WO2022079308A1 - Chimeric constructs useful in vaccination and cancer therapy - Google Patents

Abstract

The present invention provides nucleic acid constructs that encodes chimeric protein comprising, from N to C term, i) an oligomerization domain of a ficolin or collectin protein, followed by a collagen-like domain of a ficolin or collectin protein; and ii) a heterologous protein or peptide of interest.

Description

CHIM ERIC CONSTRUCTS USEFUL IN VACCINATION AND CANCER THERAPY

The present invention relates to chimeric constructs that are particularly useful in vaccination against infectious diseases and treatment of cancers.

Background of the invention

One of the common features among pathogens is the presence of large numbers of identical molecules on their surfaces. Antibodies of the immune system lock onto these surface proteins and clear the pathogen from circulation. For a primo infection, the antibodies, or immunoglobulins (Ig), that engage with the pathogen are the IgMs. The affinity of the IgM antigen binding domain for cognate antigen is generally low. To overcome this hurdle, 5 IgM molecules concatemerize by means of the J chain, or the formation of hexameric IgM rosettes. The resulting pentameric and hexameric IgM gives overall valencies of 10 (2x5) and 12 (2x6) respectively. In the context of antibodies, valency is synonymous with the number of antigen recognition sites on the molecule. For an IgG it is 2. The avidity of the immunoglobulin for the antigen is the measure of the overall strength of interaction between these two molecules and is related to the valency. As an infection progresses, immune responses are ramped up and there is a shift from low affinity/high valency (or avidity) IgMs to high affinity/lower valency (or avidity) IgGs.

Bearing these mechanisms in mind, the inventors now propose nucleic acid and protein constructs which show high valency, making them particularly useful in vaccination and immunotherapy.

Summary of the invention

The inventors propose to fuse proteins, peptides or epitopes to the collagenous triple helix domains of ficolins or collectins, so that the chimeric proteins will oligomerize to show valencies of between 9 to 18. The present invention thus provides a nucleic acid construct that encodes a chimeric protein comprising, from N to C term, i) an oligomerization domain of a ficolin or collectin protein followed by a collagen-like domain of a ficolin or collectin protein; and ii) a heterologous protein or peptide of interest.

In a particular embodiment, the heterologous protein or peptide of interest may be an antigenic protein or peptide of an infectious microorganism, including a virus, a bacterium, or a parasite. Such constructs are useful in vaccination.

SUBSTITUTE SHEET (RULE 26) In another embodiment, the heterologous protein or peptide of interest is a paratope fragment or a scFv fragment of an antibody.

In a particular aspect, the heterologous protein or peptide of interest binds an immune checkpoint.

Such constructs are particularly useful in cancer immunotherapy.

The invention further provides a vector that comprises the nucleic acid as described herein, wherein the sequence that encodes the chimeric protein is operatively associated with regulatory sequences that allow expression of the chimeric protein.

Another aspect of the invention is a host cell transduced with the nucleic acid or the vector, so that the host cell is capable of expressing the chimeric protein.

A further subject of the invention is a chimeric protein that is encoded by the nucleic acid as described herein, wherein the chimeric protein is preferably in a multimerized form.

The constructs of the invention provide an increase of the avidity of the heterologous protein or peptide for its target through the multimerization of the former. The present invention allows to increase many times the avidity of a paratope for its specific epitope or to increase the antigenicity of a particular protein or antigen.

Legends to the Figures

Figure 1 shows a schema of ficolin and collectin single chain structures.

Figure 2.A shows a multimerization of single chains into helical collagen trimers, followed by a hexamerization (Adapted from Beltrame et al., 2015)

Figure 2.B shows different natural multimeric structures of ficolins and collectins (Adapted from Lu et al., 2002).

Figure 3.A shows a schema recombinant human H-ficolin (FCN3) where the fibrinogen domain was replaced by the DI and D2 domains of ILT2 and/or ILT4 single chain constructs. (Adapted from Endo et al., 2007).

Figure 3.B shows a Western blot of comparing the cell lysate and the cell culture supernatant (SN) of a 293T cell line transfected with the FNC3-ILT2/4 constructs.

Figure 3.C shows an ELISA comparing relative avidities for HLA-G of a dimeric ILT4 receptor versus FNC3-ILT4.

Figure 4.A shows a schema of the lentiviral FNC3-ILT2/4 vector construct and a Western blot analysis of constructs expression on transduced FNC3-ILT2/4 293T cell lines.

Figure 4.B shows the protocol of mice immunization. Figure 4.C shows ELISA results when using commercial ILT2-Fc or ILT4-Fcas antigen (Ag). Serum dilution = 1/100 and n = 4 mice.

Figure 4.D shows ELISA results when limiting dilution serum titers of greater than 1/10,000. Dil = serum dilution, using either commercial ILT2-Fc or ILT4-Fc as Ag.

Figures 5A to 5F shows Western blots of transfected cell lines with different ficolin or collectin recombinant proteins bearing a variety of foreign cargos, either FLAG-tagged or V5-tagged. 5.A to D: Cell lysates were treated with DTT and denatured by heat and separated by SDS- PAGE. 5.E shows Western blot results of cell lysates and SN of 293 T and HeLa cell lines transfected with a hFCN3-Para7 in reducing conditions and separated in an SDS-PAGE. 5.F show a schema of the chain hFCN3-Calif construct and the corresponding Western blot results of cell lysates and SN of 293T and HeLa cell lines transfected with a hFCN3-Calif in reducing conditions and separated on a SDS-PAGE gel.

Figure 6 shows Western blot analysis of an immunoprecipitation performed using supernatant from 293 T cell lines co-transfected with FCN3-ILT4-FLAG tagged construct and FCN-ILT4- V5 tagged construct. Secreted mixed complexes present in SN were immuno-precipitated with anti-FLAG beads and the blotted with an anti-V5 primary antibody. V5 tagged human APOBEC3A construct is used as negative interaction control.

Figure 7.A shows a schematic drawing of the molecule with the extra cysteine bridge introduced to crosslink gpl20 and the gp41 ectodomain.

Figure 7.B shows western blots of transfected cells with the human FCN3 construct using SOSIP from the BG505 strain of HIV (GenBank accession # KX462847).

Cell lysates were either treated with DTT and denatured by heat or not reduced by DTT but denatured by heat prior to SDS-PAGE separation. Running gels were incubated for 15 minutes at room temperature in 25 mM DTT solution to allow the transfer of high molecular weight complexes.

Figure 8.A shows the protein sequence of FCN3-ILT2-V5 construct (SEQ ID:4).

Figure 8.B shows the protein sequence of FCN3-ILT4-V5 construct (SEQ ID:6).

Figure 8.C shows the protein sequence of MuFAT4 (Murine FCNA - GlySer linker - ILT4 DIDI - spacer - FLAG) (SEQ ID:8).

Figure 8.D shows the protein sequence of MuFBT4 (Murine FCNB - GlySer linker - ILT4 DIDI - spacer - FLAG) (SEQ ID: 10) .

Figure 8.E shows the protein sequence of HuFlT4 (FCN1- GlySer linker - ILT4 D1D2 - spacer - FLAG) (SEQ ID: 12). Figure 8.F shows the protein sequence of HuF2T4 (Human FCN2- GS linker - D1D2 ITL4 - spacer - FLAG) (SEQ ID: 14).

Figure 8.G shows the protein sequence of HuF3T4F (Human Ficolin 3 - GlySer- ILT4 D1D2 - short spacer - FLAG) (SEQ ID: 16).

Figure 8.H shows the protein sequence of HuF3para7 (Human FCN3- GlySer spacer - 15E7 paratope - short spacer - FLAG - His6) (SEQ ID: 18).

Figure 8.1 shows the protein sequence of HuF3 Calif (Human ficolin 3 - GS spacer - influenza A strain California hemagglutinin (HA) ectodomain - linker - FLAG) (SEQ ID:20). Figure 8. J shows the protein sequence of HuMBLT4 (MBL collagen domain - GS linker - D1D2 ITL4 - spacer - FLAG) (SEQ ID:22).

Figure 8.K shows the protein sequence of HuSPDT4 (Human SP-D collagen domain -

GlySer spacer - ILT4 DIDI - spacer - FLAG) (SEQ ID:24).

Figure 8.L shows the protein sequence of PFT4 (Pig FCN collagen domain - GS spacer - D1D2 domains of human ILT4- spacer - FLAG) (SEQ ID:26).

Figure 8.M shows the protein sequence of Human H-ficolin HIV SOSIP construct (FCN3 GlySer spacer - SOSIP - GlySer - PADRE - spacer - FLAG) (SEQ ID:28).

Detailed description of the invention

Definitions

The term "isolated polynucleotide" is defined as a polynucleotide removed from the environment in which it naturally occurs. For example, a naturally-occurring DNA molecule present in the genome of a living bacteria or as part of a gene bank is not isolated, but the same molecule separated from the remaining part of the bacterial genome, as a result of, e.g., a cloning event (amplification), is isolated. Typically, an isolated DNA molecule is free from DNA regions (e. g., coding regions) with which it is immediately contiguous at the 5' or 3' end, in the naturally occurring genome. Such isolated polynucleotides may be part of a vector or a composition and still be defined as isolated in that such a vector or composition is not part of the natural environment of such polynucleotide.

The terms “antigenic protein” and “antigenic peptide” refer to protein or protein fragments that may be specifically bound by the products of specific humoral or cellular immunity, such as an antibody molecule or a T-cell receptor. An antigenic peptide typically comprises between 4 and 40 amino acids, preferably between 8 and 30 amino acids, still preferably between 10 and 20 amino acids. The term “immunogenic” means that the composition or construct to which it refers is capable of inducing an immune response upon administration. "Immune response" in a subject refers to the development of an innate and adaptive immune response, including a humoral immune response, a cellular immune response, or a humoral and a cellular immune response to an antigen. A "humoral immune response" refers to one that is mediated by antibodies. A "cellular immune response" is one mediated by T-lymphocytes. It includes the production of cytokines, chemokines and similar molecules produced by activated T-cells, white blood cells, or both. Immune responses can be determined using standard immunoassays and neutralization assays for detection of the humoral immune response, which are known in the art.

In the context of the invention, the immune response preferably encompasses stimulation or proliferation of cytotoxic CD8 T-cells and/or CD4 T-cells and can be determined using immunoassays such as the ELISpot assay, the in vivo cytotoxicity assay or the cytokine secretion binding assay.

The term “vaccine”, when referring to an infectious disease, means any preparation having an active ingredient of an immunogenic material suitable for the stimulation of active immunity in mammals without inducing the disease. It consists on an antigenic preparation with which prevention of infections may be achieved by vaccination of a host.

The “subject” or “patient” to be treated may be any mammal, preferably a human being. The human subject may be a child, an adult or an elder.

As used herein, the term “treatment” or “therapy” or “immunotherapy” refers to any of the alleviation, amelioration and/or elimination, reduction and/or stabilization (e.g., failure to progress to more advanced stages) of a symptom, or of a symptom thereof. When used in connection with therapy of cancers, the term thus includes achievement of an efficient anti tumoral immune response observed in cancer patients.

As used herein, the term “prevention” or “preventing” refers to the alleviation, amelioration and/or elimination, reduction and/or stabilization (e.g., failure to progress to more advanced stages) of a prodrome, i.e. any alteration or early symptom (or set of symptoms) that might indicate the start of a disease before specific symptoms occur.

The term "scFv" refers to a protein comprising at least one antibody fragment comprising a variable region of a light chain and at least one antibody fragment comprising a variable region of a heavy chain, wherein the light and heavy chain variable regions are contiguously linked, e.g., via a synthetic linker, e.g., a short flexible polypeptide linker, and capable of being expressed as a single chain polypeptide, and wherein the scFv retains the specificity of the intact antibody from which it is derived. Unless specified, as used herein a scFv may have the VL and VH variable regions in either order, e.g., with respect to the N- terminal and C-terminal ends of the polypeptide, the scFv may comprise VL-linker-VH or may comprise VH-linker-VL. The linker may comprise portions of the framework sequences.

The terms “derive from” and “derived from” as used herein refers to a compound having a structure derived from the structure of a parent compound or protein and whose structure is sufficiently similar to those disclosed herein and based upon that similarity, would be expected by one skilled in the art to exhibit the same or similar properties, activities and utilities as the claimed compounds. For example, a scFv derived from a monoclonal antibody refers to an antibody fragment that shares the same properties that the monoclonal antibody, e.g. shares identical or similar VH and VL and/or recognizes the same epitope.

As used herein, "bind" or "binding" refer to peptides, polypeptides, proteins, fusion proteins and antibodies (including antibody fragments) that recognize and contact an antigen. Preferably, it refers to an antigen-antibody type interaction. The terms "specific binding" or "specifically binding," can be used in reference to the interaction of an antibody, a protein, or a peptide with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope). As used herein, the term “specific binding” means the contact between an antibody and an antigen with a binding affinity of at least 10'⁶ M. In certain aspects, antibodies bind with affinities of at least about 10" ⁷ M, and preferably 10'⁸ M, 10'⁹ M, 10'¹⁰ M.

Ficolins and collectins

Ficolins are a group of oligomeric proteins consisting of both a collagen (Col)-like segment and a fibrinogen (Fi)-like globular domain with lectin (In) binding activity, hence the name Fi+Col+In. Ficolins are secreted proteins and are found in blood, lungs and other body fluids. Collectins are a group of oligomeric proteins consisting of both a collagen (Col)-like segment and C-type lectin binding domain, hence the name Col+Lectin. The term “C-type” refers to the need for calcium ions (Ca²⁺) to assist sugar binding. Collectins are secreted proteins and are found in blood, lungs and other body fluids.

Interestingly, many of these molecules have high valency for sugar binding - valencies of between 9 to 18, typically between 12 to 18. The term “valency” defines the number of binding domains in a macromolecule. Ficolins and collectins are naturally high valency molecules by virtue of the multimerization of trimers made up identical single protein chains into higher order dimers, trimers, tetramers and hexamers. The overall structure of single ficolin and collectin protein chains is the following:

• An N-terminal signal peptide sequence allowing secretion ultimately into the extracellular space;

• Followed by a domain permitting oligomerization into nonamers (9 protein chains coming together to form a single large or macromolecule) or octadecamers (18 protein chains coming together to form a single large or macromolecule) which involves formation of cysteine bridges;

• Followed by a collagen like domain of variable length - between 5-59 Gly-Xxx-Yyy trimeric amino acid motifs where Gly is glycine, Xxx is frequently proline and Yyy is frequently hydroxyproline;

• Followed by a lectin domain (fibrinogen-like for ficolins, C-type for collectins) at the C- terminus.

See Figure 1 for a schematic diagram of ficolin and collectin protein sequences.

As ficolins and collectins share a common collagen like structure, they are sometimes referred to as collagenous proteins. Collagen chains spontaneously associates to form a trimeric molecule called the collagen helix. This is an intrinsic property of the Gly-Xxx-Yyy motif. Through the presence of cysteine residues in the small oligomerization domain these collagen helices to further associate into dimers, trimers, tetramers and hexamers.

The lectin domain at the C-terminal end of the molecule binds carbohydrate molecules on bacteria and even viruses. The crucial aspect of these high valency ficolins and collectins is that they increase the effective avidity of a single lectin domain for its sugar target from the submicromolar range to the picomolar range. In this sense they parallel perfectly IgM molecules that make up for intrinsic low affinity for a protein antigen by penta- and hexamerization.

There are three human ficolins, L-ficolin (gene name FCN1), M-ficolin (FCN2) and H-ficolin (FCN3) (Table 1 below).

They are each made up of a unique protein chain, that first trimerizes and then oligomerizes. L- and M- ficolin exist as multimers up to tetramers of trimers while H-ficolin exists as multimers up to a hexamer of trimers. Accordingly, the former has a maximal valency of 12 while the latter has a maximal valency of 18. As seen by electron microscopy (Lacroix et al., 2009) they show structures much like a bunch of tulips - the collagen helices representing the stalks and the globular fibrinogen like domains the tulip heads (Figure 2. A). H-ficolin is the most abundant in serum followed by L-ficolin. M-ficolin is found in serum in minute quantities and is usually attached to leukocytes.

The human genome encodes 7 collectin genes (Table 2 below), perhaps the most well-known being that encoding the mannan binding lectin 2, or MBL2, which is encoded by the COLECI gene. MBL2 is a single chain that first forms collagen helical trimers which oligomerize into molecules with a maximal valency of 18, like H-ficolin. The human surfactant proteins SP-A1, SP-A2 and SP-D found primarily in the lung are made up of a single protein chain that forms collagen helical trimers, which subsequently tetramerize to give a dodecamer - a molecule with a valency of 12. MBL2 is able to fix complement via the MASP1 and MASP2 proteins, just like the human ficolins, while SP-A and SP-D are unable to do so (Holmskov et al., 2003).

In a preferred embodiment of the invention, the ficolin or collectin is a human ficolin or collectin.

Still preferably, the oligomerization domain and/or the collagen-like domain are from human L ficolin, human M ficolin, or human MBL.

In still a preferred embodiment, the oligomerization domain is represented by SEQ ID NO: 1. In still a preferred embodiment, the collagen-like domain is represented by SEQ ID NO: 2.

Through genomic analyses these molecules can be traced back through mammals, birds, reptiles and even to early forms of lobe-finned fishes such as coelacanths which is very early in evolutionary terms of immune responses, comparable to the earliest immunoglobulin like molecules.

Table 1 lists some typical ficolins in tetrapods (Garred et al., 2010). The list is not exhaustive. huFCNl, huFCN2 and huFCN3 can be found in all primates, i.e. chimps, gorillas, orangs, macaques and prosimians i.e. lemurs.

Table 1.

Table 2 lists some typical collectins in tetrapods. The list is not exhaustive.

Table 2.

There is a small group of ficolin like molecules among some invertebrates such as mosquitos, sea urchins and sea squirts. These are listed in Table 3 (Garred et al., 2010). Table 3.

Ficolin and collectin molecules from a wide variety of different animals can be used as backbone for different purposes, (i) Such molecules can be used and changed in different phases of vaccination to avoid immunization against it. This way vaccination could proceed without impairment of vaccination by the scaffolds, (ii) With similar criteria, different vaccinations against different viruses could need different scaffolds to avoid crossed boosting between vaccinations, e.g.: for antigen A, a ficolin from a camel could be used; for antigen B, a ficolin from a mouse could be used; for antigen C, a collectin from an elephant could be used, and so on.

Tables 1 and 2 provide non-exhaustive lists of ficolin and collectins molecules that have been found in the literature, data bases or else by data mining of genomes using BLAT and BLAST searches. The literature shows that in evolutionary terms they go back to some early forms of fishes, much like immunoglobulins themselves. For example, it was easy to find a ficolin and collectin equivalent for the coelacanth (Latimeria sp.), a rare lineage of fishes that goes back to around 360 million years. This means that a vast array of ficolin and collectin collagen helix scaffold proteins exist in nature from coelacanths to humans and that there will be more than enough to make vaccines for human immunization.

In the present invention, the oligomerization domain and the collagen-like domain in the chimeric protein can derive from the same ficolin or collectin, or alternatively the oligomerization domain may derive from one ficolin or collectin (e.g. from a first species) and the collagen-like domain may derive from another one ficolin or collectin (e.g. from a second species).

Heterologous protein or peptide of interest

The invention provides a nucleic acid construct that encodes a chimeric protein comprising a heterologous protein or peptide of interest. In the context of the present invention, the term “heterologous” means that the protein or peptide of interest is not a ficolin or collectin protein, nor derived therefrom. In particular, the protein or peptide of interest is not, and does not comprise, a lectin binding domain.

The protein or peptide of interest may yet be a protein or peptide that derives from the same species as the species from which the ficolin or collectin oligomerization and collagen-like domains derive.

In a particular embodiment, the heterologous protein or peptide of interest is an antigenic protein or peptide.

In a preferred embodiment, the heterologous protein or peptide of interest is an antigenic protein or peptide of an infectious microorganism, especially a virus.

In particular, the virus may be selected from the group consisting of Arenaviruses (e.g. Lassa fever virus), Bunyaviruses (e.g. Rift valley fever virus), Coronaviruses (e.g. SARS-CoV-1 & - 2 or MERS-CoV), Filoviruses (e.g. Ebola virus, Marburg virus), Hepevirus (e.g. Hepatitis E virus), Nairovirus (e.g. Crimean-Congo hemorrhagic fever virus), Orthomyxoviruses (including influenza viruses such as influenza A and influenza B viruses), Paramyxoviruses (e.g. Nipah virus), Pneumovirues (e.g. Metapneumovirus, Respiratory syncytial virus), Retroviruses (e.g. HIV), and Togaviruses (e.g. Chikungunya virus).

Preferably, the antigenic protein or peptide is a viral envelope protein, or an antigenic fragment thereof.

Preferred target viruses are SARS-CoV-2, influenza virus and HIV.

In a particular embodiment, the viral envelope protein is a glycoprotein S of SARS-CoV-2, or an antigenic fragment thereof, for example, but not exclusively, the receptor binding domain. Other viral envelope proteins of interest include those belonging to Adenoviruses, Asfarviruses, Herpesviruses, Flaviviruses and Poxviruses.

In another particular embodiment, the viral envelope protein is an Influenza hemagglutinin (HA) protein or an antigenic fragment thereof, such as the HA1 and HA2 domains in pre- and post-fusion conformations. Generally speaking, trimeric viral envelop proteins are of special interest. By coupling trimeric viral envelope proteins to self-associating collagenous triple helix, the individual components of the metastable viral trimer cannot dissociate because they are covalently coupled one to the other. Thus, the full immunogenicity of the key antigenic structure is retained. Typical examples are HIV gpl20-gp41 proteins.

The collagen like helix ensures that the envelope proteins form stable trimers while the oligomerizing domain increases the valency. Such high valency allows good induction of immunity. Being covalently linked to the ficolin or collectin domains, the envelope trimers cannot fall apart, either spontaneously as is the case for some HIV isolates or be torn apart by antibodies within germinal centers.

In another embodiment, the heterologous protein or peptide of interest that can be fused to the collagen-like domain of a ficolin or collectin protein may derive from a bacterium or a parasite. As an example, one may use the Plasmodium falciparum circumsporozite protein (CSP), more particularly at least a part of the repeat sequence coupled with the C-terminal region encoding a number of CD4 and CD8 T cell epitopes.

More generally antigenic protein or peptides may derive from a microorganism that is a causative agent of a disease listed in Table 4. On the left is a list of infectious agents for which certain vaccines are available. On the right the list for which no vaccine has been not marketed yet.

Table 4.

In another embodiment, the heterologous protein or peptide of interest is an antibody recognition site, such as a paratope fragment or a scFv fragment of an antibody, e.g. an antibody that specifically binds an immune checkpoint molecule or a viral, bacterial or parasitic antigen.

In a particular embodiment, the heterologous protein or peptide of interest binds an immune checkpoint molecule.

Any immune checkpoint may be targeted, including but not limited to, CTLA-4, PDL1, PDL2, PD1, B7-H3, B7-H4, BTLA, HVEM, TIM3, GAL9, LAG3, VISTA, KIR, 2B4, CD160, CGEN- 15049, CHK1, CHK2, A2aR, and the B-7 family of ligands.

Fusing the collagen-like domain of a ficolin or collectin protein to antibody recognition sites specific for immune checkpoints results in molecules with valencies of 9 to 18, especially 12 or 18, that will irreversibly or strongly bind to tumor cells (namely with a Kd of 10'¹⁰ to 10'¹² or lower) thereby allowing recruitment of complement, and lysis of the tumor cells. In a preferred embodiment, the heterologous protein or peptide of interest binds HLA-G. The HLA-G binding capacity is a feature of the first two domains of the ILT2 or ILT4 molecules that are composed of four domains. Accordingly, the heterologous protein or peptide of interest may be ILT2 or ILT4, or a HLA-G binding domain thereof. More particularly such chimeric protein of the invention with domain DI and/or D2 of either ILT2 or ILT4 can be designed, to strongly bind to the tumor cells, the apparent dissociation constant moving from nanomolar to femtomolar.

In a particular embodiment, the heterologous protein or peptide of interest binds to a molecule of therapeutic interest, including, but not limited to type I, II and III interferons, interleukins like IL-6, IL- 10.

Other examples of targets to which the heterologous protein or peptide of interest may bind, are listed below: integrin receptor, alpha-4 integrin, IL 12, IL23, IL6R, IL23, IL 17 A, IL5, IL4RA, IL2R, IL2RA, IL17RA, IL5RA, IL1B, HER2, EGFR, CD20, CD22, CD4, CD33, CD30, CD19, CD52, CD79B, CD38,VEGF ,VEGFR1, VEGFR2, PD-1, PD-L1, PDGFRA, CTLA-4, TNF, TNF alpha, PCSK9, CGRP receptor, SLAMF7, Complement component 5, GD2, RANK, PSMA, FGF23, BLyS, PCSK9, GPIIb/IIIa, CCR4.

Methods for treating cancers or autoimmune or inflammatory diseases, by targeting any of those molecules are described in greater details below.

Peptide Linker

The heterologous protein or peptide of interest is linked to the collagen-like domain may be fused in frame (directly) or through a peptide linker.

The term “linker” refers to a (poly)peptide comprising 4 to 80 amino acids, preferably 4 to 30, 4 and 18 amino acids or 5 to 15 amino acids. Suitable linkers are known in the art.

In a particular embodiment the peptide linker comprises or consists of a sequence of glycine residues, or of a sequence comprising glycine and serine residues, for instance the linker may comprise GGGS (SEQ ID NO: 30) repeats. However, an artisan skilled in the art will recognize that other sequences following the general recommendations (Argos, 1990; Georges and Heringa, 2002) can also be used. Linkers composed of small, non-polar (e.g. Gly) or polar (e.g. Ser or Thr) amino acids provide flexibility, and allows for mobility of the connecting functional domains. Constructs

The nucleic acid construct of the invention is in an isolated form.

The nucleic acid may be DNA or RNA, but is preferably DNA, still preferably double stranded DNA.

The nucleic acid construct of the invention encodes a chimeric protein and as such it is not a naturally-occurring genomic nucleic acid.

Furthermore, in a preferred embodiment, it does not comprise introns.

According to the invention, the chimeric construct may further encode an N-term signal peptide. Signal peptide sequences exist at the N-terminus of many secretory proteins and membrane proteins and have typically a length of 15 to 30 amino acids, often rich in hydrophobic amino acids (Phe, Leu, He, Met and Vai).

According to the present invention, the signal peptide preferably is a signal peptide of a ficolin or collectin.

In another embodiment, the heterologous peptide of interest is further fused to a carrier protein, preferably wherein the heterologous peptide and the carrier protein altogether comprise at least 60 amino acids, or more, e.g. about 68 amino acids.

This is especially useful when the heterologous peptide of interest is a short peptide (e.g. less than 20 amino acids). In a preferred embodiment the heterologous peptide of interest is fused at the C-terminus of the carrier protein (which in turn is linked, by its N-terminus, to the collagen-like domain of a ficolin or collectin protein).

Such “carrier” proteins include e.g. a soluble secreted protein like human lysozyme or a domain of a secreted protein such as the DI domain of the human proteins ILT2 or ILT4, for example.

Production of the chimeric protein

In a preferred embodiment, the chimeric protein can be produced by DNA recombinant technique in a suitable expression vector.

In a still preferred embodiment, the chimeric protein is expressed in vivo, after administering the subject with a nucleic acid encoding said chimeric protein. Vectors and compositions are described in greater details below.

The chimeric protein assembles by cysteine disulphide bonds. The multimerization leads to the formation of high molecular weight molecules (typically more than 500kDa).

It is herein described a method for producing a recombinant multimerized protein comprising: a) transfecting host cells with a vector allowing expression of a nucleotide sequence coding for a chimeric protein comprising, from N to C term, i) an oligomerization domain followed by a collagen-like domain of a ficolin or collectin protein; and ii) a heterologous protein or peptide of interest, b) culturing transfected cells under conditions which are suitable for expressing the nucleotide sequence coding for the chimeric protein and for multimerization of the protein; c) recovering, and preferably purifying, the multimerized protein formed.

The expression vector is selected as a function of the host cell into which the construct is introduced. Preferably, the expression vector is selected from vectors that allow expression in eukaryotic cells, especially from chromosomal vectors or episomal vectors or virus derivatives, in particular vectors derived from plasmids, yeast chromosomes, or from viruses such as baculovirus, papovavirus or SV40, retroviruses or combinations thereof, in particular phagemids and cosmids. In a particular embodiment, it is a vector allowing the expression of baculovirus, capable of infecting insect cells.

The vector comprises all of the sequences necessary for the expression of the sequence coding for the fusion polypeptide. In particular, it comprises a suitable promoter, selected as a function of the host cell into which the construct is to be introduced.

Within the context of the invention, the term "host cell" means a cell capable of expressing a gene carried by a nucleic acid which is heterologous to the cell and which has been introduced into the genome of that cell by a transfection method.

Preferably, a host cell is a eukaryotic cell. A eukaryotic host cell is in particular selected from yeast cells such as S. cerevisiae, filamentous fungus cells such as Aspergillus sp., insect cells such as the S2 cells of Drosophila or sf9 of Spodoptera, mammalian cells and plant cells. Mammalian cells which may in particular be cited are mammalian cell lines such as CHO, COS, HeLa, HEK-293T, C127, 3T3, HepG2 or L(TK-) cells. In a preferred implementation, said host cells are selected from eukaryotic cell lines, preferably Sf9 insect cells.

Any transfection method known to the skilled person for the production of cells expressing a heterologous nucleic acid may be used to carry out step a) of the method. Transfection methods are, for example, described in Sambrook et al, 2001, "Molecular Cloning: A Laboratory Manual", 3rd edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. Alternatively, the chimeric protein can be produced by chemical peptide synthesis. For instance, the protein can be produced by the parallel synthesis of shorter peptides that are subsequently assembled to yield the complete sequence of the protein with the correct disulfide bridge.

Vectors

The genetic constructs of the invention may be DNA or RNA, and are preferably doublestranded DNA. The genetic constructs of the invention may also be in a form suitable for transformation of the intended host cell or host organism, in a form suitable for integration into the genomic DNA of the intended host cell or in a form suitable for independent replication, maintenance and/or inheritance in the intended host organism. For instance, the genetic constructs of the invention may be in the form of a vector, such as for example a plasmid, cosmid, YAC, a viral vector or transposon. In particular, the vector may be an expression vector, i.e. a vector that can provide for expression in vitro and/or in vivo (e.g. in a suitable host cell, host organism and/or expression system).

In a preferred but non-limiting aspect, a genetic construct of the invention comprises i) at least one nucleic acid of the invention; operably connected to ii) one or more regulatory elements, such as a promoter and optionally a suitable terminator; and optionally also iii) one or more further elements of genetic constructs such as 3'- or 5'-UTR sequences, leader sequences, selection markers, expression markers/reporter genes, and/or elements that may facilitate or increase (the efficiency of) transformation or integration.

In a particular embodiment, the genetic construct can be prepared by digesting the nucleic acid polymer with a restriction endonuclease and cloning into a plasmid containing a promoter such as the SV40 promoter, the cytomegalovirus (CMV) promoter or the Rous sarcoma virus (RSV) promoter.

Other vectors include retroviral vectors, lentivirus vectors, adenovirus vectors, vaccinia virus vectors, pox virus vectors, measles virus vectors and adenovirus-associated vectors.

Preferably, the vector is an integrative lentiviral vector. Non-integrative lentiviral vectors can also be used. Lentiviral vectors have the added advantage over vectors derived from oncoretroviruses in that they can transduce non-proliferating cells and present low immunogenicity. In general, a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers such as described in WO 01/96584; WO 01/29058; and US 6,326,193. Pharmaceutical compositions and vaccines

Pharmaceutical, immunogenic or vaccine compositions, can be prepared, comprising at least one of said nucleic acid, vector, or chimeric protein.

Optionally, in a particular embodiment, the composition comprises several different nucleic acid constructs, vectors or chimeric proteins as defined above, each encoding or comprising a distinct heterologous protein or peptide of interest. For instance, the composition may comprise a nucleic acid construct encoding a first heterologous protein or peptide of interest, and another nucleic acid construct encoding a second heterologous protein or peptide of interest.

The compositions can comprise a pharmaceutically acceptable carrier or excipients that are suitable for administration in humans or mammals (i.e. non-toxic, and, if necessary, sterile). Such excipients include liquid, semisolid, or solid diluents that serve as pharmaceutical vehicles, isotonic agents, stabilizers, or any adjuvant. Diluents can include water, saline, dextrose, ethanol, glycerol, and the like. Isotonic agents can include sodium chloride, dextrose, mannitol, sorbitol, and lactose, among others. Stabilizers include albumin, among others.

When used as a vaccine, the composition may comprise any adjuvant, including oil-based adjuvants such as Freund's Complete Adjuvant and Freund's Incomplete Adjuvant, mycolate- based adjuvants, bacterial lipopolysaccharide (LPS), peptidoglycans, proteoglycans, aluminum hydroxide, saponin, DEAE-dextran, neutral oils (such as miglyol), vegetable oils (such as arachis oil), Pluronic® polyols.

The nucleic acid or composition can be administered directly or they can be packaged in liposomes or coated onto colloidal gold particles prior to administration. Techniques for packaging DNA vaccines into liposomes are known in the art, for example from Murray, 1991. Similarly, techniques for coating naked DNA onto gold particles are taught in Yang, 1992, and techniques for expression of proteins using viral vectors are found in Adolph, 1996.

For genetic immunization, the compositions are preferably administered intradermally, subcutaneously, intramuscularly, into tumors or in any types of lymphoid organs by injection or by gas driven particle bombardment, and are delivered in an amount effective to stimulate an immune response in the host organism. In a preferred embodiment of the present invention, administration comprises an electroporation step, also designated herein by the term “electrotransfer”, in addition to the injection step (as described in Mir 2008, Sardesai and Weiner 2011). Alternatively, needle free devices can be used to deliver DNA and/or RNA.

Appropriate dosage and regimen may be determined by physicians. For instance, a series of dosages of increasing size, starting at about 5 to 30 pg, or preferably 20-25 pg, up to about 500 pg to about 5 mg, preferably up to 500-1500 pg, 500-1200 pg, or 500-1000 pg, may be administered to the subject and the resulting immune response is observed, for example by detecting the cellular immune response by an fFNy Elispot assay (as described in the experimental section), by detecting CTL responses using an in vivo lysis assay or a chromium release assay or detecting Th (helper T-cell) response using a cytokine release assay.

The compositions that comprise or are capable of expressing a chimeric protein comprising an antigen of an infectious microorganism are particularly useful in vaccination. Indeed, the chimeric constructs and compositions described herein are immunogenic and are capable of inducing neutralizing antibodies.

Other compositions or nucleic acid constructs that comprise or are capable of expressing a chimeric protein comprising a molecule that, e.g., binds an immune checkpoint molecule, are useful in cancer immunotherapy. Such chimeric constructs and compositions described herein are capable of binding HLA-G.

In a preferred embodiment, the regimen comprises one to three injections, preferably repeated three or four weeks later.

In a particular embodiment, the vaccination schedule can be composed of one or two injections followed three or four weeks later by at least one cycle of three to five injections. In another embodiment, a primer dose consists of one to three injections, followed by at least a booster dose every year, or every two to five years for instance. These are examples only, and any other vaccination regimen is herein encompassed.

Anti-tumoral treatments

The nucleic acid, protein or composition as described above is useful in a method for preventing or treating a tumor in a patient.

A method for preventing or treating a tumor in a patient is described, which method comprises administering an effective amount of said nucleic acid, protein or composition in a patient in need thereof.

The tumor may be any undesired proliferation of cells, in particular a benign tumor or a malignant tumor, especially a cancer.

The cancer may be at any stage of development, including the metastatic stage. The cancer may be chronic or non-chronic (acute).

In a particular embodiment, tumor is a solid cancer or a carcinoma. Examples include melanoma, brain tumor such as glioblastoma, neuroblastoma and astrocytoma and carcinomas of the bladder, breast, cervix, colon, lung, especially non-small cell lung cancer (NSCLC), pancreas, prostate, head and neck cancer, or stomach cancer.

In another embodiment, the tumor may be a liquid tumor, e.g. a hematopoietic tumor or leukemia, such as a chronic or acute lymphocytic leukemia, chronic or acute myeloid leukemia, lymphoma including Hodgkin's disease, multiple myeloma, malignant myeloma.

In a particular embodiment, the treatment according to the invention may be combined with conventional therapy, including chemotherapy, radiotherapy or surgery. Combinations with adjuvant immunomodulating molecules could also be useful.

Treatments of autoimmune and/or inflammatory diseases

The nucleic acid, protein or composition as described above is useful in a method for treating an autoimmune and/or inflammatory disease in a patient.

A method for treating an autoimmune and/or inflammatory disease in a patient is described, which method comprises administering an effective amount of said nucleic acid or composition in a patient in need thereof.

Autoimmune diseases include e.g. systemic lupus erythematosus, multiple sclerosis, rheumatoid arthritis, Sjogren's syndrome, type I diabetes and inflammatory bowel disease.

The examples and figures illustrate the invention without limiting its scope.

EXAMPLES

Materials and methods:

Recombinant H-ficolin ILT2/ILT4 constructs

Figure 3.A shows a schematic drawing of recombinant human H-ficolin ILT2 and/or ILT4 single chain constructs.

A glycine-serine spacer was introduced between the collagen like domain of H-ficolin and the D1D2 domains. Codon usage was optimized using an in-house method eliminating infrequently used codons (generally <16%) while runs of C and G were eliminated to help with the synthesis. A V5 tag from the dog SV5 virus was added followed by a six histidine residue tag should purification be necessary. Restriction sites were generally purged from the domain coding sequences and added around them in the form of small linker or spacer sequences to make cassettes which subsequently facilitate sub-cloning. The entire coding region was flanked by BamHI and Xhol sites. The gene was synthesized and the ensemble cloned into pcDNA3.1+.

The protein and nucleic acid sequences of the transgenes used in this application are listed in sequence listing. The other antigens spliced onto the ficolin and collectin carrier molecules are:

• the D1+D2 domains of human ILT2 and/or ILT4 receptor molecule for HLA-G.

• the exodomain of the pandemic 2009 influenza A hemagglutinin molecule.

• the ectodomain of the HIV-1 gpl20-gp41 envelope protein.

• a single chain Fv (scFv) from the mouse immunoglobulin 15E7 specific for the alpha 3 domain of HLA-G.

Some constructs had the FLAG or HA tags instead of V5, most included a six histidine residue tag.

Cell transfection

Approximately 800,000 HeLa, HEK-293T were seeded into 6-well plates and transfected with 2 pg of plasmid using the jetPRIME transfection kit (Polypus Transfection™) according to manufacturer’s instructions. For cotransfections, a plasmid ratio of 1 : 1 was used.

Western blotting

Cells were harvested at 24, 48 or 72 hours after transfection. Protein extraction and Western blot analysis were carried out according to standard procedures. Immunoprecipitation experiments were performed using Anti-FLAG® M2 Magnetic Beads (Sigma), and a magnetic stand, according to manufacturer’s instructions. For high molecular weight complexes detection, sample were either treated with or without reducing agent (25 mM DTT) prior to SDS page separation. Incubation of migration gel with a solution of 25 mM DTT for 15 minutes at room temperature was performed to allow in gel denaturation and protein transfer. After blocking, membranes were probed with either a 1 :5000 dilution of anti V5-tag horseradish peroxidase (HRP)-coupled antibody (Invitrogen), a 1 : 15000 dilution of anti P-actin (sigma), or 1 :5000 dilution of anti-FLAG HRP coupled antibody (Sigma). The membrane was subjected to detection by SuperSignal™ West Pico chemiluminescent substrate (ThermoFisher Scientific).

Lentiviral vector production HIV-1 derived vector particles production was previously described (Coutant et al. 2008). Briefly, Vectors were generated by transient calcium phosphate co-transfection of HEK-293T cells (ATCC) with a vector plasmid pTRIP encoding the vector RNA, an envelope expression plasmid pCMV encoding VSV glycoprotein from either serotype Indiana (IND) or New Jersey (NJ) and an encapsidation plasmid p8.7 to produce an Integrative Lentiviral Vector particles (ILV). To concentrate vector particles, the supernatant was ultracentrifuged (Ih at 22000g 4°C) and recovered in PBS 2,5%sucrose. Functional titer was determined by quantitative PCR after transduction of 293T cells as previously described (Coutant et al. 2008) and was expressed as transduction unit (TU)/mL of vector.

Immunization

10-week-old C57/BL6J mice were immunized by intra-peritoneal (IP) injection of 5.10⁶ TU of ILV in 200 pl of PBS. VSV-G New Jersey pseudotyped vectors were used for the 1st injection (day 0) while the VSV Indiana envelope for 2nd injection (day 29). Blood was recovered at days 0, 14, 28 and 42 from the retromandibular vein.

ELISA format and serological testing

A 96 wells ELISA plate was used. Tested proteins were FNC3-ILT2 or FCN3-ILT4 (produced and purified in house) and ILT2-Fc or ILT4-Fc (R&D Systems). These were diluted at 1/5, 1/10, 1/50, 1/100, 1/500, 1/1000, and 1/10000 with distilled water. Purified proteins (unknown concentration for FNC3-ILT2 or FCN3-ILT4 and 0.2 mg/ml for ILT2-Fc and ILT4-Fc) and successive dilutions were transferred to the plate for coating at 50 pl/well 4°C, in the dark overnight. The plate was then blocked by a PBS BSA 0.5% solution, 2 hours under shaking, in the dark at RT. After washing 3 times in PBS, the target protein, HLA-G SN was incubated 2 hours under shaking, in the dark at RT. After washing 3 times in PBS, primary antibody 4H84 (0.2 mg/ml, Santa Cruz Biotechnologies, USA) was added at 1/1000 (50 pl/well) using PBS BSA 0.5% for the different dilutions. Incubation phase was repeated with 2 h shaking in the dark at RT. Following washing 3 times in PBS, secondary antibody anti-mouse IgG-HRP (Sigma Aldrich, USA) was used at 1/2000, in 50 pl/wells before another incubation step with the same parameters for 2 h. Finally, the plate was revealed using the Ultra- TMB -ELISA reagent (100 pl/well) (ThermoFisher, USA) during 20 minutes in the dark and the reaction was stopped using the stop solution (100 pl/well) (ThermoFisher, USA). Absorbance at 450 nm was measured on a Glomax-Multi Detection System (Promega, France).

Hemagglutination inhibition and microneutralization assay Serum titers were measured with a microtiter hemagglutination inhibition (HI) assay. Briefly, after treatment with receptor-destroying enzyme, serial 2-fold dilutions of serum (starting at 1 : 10) were tested against 4 hemagglutinin units of antigen in human O+ Rh- red blood cells. The HI titers were defined as the reciprocal of the highest serum dilution that completely inhibited hemagglutination. Seroprotection was defined as an HI titer >40. Seroconversion was defined as either an HI titer <10 at DO and >40 after vaccination or an HI titer >10 at DO with a >4-fold increase after vaccination.

Seroneutralization test

Neutralizing Antibody titers were measured by microneutralization (MN) assays. Serum samples were first heat-inactivated at 56°C for 30 minutes. Serial 2-fold dilutions of serum (from 1 : 10) were added separately to 103 TCID50 of each of the three vaccine strains and incubated at 37°C for 2 hours before transfer onto 96-well microtiter plates containing confluent MDCK (Madin-Darby canine kidney) cells. The neutralization titer was expressed as the reciprocal of the highest serum dilution that blocked virus infection after 3 days of culture.

Example 1: Ficolin ILT2 and ILT4 constructs

Transfection of 293T cell line with the ficolin ILT2 and ILT4 constructs gave rise to recombinant proteins of apparent molecular weight of 34-40 kDa. Cell lysate fractions and SN showed a band of ~40 kDa for the ILT2 construct when analyzed by Western blotting; while the MW of ficolin ILT4 construct was ~34 kDa (Figure 3.B). The calculated MWs of the precursor and mature forms of both the chimeric ILT2 and ILT4 constructs are -34.7 and -32.1 kDa respectively. Ficolins are post transcriptionally modified and include hydroxylation of proline residues and glycosylation of a lysine residue in the collagenous domain, while the D1+D2 domains of ILT2 encode a single N-linked glycosylation site and ILT4 none. N- glycosylation of the ILT2 construct would explain the broad band for the ILT2 construct with respect to the ILT4.

These constructions where afterwards tested in an ELISA against commercial molecules of ILT2-Fc and ILT4-Fc. This assay allowed demonstration that multimerization of D1D2 domains of these molecules is translated into a higher avidity for the target (HLA-G) than the dimeric commercial forms. These results are shown in Figure 3.C.

As the recombinant proteins were well expressed the constructs were subcloned into the pTRIP lentiviral vector via the flanking BamHI and Xhol sites. Lentiviral stocks titered out to around 10⁸-10⁹ TU/ml (Figure 4.A). The pFLAP CMV HLA-G a3 construct was used as negative control. Using the protocol outlined in Figure 4.B, C57/BL6J mice aged of 10 weeks were immunized by intra-peritoneal (IP) injection of 5.10e6 TU of ILV in 200 pl of PBS and then boosted at day 29. Sera were drawn at days 0, 14, 28 and 42 from the retromandibular vein.

A direct ELISA to test the presence of anti-ILT2 or ILT4 antibodies generated in the immunized mice was carried out using commercially available ILT2-Fc or ILT4-Fc D1D2 bodies as coating antigen. As can be seen in Figure 4.C, good antibody responses were obtained by 2 weeks (D14) for both constructs compared to controls; indeed, they were saturating at a 1/100 dilution. The antibodies were tested by limiting dilution serum titers of greater than 1/10,000 for the FCN3-ILT2 construct for all animals by day 14 (Figure 4.D). By day 28 they well over a 1/10,000 dilution. Upon boosting at day 28 and analyzed at day 42 levels in three animals were not boosted, while only for animal M4 was there sign of a booster effect. By contrast for the FCN3-ILT4 construct titers were >1/100,000 by day 14.

Responses were target-specific with mouse antibodies reacting to ILT2 predominantly reacting to ILT2-Fc and not to ILT4-Fc. The very slight increase in heterologous titers is not surprising as the D1D2 domains of ILT2 and ILT4 are only 17% divergent at the amino acid level. This does not affect the conclusion that the sera are remarkably specific.

Example 2: Other human and mammalian ficolin and collectins scaffolds allow efficient secretion of chimeric proteins

Given the success of secretion of the FCN3-ILT2/4 constructs and their ability to induce robust immune responses in the mouse, the D1D2 domains of the human ILT4 molecules were spliced onto the collagenous domains of a number of human and mammalian ficolins and collectins.

These collagenous domains of these constructs were derived from:

Human L-ficolin (L-ficolin encoded by the human FCN1 gene)

Human M-ficolin (M-ficolin encoded by the human FCN2 gene)

Human mannose binding protein (MBL encoded by the human MBL gene)

Human surfactant protein A (SP-A encoded by the human SFTPA1 gene) Human surfactant protein D (SP-D encoded by the human SFTPD gene) Mouse mannose binding protein (MBP encoded by the mouse MBL2 gene) Mouse ficolin A (ficolin A encoded by the mouse FCNA gene) Mouse ficolin B (ficolin B encoded by the mouse FCNB gene) Pig ficolin 2 (ficolin 2 encoded by the pig FCN2 gene)

The amino acid and nucleic acid sequences of the above constructs are given in the sequence listing. As the collagenous domain for human SP-D is exceptionally long relative to the other molecules, 59 glycine repeats (GXY) compared to 11-24, it was cut back in length to 12 glycine repeats. Otherwise there were no other changes apart from the C-terminal tag that was changed to FLAG which is sometimes a more robust tag.

Following transfection of 293T cells by recombinant ficolin and collectin constructs cell pellets and culture supernatants were analyzed by SDS-PAGE using a dithiothreitol (DTT) as a reducing agent, meaning the proteins were fully reduced to monomers. Proteins were tested by Western blotting and revealed using an antibody specific for the FLAG tag. Figure 5.A to D shows that a number of various ficolin and collectin collagen like molecules can be used to vector the D1D2 domains of ILT4, notably mouse Ficolin A and B, human MBL; human ficolin 2, human surfactant protein D (SPD) and pig ficolin. The sequences of these constructs are given in the sequence listing. While the degree of secretion varied in other experiments using the same cell line or a different cell line good secretion was obtained meaning that these differences are local and experimental rather than fundamental. This was true for the same cargo, D1D2 domains of human ILT4 by different ficolins of collectins, or different cargos carried by the same collagen transporter, human H-ficolin.

Other Western blot analyses were performed to test the FCN3-Para7 (anti-HLA-G ScFv) and FCN3-Calif (ectodomain of the 2009 pandemic strain (A/California/7/2009 H1N1), respectively shown in Figure 5.E and Figure 5.F.

Example 3: Multimerization of recombinant ficolin and collectins

To show that these molecules assembled into high molecular weight molecules cross linked by cysteine disulphide bridges amongst different collagen scaffolds, a human FCN3-ILT4 construct with a FLAG tag was made. This was co-transfected with the human FCN3-ILT4- tagged construct. Cell lysates and culture supernatants were run on a denaturing gel and studied by Western blot (Figure 6). The crucial experiment is in the bottom two panels. The culture supernatants were first immunoprecipitated with anti-FLAG antibodies and then loaded on the gel. The blot was then probed with anti-V5 antibodies. As can be seen from the bottom part of the Figure 6, anti-FLAG antibodies pulled down V5 tagged human FCN3-ILT4. This is only possible if they assemble into high molecular weight complexes. To show multimerization using a completely different example, the inventors made a human FCN3 construct using SOSIP from the BG505 strain of HIV. Figure 8.M shows the annotated sequence of the construct and Figure 7.A shows a schematic of the molecule with the extra cysteine bridge introduced to crosslink gpl20 and the gp41 ectodomain. Figure 7.B shows that this high molecular weight (HMW) complex - the longest tested to date made up of 730 residues for the mature monomer (MWcalc 140 kDa) - is well synthesized and correctly processed by furin. When a non-reduced (i.e. -N/R) the majority of the FL AG-tagged protein was in the stacking gel. This is not surprising given that the MWcalc for the octadecameric complex is 2.5 MDa.

The molecular weights of the multimeric molecules are frequently >500 kDa and cannot be accurately assessed by gel electrophoresis. For example, many of the bands corresponding to multimeric forms are in the stacking gel. To get around this mini-derivatives were made of human H-ficolin corresponding to the oligomerization and collagenous domains only followed by a FLAG, V5 or HA tag. The annotated sequences corresponding to these constructs are given in the sequence listing.

Example 4: Influenza vaccination

With the above data, the inventors decided to approach influenza A vaccination. Protective antibodies to influenza are generally those that target the hemagglutinin (HA) protein. The inventors made a human H-ficolin (FCN3) construct with the ectodomain of the 2009 pandemic strain (A/Califomia/7/2009 (H1N1) pdm09-like virus, GenBank accession number FJ966082). The nucleotide sequence can be found in the sequence listing and the protein sequence of the construct in Figure 5.F. The latter shows a schematic drawing of the human ficolin (FCN3) and HA1/ HA2 construct and a Western blot confirming the correct expression of such construct in 293T and HeLa cell lines. The construct was well synthesized and secreted.

The construct was subcloned in the integrating pTRIP-CMV-WPRE vector (just like the FCN3- ILT2/4 constructs) via BamHl and Xhol sites, and a high titer stock of virus was made. Five C57BL/6j females were injected intraperitoneally at day zero and boosted one month later with 5X10⁵TU of lentiviral vector and boosted one month later. Sera were taken at days 0, 14, 28 and 42.

When antibodies were tested in a micro-hemagglutination assay antibody titers were very low. This assay privileges detection of antibodies to the crown of the viral hemagglutinin molecule which is involved in receptor binding. When the same sera were tested in a microneutralization assay titers were in the 1/20-1/640 range for the homologous A/Califomia/7/2009 (H1N1) pdm09-like virus. Such titers are sufficient to protect mice from a lethal challenge of virus. When tested against a number of different influenza H1N1 strains reciprocal serum titers were in the 1/20-1/40 range. Surprisingly the sera also proved reactive to the influenza A H3N2 strain. The titers are lower than for human reference sera used as positive control (See Tables 5 a, b, c, d, e, f and g below).

Ln

TABLES 5 a, b, c, d, e, f and g show the results of a test of sero-neutralization. Mice were immunized with the recombinant human H-ficolin-HAl/HA2 construct. The neutralizing ability of antibodies are measured and related to higher in sera titers, represented by “No”, as “neutralized virus”. The mention “Yes” represents the virus presence. Taken together these findings suggest that the antibodies are directed more to the stalk of the hemagglutinin rather than the crown, a feature with broadly cross reacting antibodies. This fits with the neutralization of the H3N3 strain.

The conclusion is that the chimeric ficolin-hemagglutinin constructs are immunogenic and induce neutralizing antibodies.

REFERENCES

• Adolph K. 1996. Ed. "Viral Genome Methods" CRC Press, Florida.

• Argos P. 1990. An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion. J Mol Biol. 211 : 943 -58. doi: 10.1016/0022-2836(90)90085-Z.

• Beltrame MH et al., 2015. The lectin pathway of complement and rheumatic heart disease, Front. Pediatrics 21 :148. doi: 10.3389/fped.2014.00148.

• Coutant F. et al. 2008, Protective antiviral immunity conferred by a nonintegrative lentiviral vector-based vaccine. PLoS ONE 3: e3973. doi: 10.1371/journal. pone.0003973.

• Endo Y, Matsushita M, Fujita T. et al., 2007. Role of ficolin in innate immunity and its molecular basis, Immunobiology 212(4-5):371-9. doi: 10.1016/j.imbio.2006.11.014.

• Garred P. et al. 2010. The genetics of ficolins. J Innate Immunity, 2:3-16. doi: 10.1159/000242419.

• George R, Heringa J. 2002. An analysis of protein domain linkers: their classification and role in protein folding. Protein Eng. 15:871-879. doi: 10.1093/protein/15.11.871

• Holmskov U, Thiel S, Jensenius JC. 2003. Collections and ficolins: humoral lectins of the innate immune defense. Annu Rev Immunol. 21 :547-78. doi:

10.1146/annurev.immunol.21.120601.140954

• Lacroix M. et al, 2009. Residue Lys57 in the collagen-like region of human L-ficolin and Its counterpart Lys47 in H-ficolin play a key role in the interaction with the mannan-binding lectin-associated serine proteases and the collectin receptor calreticulin. J Immunol. 182:456- 65. doi: 10.4049/jimmunol.182.1.456

• Lu J et al., 2002. Collectins and ficolins: sugar pattern recognition molecules of the mammalian innate immune system, Biochim Biophys Acta 1572(2-3):387-400. doi: 10.1016/s0304-4165(02)00320-3.

• Mir LM. 2008. Application of electroporation gene therapy: past, current, and future. Methods Mol Biol. 423:3-17. doi: 10.1007/978-l-59745-194-9_l.

• Murray EJ. 1991. Ed. "Gene Transfer and Expression Protocols" Humana Pres, Clifton, N.J. • Sardesai NY, Weiner DB. 2011. Electroporation delivery of DNA vaccines: prospects for success. Curr Opin Immunol. 23:421-429. doi: 10.1016/j.coi.2011.03.008.

• Yang NS. 1992. Gene transfer into mammalian somatic cells in vivo. Crit Rev Biotech.

12:335-356. doi: 10.3109/07388559209040627. • Sambrook J. et al., 2001. "Molecular Cloning: A Laboratory Manual", 3rd edition, Cold

Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

Claims

32

CLAIMS A nucleic acid construct that encodes a chimeric protein comprising, from N to C term, i) an oligomerization domain of a ficolin or collectin protein, followed by a collagen-like domain of a ficolin or collectin protein; and ii) a heterologous protein or peptide of interest. The nucleic acid construct of claim 1, wherein the heterologous protein or peptide of interest is an antigenic protein or peptide of an infectious microorganism, including a virus, a bacterium, or a parasite (e.g. Plasmodium falciparum). The nucleic acid construct of claim 2, wherein the antigenic protein or peptide is a viral envelope protein, or an antigenic fragment thereof, preferably wherein the viral envelope protein, or antigenic fragment thereof, is a viral envelope protein, or an antigenic fragment thereof of a virus selected from the group consisting of Arenaviruses (e.g. Lassa fever virus), Bunyaviruses (e.g. Rift valley fever virus), Coronaviruses (e.g. SARS-CoV-1 & -2 or MERS-CoV), Filoviruses (e.g. Ebola virus, Marburg virus), Hepevirus (e.g. Hepatitis E virus), Nairovirus (e.g. Crimean-Congo hemorrhagic fever virus), Orthomyxoviruses (including influenza viruses such as influenza A and influenza B viruses), Paramyxoviruses (e.g. Nipah virus), Pneumoviruses (e.g. Metapneumovirus, Respiratory syncytial virus), Retroviruses (e.g. HIV), and Togaviruses (e.g. Chikungunya virus). The nucleic acid construct of claim 3, wherein the viral envelope protein is selected from the group consisting of a glycoprotein S of SARS-CoV -2, or an antigenic fragment thereof, an Influenza hemagglutinin (HA) protein or an antigenic fragment thereof, and an HIV (gpl20-gp41) protein or an antigenic fragment thereof. The nucleic acid construct of any of claims 1 or 2, wherein the heterologous protein or peptide of interest is a paratope fragment or a scFv fragment of an antibody. 33

6. The nucleic acid construct of any of claims 1 or 2, or 5, wherein the heterologous protein or peptide of interest binds an immune checkpoint molecule, preferably wherein the heterologous protein or peptide of interest binds HLA-G.

7. The nucleic acid construct of any of claims 1 to 6, wherein the heterologous protein or peptide of interest is linked to the collagen-like domain by means of a peptide linker, preferably wherein the peptide linker comprises between 4 and 18 amino acids, still preferably wherein the peptide linker consists of a sequence of glycine and serine residues.

8. The nucleic acid construct of any of claims 1 to 7, wherein the oligomerization domain and the collagen-like domain derive from the same ficolin or collectin.

9. The nucleic acid construct of any of claims 1 to 8, wherein the ficolin or collectin is a mammalian ficolin or collectin, preferably human H-ficolin, human L-ficolin, human M-ficolin, or human MBL.

10. The nucleic acid construct of any of claims 1 to 9, wherein said heterologous peptide of interest is further fused to a cargo protein, preferably wherein the peptide and the cargo protein altogether comprise at least 60 amino acids.

11. A vector that comprises the nucleic acid of any of claims 1 to 10, wherein the sequence that encodes the chimeric protein is operatively associated with regulatory sequences that allow expression of the chimeric protein.

12. A host cell into which the nucleic acid of any of claims 1 to 10 or the vector of claim 11 has been inserted, so that the host cell is capable of expressing the chimeric protein.

13. A chimeric protein that is encoded by the nucleic acid of any of claims 1 to 10, wherein the chimeric protein is preferably in a multimerized form.

14. A pharmaceutical or vaccine composition comprising at least one nucleic acid construct of any of claims 1 to 10, vector of claim 11 or chimeric protein of claim 13, in association with a pharmaceutically acceptable carrier, optionally wherein the composition comprises several different nucleic acid constructs of any of claims 1 to 10, vectors of claim 11 or chimeric proteins of claim 13, each encoding or comprising a distinct heterologous protein or peptide of interest. 15. The nucleic acid construct of any of claims 1 to 10, vector of claim 11 or chimeric protein of claim 13, for use in vaccination or cancer immunotherapy.