2X3-[FWHY] wherein Y stands for tyrosine. In some cases, the putative motif may be [FWHY]-X2-[ILMV] or [ILMV]-X2-[FWHY] or [FWHY]-X2X3X4-[ILMV] or [ILMV]-X2X3X4-[FWHY].
The term “immune disorders” or “immune diseases” refers to diseases wherein a reaction of the immune system is responsible for or sustains a malfunction or non-physiological situation in an organism. Immune disorders in the context of the present invention refer to pathology induced by infectious agents and tumor surveillance.
The term “subject” refers to mammals including primates and non-primates.
The present invention provides ways to suppress or eliminate, in a subject, an infection with an intracellular pathogen or a tumor, or to increase the immunogenicity of antigens such as some infectious agents and allergens used for vaccination strategies.
In particular, the invention provides ways to increase the expansion and functional activity of CD4+ NKT cells. Such cells are usually classified into two distinct subsets, namely type 1 for NKT cells carrying an invariant TCR alpha chain (Valpha14 in the mouse, Valpha24 in humans), or type 2 NKT cells which present with a diverse alpha chain repertoire. However, recent evidence has suggested that alternative subsets of NKT cells which do not fit in the type 1 or type 2 category. It is the purpose of the present invention to include these non conventional NKT cells, provided they carry the CD4 co-receptor. Upon presentation of an antigen bound to CD1d, NKT cells are rapidly activated, acquire cytolytic properties and secrete a number of cytokines thought to be determinant in influencing other cells from both the innate and adaptive immune systems.
In the context of the present invention, we made the unexpected observation that peptides can be presented by the CD1d molecule and can activate NKT cells recognizing the complex made between CD1d and the peptide. A characteristic of the CD1d molecule is that it is made of two anti-parallel alpha chains forming a cleft sitting atop of a platform made of two anti-parallel beta chains. The cleft is narrow and deep and accept only hydrophobic residues, classically deemed to be only lipids.
The cleft can accommodate a sequence of 7 aminoacids characterized as a hydrophobic residue in position (P) 1 and 7, and an aliphatic residue in P4. P1 is obligatory a hydrophbic residue, such as F, W, H or Y. However, P7 is permissive and can contain alternative residues provided they are not polar. Residues in P4 are preferably aliphatic but this is optional. A general sequence for a CD1d binding motif is therefore [FWTHY]-X2X3-[ILMV]-X5X6-[FWTHY]. It should however be clear for those skilled in the art that the motif is symmetrical and that P7 can be considered as P1, and P1 can be considered as P7. The general sequence of a CD1d binding motif is provided here as a general indication without any limiting intention. Peptides and polypeptides of the invention are defined according to their capacity to activate NKT cells by presentation into CD1d molecule.
Many peptides or polypeptides do not naturally carry a CD1d binding motif. However, the present invention also covers peptides or polypeptides which already carry at least one CD1d motif in their natural sequence, as it may be found advantageous to increase the number of said motifs to increase suppression of infections with intracellular pathogens or tumor cells, or to increase immunogenicity to antigens from infectious agents or from allergens.
The present invention relates to the production of peptides or polypeptides which are modified by generating at least one new CD1d binding motif within the natural sequence of said peptides or polypeptides, or by adding at least one CD1d binding motif to said peptide or polypeptide, regardless of the fact that they already carry such a motif.
In a further aspect, the invention also covers the use of at least one isolated hydrophobic peptide or polypeptide comprising at least one CD1d binding motif represented by the general [FW]-X2X3-[ILMV]-X5X6-[FWTHY] sequence motif for increasing in a subject elimination of cells infected with intracellular pathogens or tumor cells, or for increasing in said subject the immunogenicity of infectious antigens or allergens used for vaccination.
In yet a further aspect, the invention also covers the use of at least one isolated peptide or polypeptide wherein at least one CD1d binding motif represented by the [FW]-X2X3-[ILMV]-X5X6-[FWTHY] sequence has been generated within the natural sequence of said peptide or polypeptide, or has been added to said natural sequence for activating in a subject NKT cells.
In yet a further aspect, the invention also covers the use of at least one isolated hydrophobic peptide or polypeptide comprising at least one new CD1d binding motif represented by the [FW]-X2X3-[ILMV]-X5X6-[FWTHY] sequence as a medicament for suppressing in a subject infection with intracellular pathogens or tumor cells, or to increase the efficiency of antigens from infectious agents or from allergens for vaccination.
A further advantage of the present invention is that addition of aromatic aminoacid residues in peptides or polypeptides creates CD1d binding motifs which are promiscuous in the sense that said motifs can bind to CD1d molecules of all or of a very large majority of subjects. This is due to the fact that the CD1d molecule itself presents a very limited degree of polymorphism. As in addition the polymorphism of NKT cell antigenic receptor is highly restricted, it should be obvious for the one skilled in the art that the same aromatic aminoacid addition is applicable to all subjects considered for application of the present invention.
This is in sharp contrast with peptide or polypeptide motifs binding to major histocompatibility class II molecules, wherein a large number of peptides can be delineated which contain the appropriate sequence. This is due to the minimum constraints imposed to MHC class II binding peptides and to the large polymorphism of class II molecules.
Peptides and polypeptides which are the object of the present invention are obtained as follows:
(1) a peptide or polypeptide is, optionally, evaluated for its capacity to activate NKT cells. This is carried out by incubating said peptide or polypeptide with a cell line expressing the CD1d molecule. Examples of such cell lines are known in the art (for instance JAWS2 cells). In a preferred embodiment, the cell line is not presenting MHC class II molecules and is transduced for hyperexpression of CD1d using a viral vector containing the DNA sequence of CD1d or any other means known in the art to introduce a gene in a cell. Methods for cell transduction are known in the art. The cell line is loaded in culture with the peptide or polypeptide. Efficient presentation of the peptide or polypeptide by the CD1d molecule is then evaluated by measuring the activation of NKT cells. Such cells can be obtained from peripheral blood by, for instance, magnetic sorting and maintained in culture with stimulants such as alpha-gal-ceramide, in the presence of cytokines such as IL-2 and IL-15 or IL-7. These methods are described in the art (see for instance Brutkiewicz Journal of Immunology 2006, 177: 769-775). Activation of NKT cells is assessed using methods such as evaluation of cytokine production. Peptides or polypeptides which show no or only limited activation of NKT cells are selected.
(2) the peptide or polypeptide aminoacid sequence is then evaluated for the presence of at least one motif corresponding to the [FWHY]-X2X3-[ILMV] or [ILMV]-X2X3-[FWHY] sequence (putative CD1d binding motif) using algorithms well known in the art such as
expasy.org/tools/scanprosite/
More particularly, said algorithms allow the prediction within a peptide or polypeptide of one or more 7 aminoacid-long sequences which correspond to the [FWHY]-X2X3-[ILMV]-XX6-[FWHY] sequence and thereby has the potential to fit into the cleft of a CD1d molecule. More particularly, said algorithms allow the prediction of aminoacid sequences corresponding to [FW]-X2X3-[ILMV] or to [ILMV]-X2X3-[FW].
(3) sequences of aminoacids identified by said algorithms are examined and modified by aminoacid substitution to increase the potential to bind to CD1d. This essentially includes the substitution of aminoacids in position P1 by a hydrophobic residue such as F, W, H or Y and/or substitution of aminoacids in position P7 by F, W, T, H or Y, when required.
(4) optionally, a putative CD1d binding motif is identified which corresponds to [FWHY]-X2-[ILMV] or [ILMV]-X2-[FWHY], or [FWHY]-X2X3X4-[ILMV] or [ILMV]-X2X3X4-[FWHY]. In such cases addition of an X3 or deletion of X4, respectively, is found advantageous to reconstitute a CD1d binding motif which comprises an aliphatic aminoacid residue in position P4. More generally, the putative CD1d binding motif could correspond to the general formula [FWHY]-R-[ILMV] or [ILMV]-R-[FWHY] wherein R represents an aminoacid or an aminoacid sequence.
(5) optionally, a CD1d motif can be added to the aminoacid sequence of the peptide or polypeptide, either in carboxy-terminal or amino-terminal end of the sequence, or anywhere within the peptide or polypeptide natural sequence
(6) optionally, peptides or polypeptides of the invention can be modified by generating at least one CD1d motif and by addition of at least one CD1d binding motif.
(7) optionally, the synthetic peptide encompassing the sequence containing a CD1d binding motif is tested in vitro using a cell line expressing the CD1d molecule as described in (1).
(8) optionally, the capacity of the peptide or polypeptide modified by substitution, addition or deletion of aminoacids as described above to bind to CD1d is tested in vitro using tetramers of the CD1d molecule to detect NKT cells specific for such peptide. One possibility is to use fluorescence-labeled tetramers and detection using fluorescence activated cell sorting (facs).
It should be clear for the one skilled in the art that substitution or addition of aminoacid residues, or addition of CD1d binding motif(s) can be carried out using a non-physiological aminoacid residues such as D-aminoacids or an organic compound.
The peptide or polypeptide containing the aminoacid substitution, addition or deletion is then produced using methods known in the art for the production of recombinant proteins using expression systems such as bacterial cells, yeast cells, insect cells, plant cells or mammalian cells.
According to the present invention medicaments are envisaged for the treatment of diseases due to intracellular pathogens. Examples of said intracellular pathogens include ssDNA, dsDNA and RNA viruses, bacteria and mycobacteria, and parasites.
Medicaments are also envisaged for the treatment of tumors.
Further, medicaments are also envisaged for vaccination strategies towards infectious agents with primarily extracellular life cycle and towards allergens.
It should be understood that any of the peptides or polypeptides envisaged in the context of the present invention may be administered in the form of gene for transgenesis, which may be carried out using viral vectors or other means known by those skilled in the art. In such a case, it may be found advantageous to alter the aminoacid sequence of the viral vector itself by adding a CD1d binding motif, thereby increasing expression of the transgene.
In a preferred embodiment, the peptide can be constituted of a CD1d binding motif encompassing the [FW]-X2X3-[ILMV]-X5X6-[FWTHY] sequence. Yet in more preferred embodiment, the said peptide also contains aminoacid flanking residues at either the aminoterminal or carboxyterminal end, or at both ends of said peptide. In yet a preferred embodiment, said peptide contains bulky aminoacid residues in flanking residues. In yet another embodiment, said peptide carries at least one class II restricted T cell epitope. In yet another embodiment, said peptide contains aminoacid flanking residues which are part of the natural sequence from which the peptide is derived.
The medicament of the invention is usually, though not necessarily, a (pharmaceutical) formulation comprising as active ingredient at least one of the peptides or polypeptides of the invention or a gene therapeutic vector capable of expressing said peptides or polypeptides. Apart from the active ingredient(s), such formulation will comprise at least one of a (pharmaceutically acceptable) diluent.
In general, administration of peptides or polypeptides of the invention increases activation of the innate immune system, more particularly activation of NKT cells, more particularly the production of cytokines associated with NKT cell activation, more particularly the cytolytic properties of NKT cells.
The route of administration for peptides or polypeptides of the present invention may vary according to the indication and/or the nature of the peptides or polypeptides. Examples are subcutaneous or intramuscular injection of vaccines for infectious disease and for allergens or for tumors, or oral, nasal or intratracheal administration for infections with intracellular pathogens. The present invention intends to cover all other possible routes of administration such as intranasal, sublingual, percutaneous, intramuscular, intrarectal or intravaginal.
As explained in detail further on, the peptides or polypeptides of the present invention can be made by chemical synthesis, which allows the incorporation of non-natural amino acids.
Another aspect of the present invention relates to methods to obtain peptides or polypeptides comprising an artificial sequence able to activate NKT cells, said method comprising the steps of:
(a) identification of peptides or polypeptides which do not, or only to a limited extend, activate NKT cells;
(b) introduction of at least one CD1d binding motif by aminoacid addition, substitution and/or deletion.
Such methods include the identification of epitopes which can be modified to carry a CD1d binding motif by aminoacid substitution, addition or deletion. Ways for in silico identification of putative NKT-cell epitopes are amply known in the art and some aspects are elaborated upon hereafter.
For instance, when said putative NKT-cell epitope is identified, synthetic peptides encompassing said sequence are produced. Alternative peptides are also synthesized which include the aminoacid substitution, addition or deletion judged to be appropriate to increase the capacity of the aminoacid sequence to bind to CD1d. The peptide encompassing the natural sequence and peptides with aminoacid substitution(s), additions, deletions or combinations of these are tested for their capacity to bind CD1d tetramers and/or to activate NKT cells by loading antigen-presenting cells expressing CD1d.
For instance, soluble CD1d molecules are obtained and made tetrameric by synthesis and/or chemical coupling. The CD1d molecule is purified by affinity chromatography. Soluble CD1d molecules are incubated with a biotin-labeled reference peptide produced according to its strong binding affinity for said CD1d molecule. Peptides to be assessed for CD1d binding are then incubated at different concentrations and their capacity to displace the reference peptide from its CD1d binding is calculated by addition of neutravidin. Methods can be found in for instance Texier et al., (2000) J. Immunology 164, 3177-3184) for peptides presented by the major histocompatibility class II molecule, but the method can easily be applied to CD1d-restricted T cell epitopes.
Optionally, the binding of the peptides of the invention to CD1d tetramers can be evaluated by incubation with NKT cells and fluorescence-activated cell sorting (facs) analysis. These methods are well described in the art.
Alternatively, antigen-presenting cells such as JAWS2 cells which express CD1d but do not express major histocompatibility class II complexes are loaded with the peptides or polypeptides of the invention and their capacity to activate NKT cells is evaluated by the proliferation of NKT cells as assessed by incorporation of tritiated thymidine. These methods are well known by the one skilled in the art. The peptides or polypeptides of the invention have a mean NKT cell stimulation index of greater than or equal to 2. A peptide having a NKT cell stimulation index of greater than or equal to 2 is considered useful as a candidate to carry out the present invention.
Aminoacid substitution(s) identified as suitable for the present invention, addition or deletion of said aminoacids are then introduced into full-length peptide or polypeptide for practicing the invention.
The peptides or polypeptides of the invention can be produced by recombinant expression in, e.g., bacterial cells (e.g. Escherichia coli), yeast cells (e.g., Pichia species, Hansenula species, Saccharomyces or Schizosaccharomyces species), insect cells (e.g. from Spodoptera frugiperda or Trichoplusia ni), plant cells or mammalian cells (e.g., CHO, COS cells). The construction of the therefore required suitable expression vectors (including further information such as promoter and termination sequences) involves meanwhile standard recombinant DNA techniques. Recombinantly produced peptides or polypeptides of the invention can be derived from a larger precursor protein, e.g., via enzymatic cleavage of enzyme cleavage sites inserted adjacent to the N- and/or C-terminus of the peptide or polypeptide, followed by suitable purification.
In view of the limited length of some of the peptides or polypeptides of the invention, they can be prepared by chemical peptide synthesis, wherein peptides are prepared by coupling the different amino acids to each other. Chemical synthesis is particularly suitable for the inclusion of e.g. D-amino acids, amino acids with non-naturally occurring side chains or natural amino acids with modified side chains such as methylated cysteine. Chemical peptide synthesis methods are well described and peptides can be ordered from companies such as Applied Biosystems and other companies. Peptide synthesis can be performed as either solid phase peptide synthesis (SPPS) or contrary to solution phase peptide synthesis. The best-known SPPS methods are t-Boc and Fmoc solid phase chemistry which is amply known to the skilled person. In addition, peptides can be linked to each other to form longer peptides using a ligation strategy (chemoselective coupling of two unprotected peptide fragments) as originally described by Kent (Schnolzer & Kent (1992) Int. J. Pept. Protein Res. 40, 180-193) and reviewed for example in Tam et al. (2001) Biopolymers 60, 194-205. This provides the potential to achieve protein synthesis which is beyond the scope of SPPS. Many proteins with the size of 100-300 residues have been synthesized successfully by this method.
The physical and chemical properties of a peptide or polypeptide of interest (e.g. solubility, stability) is examined to determine whether the peptide is/would be suitable for use in therapeutic compositions. Typically this is optimized by adjusting the sequence of the peptide. Optionally, the peptide can be modified after synthesis (chemical modifications e.g. adding/deleting functional groups) using techniques known in the art.
The production of genetically-modified peptides or polypeptides relies on methods well known by those skilled in the art, including cloning, site-directed mutagenesis and growth.
The present invention also relates to nucleic acid sequences encoding the peptides or polypeptides of the invention and methods for their use, e.g., for recombinant expression or in gene therapy. In particular, said nucleic acid sequences are capable of expressing peptides of the invention.
In gene therapy, recombinant nucleic acid molecules encoding the peptides or polypeptides of the present invention can be used as naked DNA or in liposomes or other lipid systems for delivery to target cells. Other methods for the direct transfer of plasmid DNA into cells are well known to those skilled in the art for use in human gene therapy and involve targeting the DNA to receptors on cells by complexing the plasmid DNA to proteins. In its simplest form, gene transfer can be performed by simply injecting minute amounts of DNA into the nucleus of a cell, through a process of microinjection. Once recombinant genes are introduced into a cell, they can be recognized by the cells normal mechanisms for transcription and translation, and a gene product will be expressed. Other methods have also been attempted for introducing DNA into larger numbers of cells. These methods include: transfection, wherein DNA is precipitated with calcium phosphate and taken into cells by pinocytosis; electroporation, wherein cells are exposed to large voltage pulses to introduce holes into the membrane); lipofection/liposome fusion, wherein DNA is packed into lipophilic vesicles which fuse with a target cell; and particle bombardment using DNA bound to small projectiles. Another method for introducing DNA into cells is to couple the DNA to chemically modified proteins. Adenovirus proteins are capable of destabilizing endosomes and enhancing the uptake of DNA into cells. Mixing adenovirus to solutions containing DNA complexes, or the binding of DNA to polylysine covalently attached to adenovirus using protein crosslinking agents substantially improves the uptake and expression of the recombinant gene. Adeno-associated virus vectors may also be used for gene delivery into vascular cells. As used herein, “gene transfer” means the process of introducing a foreign nucleic acid molecule into a cell, which is commonly performed to enable the expression of a particular product encoded by the gene. The said product may include a protein, polypeptide, anti-sense DNA or RNA, or enzymatically active RNA. Gene transfer can be performed in cultured cells or by direct administration into mammals. In another embodiment, a vector comprising a nucleic acid molecule sequence encoding a peptide according to the invention is provided. In particular embodiments, the vector is generated such that the nucleic acid molecule sequence is expressed only in a specific tissue. Methods of achieving tissue-specific gene expression are well known in the art, e.g., by placing the sequence encoding an immunogenic peptide of the invention under control of a promoter, which directs expression of the peptide specifically in one or more tissue(s) or organ(s). Expression vectors derived from viruses such as retroviruses, vaccinia virus, adenovirus, adeno-associated virus, herpes viruses, RNA viruses or bovine papilloma virus, may be used for delivery of nucleotide sequences (e.g., cDNA) encoding peptides, homologues or derivatives thereof according to the invention into the targeted tissues or cell population. Methods which are well known to those skilled in the art can be used to construct recombinant viral vectors containing such coding sequences. Alternatively, engineered cells containing a nucleic acid molecule coding for a peptide or polypeptide according to the invention may be used in gene therapy.
The medicament of the invention is usually, but not necessarily, a (pharmaceutical) formulation comprising as active ingredient at least one of the peptides or polypeptides of the invention, a gene therapeutic vector capable of expressing said peptide or polypeptide. Apart from the active ingredient(s), such formulation will comprise at least one of a (pharmaceutically acceptable) diluent. Typically, pharmaceutically acceptable compounds can be found in, e.g., a Pharmacopeia handbook (e.g. US-, European- or International Pharmacopeia). The medicament or pharmaceutical composition of the invention normally comprises a (prophylactically or therapeutically) effective amount of the active ingredient(s) wherein the effectiveness is relative to the condition or disorder to be prevented or treated.
The medicament or pharmaceutical composition of the invention may need to be administered to a subject in need as part of a prophylactic or therapeutic regimen comprising multiple administrations of said medicament or composition. Said multiple administrations usual occur sequentially and the time-interval between two administrations can vary and will be adjusted to the nature of the active ingredient and the nature of the condition to be prevented or treated. The amount of active ingredient given to a subject in need of a single administration can also vary and will depend on factors such as the physical status of the subject (as for instance weight and age), the status of the condition to be prevented or treated, and the experience of the treating doctor, physician or nurse.
The term “diluents” refers for instance to physiological saline solutions. The term “pharmaceutically acceptable carrier” means any material or substance with which the active ingredient is formulated in order to facilitate its application or dissemination to the locus to be treated, for instance by dissolving, dispersing or diffusing the said composition, and/or to facilitate its storage, transport or handling without impairing its effectiveness. They include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents (for example phenol, sorbic acid, chlorobutanol), isotonic agents (such as sugars or sodium chloride) and the like. Additional ingredients may be included in order to control the duration of action of the active ingredient in the composition. The pharmaceutically acceptable carrier may be a solid or a liquid or a gas which has been compressed to form a liquid, i.e. the compositions of this invention can suitably be used as concentrates, emulsions, solutions, granulates, dusts, sprays, aerosols, suspensions, ointments, creams, tablets, pellets or powders. Suitable pharmaceutical carriers for use in said pharmaceutical compositions and their formulation are well known to those skilled in the art, and there is no particular restriction to their selection within the present invention. They may also include additives such as wetting agents, dispersing agents, stickers, adhesives, emulsifying agents, solvents, coatings, antibacterial and antifungal agents (for example phenol, sorbic acid, chlorobutanol), isotonic agents (such as sugars or sodium chloride) and the like, provided the same are consistent with pharmaceutical practice, i.e. carriers and additives which do not create permanent damage to mammals. The pharmaceutical compositions of the present invention may be prepared in any known manner, for instance by homogeneously mixing, coating and/or grinding the active ingredients, in a one-step or multi-steps procedure, with the selected carrier material and, where appropriate, the other additives such as surface-active agents. They may also be prepared by micronisation, for instance in view to obtain them in the form of microspheres usually having a diameter of about 1 to 10 μm, namely for the manufacture of microcapsules for controlled or sustained release of the active ingredients.
Peptides or polypeptides, homologues or derivatives thereof according to the invention (and their physiologically acceptable salts or pharmaceutical compositions all included in the term “active ingredients”) may be administered by any route appropriate to the condition to be prevented or treated and appropriate for the compounds, here the peptide or polypeptide to be administered. Possible routes include regional, systemic, oral (solid form or inhalation), rectal, nasal, topical (including ocular, buccal and sublingual), vaginal and parenteral (including subcutaneous, intramuscular, intravenous, intradermal, intraarterial, intrathecal and epidural). The preferred route of administration may vary with for example the condition of the recipient or with the condition to be prevented or treated.
The formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. Formulations of the present invention suitable for oral administration may be presented as discrete units such as capsules, cachets or tablets each containing a predetermined amount of the active ingredient; as a powder or granules; as solution or a suspension in an aqueous liquid or a non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion. The active ingredient may also be presented as a bolus, electuary or paste. A tablet may be made by compression or moulding, optionally with one or more accessory ingredients. Compressed tablets may be prepared by compressing in a suitable machine the active ingredient in a free-flowing form such as a powder or granules, optionally mixed with a binder, lubricant, inert diluent, preservative, surface active or dispersing agent. Moulded tablets may be made by moulding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent. The tablets may optionally be coated or scored and may be formulated so as to provide slow or controlled release of the active ingredient therein.
The present invention will now be illustrated by means of the following examples, which are provided without any limiting intention. Furthermore, all references described herein are explicitly included herein by reference.
Mycobacterium tuberculosis is responsible for thousands of deaths every year. The only available vaccination, the Calmette-Guérin Mycobacterium bovis-based vaccine (BCG), is not efficient. One candidate for improving vaccination is the 6 kDa early secretory antigen target (ESAT-6) produced by M. tuberculosis, which is one of the main antigens recognized both by humans and animals such as mice.
The sequence of ESAT-6 (SEQ ID1) was analyzed using computer algorithms to identify CD1d binding motifs corresponding to the [FW]-X2X3-[ILMV]-X5X6-[FWTHY] sequence. None of such motif was found. A mutation A to F and G to F was introduced by standard mutagenesis methods in position 14 and 20, respectively, which generated a CD1d binding motif susceptible to activate NKT cells (mutated ESAT-6; SEQ ID2).
C57BL/6 mice are immunized with ESAT-6 (SEQ ID1) or mutated ESAT-6 of SEQ ID NO:2 together with an adjuvant such as alum. Four injections of 50 μg of the peptide are made at fortnight intervals. Two weeks after the last immunization, mice are sacrificed and CD4+ T lymphocytes prepared from the spleen by a combination of density gradient centrifugation and selection on antibody-coated magnetic beads.
CD4+ T cells are then activated and expanded in vitro using JAWS2 cells as antigen-presenting cells loaded with mutated ESAT-6 of SEQ ID2. JAWS2 cells do not express major histocompatibility class II determinants, preventing thereby activation of class II restricted CD4+ T cells, but JAWS2 cells express CD1d and can therefore be used to assay the capacity of peptides to activate NKT cells. It is observed that only NKT cells obtained from mice immunized with the mutated ESAT-6 (SEQ ID2) are activated by loaded JAWS2 cells, while NKT cells form mice immunized with ESAT-6 (SEQ ID1) are not activated.
To evaluate the cytolytic properties of CD4+ NKT cells activated by mutated ESAT-6 of SEQ ID2, JAWS2 cells were analyzed after 18 h incubation with NKT cells for induction of apoptosis. Thus, annexin V binding to the surface of apoptotic cells is detected by addition of a fluorescence-labeled annexin V. Results indicate that JAWS2 cells incubated with NKT cells obtained from mice immunized with mutated ESAT-6 (SEQ ID2) are induced into apoptosis.
These results therefore show that single aminoacid substitutions generating a CD1d binding motif are sufficient to elicit activation of NKT cells and apoptosis of antigen-presenting cells.
EG7 tumor cells (H-2b) are derived from a thymoma transduced with an ovalbumin(ova)-containing construct. A CD1d restricted ova epitope is presented by such cells, but this is known to be insufficient to trigger NKT activation and tumor cell killing (Castano et al, Science 1995, 269: 223-226).
A search was made using computer algorithms to identify alternative epitopes which could be altered by aminoacid substitution to generate new CD ld binding motifs. Two sequences were identified in position 16-22 (FKELKVH, SEQ ID NO: 9) and 181-187 (FKGLWEK, SEQ ID NO: 10). H22 and K187 were mutated to Fin the ova sequence thereby generating a protein of SEQ ID4.
Immunization of mice with ova of SEQ ID4 was carried out using 50.1 g of ova in alum administered subcutaneously on 4 occasions separated by an interval of 10 days. A control group was immunized with ova in natural sequence (SEQ ID3). All mice were then engrafted with 106 EG7 tumor cells injected in the flank and the growth of the tumor was followed over time. Mice preimmunized with ova of SEQ ID4 rejected the tumor while control mice preimmunized with ova in natural SEQ ID3 did not.
In vitro killing of EG7 cells was evaluated using NKT cells prepared from the spleen using magnetic bead sorting. The NKT cells were first stimulated for 4 h in vitro with antigen-presenting cells loaded with ova of SEQ ID4. EG7 cells were labeled at membrane level with 1 μM DiOC18 (3,3′-dioctadecycloxacarbocyanine perchlorate from Invitrogen). EG7 cells (1×105 per well) were then cultured for 18 h at 37° C. in the presence of NKT cells obtained from each one of the 2 mouse groups, using ratios of 1/1 to 1/5 (EG7 cells versus NKT cells). After 18 h, cells were harvested and stained for Annexin V and 7-AAD following manufacturer's instructions (Apoptosis Detection kit; BD Biosciences) and analyzed on a FACSCantoII flow cytometer (BD Biosciences). Results show that EG7 cells incubated with NKT cells obtained from mice immunized with ova of SEQ ID4 are induced into apoptosis, while NKT cells obtained from control mice immunized with ova of SEQ ID3 did not induce a significant degree of tumor cell apoptosis.
Influenza virus hemagglutinin is a major antigen used for vaccination purposes. The efficacy of vaccination is however limited by the relatively weak immunogenicity of hemagglutinin.
The sequence of hemagglutinin (SEQ ID5) contains 3 sequences that are suitable for mutation to obtain aminoacid sequences encoding a CD1d binding motif of the [FW]-X2X3-[ILMV]-X5X6-[FWTHY] format. cDNA of hemagglutinin was obtained and 3 mutations were introduced by standard mutagenesis methods to replace the aminoacid in position 7 of the CD1d binding motif into F (phenylalanine). These mutations corresponded to V314F, A348F and K459F, in which valine, alanine and lysine in position 314, 348 and 459, respectively, were mutated to phenylalanine. Mutated hemagglutinin of SEQ ID6 was produced by recombinant technology.
Mice were immunized 4 times with either hemagglutinin of SEQ ID5 or SEQ ID6 by the subcutaneous route at 1 week intervals. Seven days after the last immunization, mice were sacrificed and CD4+ T cells were prepared from the spleen using magnetic bead sorting. JAWS2 cells were loaded with mutated hemagglutinin of SEQ ID6 by incubation for 18 h at room temperature. The cells were then washed and incubated in the presence of CD4+ T cells obtained from mice immunized with either hemagglutinin of SEQ ID5 or hemagglutinin of SEQ ID6. It is observed that a significant proportion of NKT cells are activated when obtained from mice immunized with hemagglutinin of SEQ ID6 but not with hemagglutinin of SEQ ID5, demonstrating that immunization with hemagglutinin of SEQ ID6 had induced an expansion of NKT cells in vivo.
Further, mutated hemagglutinin of SEQ ID6 is used for vaccination. It is observed that mice immunized with hemagglutinin of SEQ ID6 produce higher concentrations of hemagglutinin specific antibodies.
Vaccination for allergic diseases is currently limited by the relative weak immunogenicity of allergens. Methods by which an increased production of allergen-specific IgG antibodies could be obtained are highly desirable.
Der p 2 is one of the major allergens from house dust mite, D. pteronyssinus, associated with allergic rhinitis and asthma throughout the world. A search within the sequence of Der p 2 using computer algorithms identified no sequence which carried a CD ld binding motif. A motif made of 7 aminoacids (FAALAAF, SEQ ID NO: 11) was added at the carboxyterminal end of the sequence of Der p 2. Such a sequence encodes a CDld binding motif corresponding to the sequence [FW]-X2X3[ILMV]-X5X6-[FWTHY]. To note, a major T cell epitope presented by major histocompatibility class II complexes is known to be located in position 24-35 of the mature Der p 2 molecule.
Two groups of C57BL/6 mice (H-2b) were immunized with either native Der p 2 (SEQ ID7) or native Der p 2 wherein a CD1d binding motif had been added (SEQ ID8), using 50 μg of protein in alum injected subcutaneously 4 times at 10 days intervals. Mice were then bled and the concentration of specific anti-Der p 2 antibodies was tested by direct binding ELISA. It is observed that the concentration of antibodies is 10-fold higher in the group of mice immunized with Der p 2 of SEQ ID8.
Further, CD4+ T cells were prepared from the spleen of each mouse from the 2 groups, using magnetic bead sorting. Such cells (106 cells/well) were cultured with dendritic cells prepared from syngeneic CD1d KO mice. Such cells can only activate class II restricted CD4+ T cells. It is observed that cells obtained from mice immunized with Der p 2 of SEQ ID8 proliferate with a stimulation index 4-fold higher than cells obtained from mice immunized with native Der p 2 (SEQ ID7).
It is therefore concluded that the presence of a CD1d binding motif increases the production of specific antibodies and the proliferation of class II restricted CD4+ T cells.
It should be understood that the examples provided here are not exhaustive and that combinations of proteins or peptides containing various numbers of aminoacid substitutions or deletions to generate new CD1d binding motifs or containing various numbers of added CD1d binding motifs are envisioned within the scope of the present invention.
| Number | Date | Country | Kind |
|---|---|---|---|
| 10192564 | Nov 2010 | EP | regional |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP2011/070907 | 11/24/2011 | WO | 00 | 6/25/2013 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2012/069572 | 5/31/2012 | WO | A |
| Number | Date | Country |
|---|---|---|
| WO 0219968 | Mar 2002 | WO |
| WO 2010037395 | Apr 2010 | WO |
| WO 2010037402 | Apr 2010 | WO |
| WO 2010065544 | Jun 2010 | WO |
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| Number | Date | Country | |
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| 20130302375 A1 | Nov 2013 | US |
