Patent Grant
12134639
This application contains a Sequence Listing submitted via EFS-Web. The entire contents of the sequence listing in ASCII text file is entitled “MAI0004US2 Sequence Listing.txt,” created on Jun. 11, 2019, and is 90 kilobytes in size and is incorporated herein by reference in its entirety.
The present invention relates to the field of cytokine-induced and/or cytokine-stimulated biological responses, more particularly to the field of IL-15-induced and/or IL-15-stimulated biological responses, and especially to the field of those biological responses which involve an IL15Rβ/γ signalling pathway.
IL-15 is a cytokine which, like IL-2, has originally been described as a T cell growth factor (1). The two cytokines belong to the four α-helix bundle family, and their membrane receptors share two subunits (the IL-2R/IL-15R β and γ chains) responsible for signal transduction (2). The IL-2Rβ/γ complex is an intermediate affinity receptor for both cytokines. It is mainly expressed by most NK cells, and can be activated in vitro by nanomolar concentrations of IL-2 or IL-15.
High affinity IL-2 and IL-15 receptors, which are expressed for example on activated T cells, and which can be activated with picomolar concentrations of either cytokine, contain in addition their own, private, a chain (IL-2Rα and IL-15Rα) that confer cytokine specificity and enhance the affinity of cytokine binding (3).
Both cytokines play pivotal roles in innate and adaptive immunity. Whereas initial in vitro experiments have shown a large functional overlap (induction of the proliferation and cytotoxicity of activated lymphocytes and NK cells, co-stimulation of B cell proliferation and immunoglobin synthesis, chemoattraction of T cells) (1,4-6), more recent experiments have indicated that the two cytokines exert complementary and even contrasting actions in vivo. Whereas IL-2 or IL-2Rα knock out in mice was associated with autoimmune phenotypes with increased populations of activated T and B cells, IL-15 and IL-15Rα knock out resulted in specific defects in NK, NK-T, intraepithelial lymphocytes and memory CD8 T cells (7,8). Furthermore, IL-2 promotes peripheral tolerance by inducing activation induced cell death (AICD), whereas IL-15 inhibits IL-2 mediated AICD (9), and, unlike IL-2, IL-15 is a survival factor for CD8 memory T cells (10). In line with these observations, it has been suggested that the major role of IL-2 is to limit continuous expansion of activated T cells, whereas IL-15 is critical for the initiation of T cell division and the survival of memory T cells (11). A novel mechanism of IL-15 transpresentation has been described, in which IL-15 and IL-15Rα are coordinately expressed by antigen-presenting cells (monocytes, dendritic cells), and IL-15 bound to IL-15Rα is presented in trans to neighboring NK or CD8 T cells expressing only the IL-15R13/γ receptor (12). IL-15 transpresentation as a co-stimulatory event occurring at the immunological synapse, now appears to be a dominant mechanism for IL-15 action in vivo (13,14). It is suggested to play a major role in tumor immunosurveillance (15).
The IL-15Rα and IL-2Rα subunits form a sub-family of cytokine receptors in that they comprise at their N-terminal extracellular parts so called “sushi” structural domains (one in IL-15Rα, two in IL-2Rα) also found in complement or adhesion molecules (16). In both cases, these sushi domains have been shown to bear most of the structural elements responsible for the cytokine binding.
Whereas IL-2Rα alone is a low affinity receptor for IL-2 (Kd=10 nM), IL-15Rα binds IL-15 with high affinity (Kd=100 pM). Shedding of IL-2Rα by proteolysis is a natural mechanism that participates in the down regulation of lymphocyte activation. IL-2Rα is cleaved by Der p1, a major mite allergen, to inhibit Th1 cells and favor an allergic environment (17), and by tumor-derived metalloproteinases to suppress the proliferation of cancer-encountered T cells (18). The soluble IL-2Rα thus generated is a competitive inhibitor of IL-2 action in vitro. However, it remains a low affinity IL-2 binder, and it is not likely to efficiently participate in down regulation of IL-2 activity in vivo.
It has been recently shown that a soluble form of the human IL-15Rα can also be naturally released from IL-15Rα positive cells by a shedding process involving MMPs (19). In contrast to soluble IL-2Rα, this soluble IL-15Rα receptor was able to bind IL-15 with high affinity, and efficiently blocks proliferation driven through the high affinity IL-15Rα/β/γ signaling complex. This result was consistent with the concept of sIL-15Rα behaving, like its homolog sIL-2Rα, as an antagonist, and with inhibitory effects of mouse sIL-15Rα in vitro or in vivo (20,21).
Here, the present inventors show that a fragment essentially consisting of the sushi domain of IL-15Ralpha (=IL-15Rα) has an opposite action.
Such a fragment is able to enhance the binding, as well as the bioactivity of IL-15 through the IL-15Rbeta/gamma (=IL-15Rβ/γ) intermediate affinity receptor, without affecting those through the high affinity receptor. In addition, the present inventors describe fusion proteins which behave as potent super-agonists of the IL-15Rβ/γ complex. Such fusion proteins comprise an IL-15Rbeta/gamma binding entity, such as IL-15 (or a conservative fragment, agonist, mimetic thereof), fused by covalence e.g., by a flexible linker, to IL-15Rα or to an IL-15Ralpha fragment which has retained the sushi domain of IL-15Ralpha.
To the best of the inventors' knowledge, there is only one prior art which reports a stimulating effect for a compound comprising an IL-15Ralpha-related element, namely the commercially available form of soluble IL-15Ralpha.
It is the Giron-Michel et al. publication, which is entitled “Membrane-bound and soluble IL-15/1L-15Ralpha complexes display differential signalling and functions on human haematopoietic progenitors” (Blood, 1 Oct. 2005, Vol. 106, No. 7, pp. 2302-2310; pre-published online in June 2005).
The Giron-Michel et al. publication discloses that (see FIG. 7 of Giron-Michel et al.):
The soluble IL-15Ralpha that is used by Giron-Michel et al. is the commercially available form of IL-15Ralpha (available from R&D Systems, under reference 147-IR). This soluble IL-15Ralpha is a modified form of soluble IL-15Ralpha, which lacks exon 3. The form of soluble IL-15Ralpha that is used by Giron-Michel et al. hence comprises the exon 2 encoded part of IL-15Ralpha, directly linked to the exon 4 encoded part of IL-15Ralpha, without comprising any exon 3 encoded part of IL-15Ralpha. The form of soluble IL-15Ralpha that is used by Giron-Michel et al. does therefore not correspond to a fragment of IL-15Ralpha, but to a modified form thereof.
The form of soluble IL-15Ralpha that is used by Giron-Michel et al. further comprises a Fc fragment (human IgG), linked thereto by covalence. A Fc fragment does not bind to IL-15Rbeta/gamma. The Giron-Michel et al. publication does therefore not disclose any compound wherein the soluble IL-15Ralpha form would be linked by covalence to an IL-15Rbeta/gamma binding entity.
The Giron-Michel et al. publication further discloses an anti-apoptotic effect, but does not disclose any effect on the proliferation and/or activation of IL-15Rbeta/gamma-positive cells. It can further be noted that the disclosed anti-apoptotic effect assay does not comprise any control samples which would contain (i) the soluble IL-15Ralpha-Fc fragment in the absence of rIL-15 or (ii) a soluble IL-15Ralpha without any Fc fragment. The disclosed anti-apoptotic effect therefore cannot be directly attributed to the IL-15Ralpha part of the compound that is used.
The Giron-Michel et al. publication does not further contain any hint to the sushi domain of IL-15Ralpha (nor to the hinge region that is absent from the soluble IL-15Ralpha form that is being used in this prior art), nor does it contain a hint to the IL-15beta/gamma signalling pathway.
The present invention describes for the first time the structural units which are necessary to, and especially advantageous for, the induction and/or stimulation of an IL-15 biological action, the specific triggering of the IL-15beta/gamma signalling pathways, and the induction and/or stimulation of the proliferation of NK and/or T cells. The present invention thereby represents a technical contribution over the prior art, which enables previously-unattained biological and medical applications.
It is therefore believed that, when analysed on an a priori basis, the Giron-Michel et al. publication does not teach the claimed invention to the person of ordinary skill in the art, and does not guide the skilled person to the claimed invention.
The present invention relates to the IL-15Rbeta/gamma signalling pathway, and to the induction and/or stimulation of the activation and/or proliferation of IL-15Rbeta/gamma-positive cells and/or prevention of apoptosis, such as NK and/or T cells.
The present invention demonstrates that the extracellular region of IL-15Ralpha can act as an agonist of IL-15 biological action, via the IL-15Rbeta/gamma signalling pathway. It notably demonstrates that it can stimulate and/or induce the proliferation and/or activation of IL-15Rbeta/gamma-positive cells and/or prevention of apoptosis, such as NK and/or T cells.
The present invention demonstrates that the minimal structural unit contained in this IL-15Ralpha extracellular region, that is required to exert such an agonist action, is the sushi domain of IL-15Ralpha extracellular region.
The present invention further demonstrates that the hinge and tail region of this IL-15Ralpha extracellular region significantly increase the efficiency of this agonist action.
The present invention further provides compounds which show a 30 to 150 fold increase in bioactivity, compared to wild-type IL-15, and which are even more potent than the simple association of IL-15 and soluble IL-15Ralpha sushi domain.
The present invention relates to the objects described in the detailed description section, and more particularly to those defined in the appended claims.
SPR sensorgrams of the binding (association and dissociation phases) of increasing concentrations of rIL-15 (1, 2.5, 5, 10, 25, 50, 100 nM) to immobilized
The present invention relates to IL-15Ralpha, and to IL-15Ralpha fragments which comprise at least one IL-15Ralpha sushi domain.
The present invention relates to products, which can be intended for stimulating the IL-15Rbeta/gamma signalling pathway, to thereby induce and/or stimulate the activation and/or proliferation and/or prevention of apoptosis of IL-15Rbeta/gamma-positive cells, such as NK and/or T cells.
The present invention relates to isolated sushi-containing polypeptides, which contain the sushi domain that is comprised in the extracellular region of an IL-15Ralpha, i.e., it relates to the isolated fragment consisting of IL-15Ralpha extracellular region, and to sub-fragments thereof that have retained the sushi domain.
The sushi-containing polypeptides of the invention can be either linked by covalence, or not linked by covalence to at least one IL-15Rbeta/gamma binding entity.
The invention more particularly relates to a covalently-linked compound which comprises at least of such a sushi-containing polypeptide, directly or indirectly linked by covalence to at least one IL-15Rbeta/gamma binding entity. Such a compound can have a 30 to 150 fold increase in bioactivity, compared to wild-type IL-15, and be more potent than the free association of IL-15 and soluble IL-15Ralpha sushi domain.
IL-15Rbeta/Gamma Binding Entity:
In addition to said at least one sushi-containing polypeptide, said covalently linked compound of the invention comprises at least one IL-15Rbeta/gamma binding entity.
Said IL-15Rbeta/gamma binding entity preferably is an IL-15, or an IL-15 fragment, mimetic, or agonist, wherein said IL-15 fragment, mimetic, or agonist has an affinity for binding to IL-15Rbeta/gamma that is not significantly lower than the one of native IL-15.
Said IL-15 can be any IL-15, e.g. a human IL-15, or a non-human mammalian IL-15, or a non mammalian IL-15.
Illustrative non-human mammalian IL-15 are monkey IL-15, or a murine IL-15 (e.g., mouse IL-15 of accession number NM_008357; rat IL-15 of accession number NM_013129), or a rabbit IL-15 (e.g., accession number DQ157152), a sheep IL-15 (e.g., accession number NM_001009734), or a pig IL-15 (e.g., accession number NM_211390). Illustrative non mammalian IL-15 is chicken (e.g., accession number NM_204571).
More preferably, said IL-15 is a human IL-15. Most preferably, the amino acid sequence of said human IL-15 is the sequence of SEQ ID NO: 48.
IL-15 does not bind IL-2Ralpha. In view of the biological and medical applications contemplated by the present invention, said IL-15 fragment, mimetic, or agonist preferably does not bind IL-2Ralpha.
The terms “agonist” and “mimetic” are herein given their ordinary meaning in the field.
A compound is termed IL-15 agonist when it induces a biological response that is of a similar or higher level than the one induced by native IL-15. Preferred agonists are those which induce an even higher level of biological response (super-agonist).
An IL-15 agonist typically has an affinity for binding to IL-15Ralpha and/or to IL-15Rbeta/gamma that is at least not significantly different from the one of native IL-15, and that is preferably significantly higher than the one of native IL-15.
A mimetic (or mimetope) of IL-15 refers to any compound that is able to mimic the biological actions of IL-15.
In the present invention, preferred IL-15 mimetics or agonists are those which are able to mimic the biological action of IL-15 through the IL-15Rbeta/gamma signalling pathway. Such a preferred IL-15 mimetic thus has the capacity of binding to the IL-15beta/gamma complex, and to thereby induce and/or stimulate the transduction of a biological signal through said IL-15Rbeta/gamma complex. Preferred IL-15 mimetics or agonists of the invention have an affinity for binding to IL-15Rbeta/gamma that is at least not significantly different from the one of native IL-15, and that is preferably significantly higher than the one of native IL-15. Appropriate agonists or mimetics have been described in e.g., the international PCT application PCT/EP2005/002367, filed on 10 Feb. 2005, in the name of INSERM.
Sushi-Containing Polypeptide:
The amino acid sequence of said at least one sushi-containing polypeptide:
An alternative definition of the definition is that it begins at the first cysteine residue (C1) after the signal peptide, and ends at the fourth cysteine residue (C4) after the signal peptide.
Said variant amino acid sequence may comprise a conservative variant sequence of IL-15Ralpha sushi domain.
Such a conservative variant sequence of IL-15Ralpha sushi domain derives from the sequence of a parent sushi domain, by at least one deletion and/or at least one substitution and/or at least one addition of amino acid, but has retained the capacity of at least one of the following features:
Preferably, said conservative variants have retained the feature described in iii. above.
Appropriate cell lines to assay the above mentioned features are IL-15Rbeta/gamma-positive IL-15Ralpha-negative cells. Illustrative of such cell lines is the cell line 32D, which can be transfected with a beta and a gamma chain (e.g., a human beta and a human gamma chain).
Alternatively, naïve or resting NK and/or T cells can be purified from a biological sample, such as a blood sample.
Preferably, said variant amino acid sequence is at least 85% identical to the amino acid sequence of such an IL-15Ralpha extracellular region, or of such a fragment of IL-15Ralpha extracellular region, over the entire length of this sequence of IL-15Ralpha extracellular region or of fragment of IL-15Ralpha extracellular region.
More preferably, this percentage of sequence identity is of at least 90%, still more preferably of at least 92%, most preferably of at least 95%, e.g., at least 96%, at least 97%, at least 98%, at least 99% or 100%.
Such variant amino acid sequences notably encompass the IL-15Ralpha polymorphisms which naturally occur within an animal species, as well as conservative variants which can be produced by the person of ordinary skill in the art.
IL-15Ralpha:
Exon 1 of IL-15Ralpha codes for the signal peptide of IL-15Ralpha.
Exon 2 of IL-15Ralpha codes for the sushi domain of IL-15Ralpha.
A 5′ terminal part of exon 3 codes for region known as the hinge region of IL-15Ralpha.
The remaining part of exon 3, as well as the other extracellular exons (i.e., exon 4, exon 5, and a 5′ part of exon 6 for human IL-15ralpha, as well as for most species) code for a region rich in glycosylation sites, also known as the tail region of IL-15Ralpha.
The remaining IL-15Ralpha exons (i.e., a 3′ part of exon 6, as well as exon 7 for human IL-15ralpha, as well as for most species) code for the transmembranar and intracytoplasmic regions of IL-15Ralpha.
Advantageously, in view of the medical applications of the present invention, said IL-15Ralpha preferably is a human IL-15Ralpha.
The amino acid sequence of said human IL-15Ralpha most preferably is the sequence of human IL-15Ralpha sequence of SEQ ID NO: 3 (267 amino acids). The extracellular region of the human IL-15Ralpha of SEQ ID NO:3 has the amino acid sequence of SEQ ID NO:40 (1 . . . 209 of SEQ ID NO:3). The signal peptide deleted form of SEQ ID NO:40 is listed as SEQ ID NO:44 (31 . . . 209 of SEQ ID NO:3).
Some human alleles of IL-15Ralpha may have a Thr amino acid (amino acid t, coded by act, acc, aca, or acg), instead of a Asn amino acid (amino acid n, encoded by aat or aac) at position 182 of SEQ ID NO: 3. Such variants are naturally-occurring, and are functional.
In the present application, such allelic naturally-occurring variants of human IL-15Ralpha are meant as equivalent to the reference human IL-15Ralpha sequences of SEQ ID NO: 3 (amino acid sequence), and SEQ ID NO: 1 or NO: 2 (cDNA and CDS sequences), and to the reference human IL-15Ralpha sequences that directly derives thereform, i.e., the extracellular region sequences of SEQ ID NO: 40 or NO:44 (amino acid sequences), and SEQ ID NO: 39 and NO:43 (CDS sequences).
The positions of the seven exons of the human IL-15Ralpha of SEQ ID NO:3 are as described in the following table 1.
In this respect, please note that the positions of exon 1 is 1 . . . 170, and that those of exon 2 is 171 . . . 365, as described in table 1 below, and that they are not 1 . . . 171 and 172 . . . 365, respectively, as declared in the sequence available under accession number U31628.
The positions of the different regions and parts of the human IL-15Ralpha of SEQ ID NO: 3 is shown in table 2 below.
In the present application, the double-point symbol (<< . . . >>) placed between a first number and a second number describes an isolated sequence which is identical to the sequence extending from position “first number” to position “second number”.
In the present application, when sequences are defined by “start” and “stop” positions, these start and stop positions are meant as included within the described sequence.
For some biological applications, such as preliminary testing, research, development, compound or cell screening, pre-clinical and clinical studies (including tests relating to pharmacological, toxicological, pharmacokinetic, or biological qualities, as well as “risk-benefit assessment” and safety related tests), non-human mammalian IL-15Ralpha can nevertheless be used.
Preferred non-human mammalian IL-15Ralpha notably comprise monkey IL-15Ralpha (e.g., a chimpanzee IL-15Ralpha), or a murine IL-15Ralpha (e.g., mouse IL-15Ralpha, rat IL-15Ralpha), or a rabbit IL-15Ralpha, or a pig IL-15Ralpha.
Illustrative IL-15Ralpha amino acid sequences of such non-human mammalian IL-15Ralpha are those encoded by the nucleic acid sequences available as accession number NM_008358 (Mus musculus IL-15Ralpha: nucleic acid sequence of SEQ ID NO: 72, amino sequence of SEQ ID NO:73), as accession number XM_521684 (Pan troglodytes IL-15Ralpha: nucleic acid sequence of SEQ ID NO: 78, amino sequence of SEQ ID NO:79), or as accession number XM_577598 (Rattus norvegicus: IL-15Ralpha: nucleic acid sequence of SEQ ID NO: 84, amino sequence of SEQ ID NO:85). See
Extracellular Region of IL-15Ralpha:
The extracellular region of IL-15Ralpha is usually defined as the region of an IL-15Ralpha sequence that extends from its first N-terminal amino acid, to the last amino acid of the tail region (or region rich in glycosylation sites). As described in more details below, the tail region of an IL-15Ralpha sequence can be determined by the skilled person, e.g., through the help of software.
Said extracellular region of IL-15Ralpha is a human IL-15Ralpha extracellular region, or a non-human mammalian IL-15Ralpha extracellular region.
Among the amino acid sequences of human extracellular IL-15Ralpha regions, the amino acid sequence of the extracellular IL-15Ralpha region of SEQ ID NO: 40 is preferred.
The amino acid sequence of the human IL-15Ralpha extracellular region of SEQ ID NO: 40, is encoded by exons 1-5, and a small 5′ part of exon 6 of human IL-15Ralpha.
Exon 1 of human IL-15Ralpha (SEQ ID NO: 8) codes for IL-15Ralpha signal peptide (nucleic acid sequence of SEQ ID NO: 4; amino acid sequence of SEQ ID NO: 5).
Exon 2 (SEQ ID NO: 9) comprises the sequence coding for the sushi domain of human IL-15Ralpha.
The last 3′ codon of exon 2 codes for the first amino acid of the hinge region. A 5′ part of exon 3 (exon 3 of SEQ ID NO: 10) codes for the hinge region of human IL-15Ralpha.
The remaining 3′ part of exon 3, plus exon 4 (SEQ ID NO: 11), exon 5 (SEQ ID NO: 12), and a 5′ part of exon 6 (699 . . . 709 of SEQ ID NO:1) code for a region rich in glycosylation sites (also known as tail region).
The sequence of SEQ ID NO: 44 is the signal peptide deleted form of the IL-15Ralpha extracellular region of SEQ ID NO: 40. In the present invention signal peptides may be used, but are optional. Such a signal peptide can be an IL-15Ralpha signal peptide, or the signal peptide of another protein. Hence, a signal peptide deleted form of an IL-15Ralpha extracellular region (such as SEQ ID NO: 44) is directly equivalent to the complete IL15Ralpha extracellular sequence (such as SEQ ID NO: 40).
Illustrative of non-human mammalian IL-15Ralpha extracellular regions, are those which have the sequence of SEQ ID NO: 74 (1 . . . 204 of Mus musculus IL-15Ralpha), of SEQ ID NO: 80 (1 . . . 286 of Pan troglodytes IL-15Ralpha), of SEQ ID NO: 86 (1 . . . 182 of Rattus norvegicus IL-15Ralpha).
Sushi Domain:
The extracellular region of IL-15Ralpha or fragment thereof that defines said at least one sushi-containing polypeptide contains an IL-15Ralpha sushi domain.
The extracellular region of IL-15Ralpha contains a domain, which is known as the sushi domain (Wei et al. 2001, J. Immunol. 167:277-282).
The sushi domain of IL-15Ralpha has a beta sheet conformation.
It is coded by exon 2 of IL-15Ralpha. It begins at the first exon 2 encoded cysteine residue (C1), and ends at the fourth exon 2 encoded cysteine residue (C4).
When considering the IL-15Ralpha protein sequence in the standard N-terminal to C-terminal orientation, the sushi domain of IL-15Ralpha can be defined as beginning at the first cysteine residue (C1) after the signal peptide, and ending at the fourth cysteine residue (C4) after the signal peptide.
Residues C1 and C4 are both included in the sushi sequence.
Hence, when the identification of the sushi domain is made on a IL-15Ralpha sequence which is deleted from its signal peptide sequence (such as e.g., the sequence of SEQ ID NO: 44), the sushi domain is then defined as beginning at the first cysteine residue (starting from the N-terminal end of the protein), and ending at the fourth cysteine residue of this IL-15Ralpha sequence.
The IL-15Ralpha sushi domain can also be determined by analysis of the aminoacid sequence of IL-15Ralpha with appropriate software such as:
The amino acid sequence of said sushi domain can be the amino acid sequence of a human IL-15Ralpha sushi domain, or of a non-human mammalian sushi domain.
Among the amino acid sequences of human IL-15Ralpha sushi domains, the amino acid sequence of the human IL-15Ralpha sushi domain of SEQ ID NO: 14 is preferred.
For example, the amino acid sequence of said fragment of extracellular region of human IL-15Ralpha can be the sequence of SEQ ID NO: 16 (it+human IL-15Ralpha sushi), or NO: 18 (t+human IL-15Ralpha sushi).
Illustrative of non-human mammalian IL-15Ralpha sushi domains, are the amino acid sequences of SEQ ID NO:75 (36 . . . -96 of Mus musculus IL-15Ralpha), of SEQ ID NO: 81 (13 . . . 73 of Pan troglodytes IL-15Ralpha), or of SEQ ID NO:87 (24 . . . 84 of Rattus norvegicus IL-15Ralpha).
Signal Peptide:
A signal peptide is a short (15-60 amino acids long) peptide chain that directs the post translational transport of a protein. Some signal peptides are cleaved from the protein by signal peptidase after the proteins are transported. Signal peptides may also be called targeting signals or signal sequences. The amino acid sequences of signal peptides direct proteins which are synthesized in the cytosol to certain organelles such as the nucleus, mitochondrial matrix, endoplasmic reticulum, chloroplast, and peroxisome.
The signal peptide of IL-15Ralpha is a N-terminal sequence of about 29-33 amino acids, e.g., 30-32 amino acids. It begins at the first N-terminal amino acid residue of IL-15Ralpha. It is determined by analysis of the N-terminal amino-acid sequence of IL-15Ralpha with appropriate software such as:
The signal peptide of Mus musculus IL-15Ralpha is a N-terminal amino acid sequence of 32 amino acids (see accession number NP_032384; sig_peptide 1 . . . 32).
The signal peptide of human IL-15Ralpha, as shown in SEQ ID NO: 5, is a N-terminal amino acid sequence of 30 amino acids, which contains one cysteine residue.
Fragment of Exon 2 Encoded Part:
Exon 2 of IL-15Ralpha contains the sushi domain, i.e., the minimal structural unit that is required by the present invention.
Said fragment of IL-15Ralpha extracellular region can comprise (or can essentially consist of):
According to the present invention, said fragment of IL-15Ralpha extracellular region has to comprise at least one IL-15Ralpha domain. Hence, a fragment of an exon 2 encoded part can be any fragment thereof, provided that it still comprises the sushi domain (from residue C1 to residue C4).
For example, the exon 2 encoded part of the human extracellular region of SEQ ID NO:40 is the sequence extending from position 31 to position 94 (i.e., SEQ ID NO:24), i.e., it is:
Fragments of this exon 2 encoded part are: t+sushi; it+sushi; t+sushi+i.
For example, said exon 2 encoded sequence can be:
Variants of such IL-15Ralpha extracellular region fragments are encompassed within the scope of the present invention.
Such variants notably include those which have conservative amino deletion and/or substitution and/or addition in their sequence.
A conservative variant sequence of an IL-15Ralpha extracellular region fragment derive from the sequence of a parent IL-15Ralpha extracellular region fragment, by at least one deletion and/or at least one substitution and/or at least one addition of amino acid, and has retained the capacity of at least one of the following features:
Preferably, said conservative variants have retained the feature described in iii. above.
Conservative variants notably comprise those which have an amino acid sequence that has an identity of at least 85% with the parent sequence, over the entire length of this parent sequence. Preferably, said percentage of identity is of at least 90%, still more preferably of at least 92%, most preferably of at least 95%, e.g., at least 96%, at least 97%, at least 98%, at least 99% or 100%.
For example, starting from the above-mentioned exon 2 encoded part of SEQ ID NO: 40, it will be apparent to the skilled person that i+sushi, i+sushi+t, i+sushi+i, it+sushi+t are conservative variants, which are technically equivalent to the parent fragment.
Fragment of Exon 2-3 Encoded Part:
According to a very advantageous embodiment of the present invention, said fragment of IL-15Ralpha extracellular region may further comprise at least one amino acid from the sequence that is encoded by exon 3 of said IL-15Ralpha.
Said fragment of IL-15Ralpha extracellular region may thus comprise, or consist of:
Exon 3 of the human IL-15Ralpha of SEQ ID NO: 3 (i.e., of the human extracellular region of SEQ ID NO: 40) is the nucleic acid sequence of SEQ ID NO: 10. The exon 3 encoded part of SEQ ID NO: 3 is the sequence of SEQ ID NO: 93, i.e., the 95 . . . 127 sequence part of SEQ ID NO: 3 or of SEQ ID NO: 40 (i.e., the amino acid sequence which extends from position 95 to position 127 of the human IL-15Ralpha sequence of SEQ ID NO: 3 or NO: 40, positions 95 and 127 being both included).
For example, said exon 3 encoded sequence can be:
A fragment of an exon 3 encoded part can be a fragment of only one amino acid, preferably of at least two amino acids, more preferably of at least three amino acids, still more preferably of at least four amino acids, most preferably of at least five amino acids.
The inventors demonstrate that an exon 3 encoded part of IL-15Ralpha, or a fragment thereof, advantageously increases the affinity and the efficiency of the resulting compound, in terms of IL-15Rbeta/gamma signal transduction, and of IL-15Rbeta/gamma-positive cell proliferation and activation.
When the sushi-containing polypeptide is intended for the production of a fusion protein, the skilled person may prefer limiting the number of exon 3 amino acid to the optimum number, i.e., to the number of amino acids which represents a fair balance between the increase in affinity and efficiency on the one hand, and the increase in molecular size and conformation difficulties on the other hand.
Hence, the skilled person may find advantageous to limit the number of exon 3 encoded amino acids that are added to said IL-15Ralpha sushi domain to a number of 30, preferably of 25, more preferably of 20, still more preferably of 18, most preferably of 17, e.g., of 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6.
Most preferred numbers of exon 3 encoded amino acids therefore are those of the intervals that result from the combination of each of the above-mentioned inferior limits to each of the above-mentioned superior limits.
Illustrative of preferred fragments of exon 3 encoded part are all fragments which derive from the exon 3 encoded part of the human IL-15Ralpha of SEQ ID NO:3 (or of SEQ ID NO:40), i.e., the part extending from position 95 to position 127, positions 95 and 127 being both included (in others words: sequence 95 . . . 127 of SEQ ID NO:3 or NO:40).
A preferred compound of the invention hence comprises at least one sushi-containing polypeptide which, in addition to said sushi domain, comprise at least one amino acid from the sequence extending from position 95 to position 127 of SEQ ID NO:3 (positions 95 and 127 being both included). It most preferably comprises:
Hence, said fragment of IL-15Ralpha extracellular region advantageously comprises the part of IL-15Ralpha extracellular region, which is encoded by exon 2 of said IL-15Ralpha, or a conservative variant thereof as above-defined, and further comprises at least one amino acid from the sequence encoded by exon 3 of said IL-15Ralpha.
More particularly, said fragment of IL-15Ralpha extracellular region can comprise (or can essentially consist of):
Still more particularly, said fragment of IL-15Ralpha extracellular region can comprise (or can essentially consist of):
The above-given definition of conservative variants applies mutatis mutandis to a conservative variant of an exon 2-3 encoded part, i.e., it is a sequence which derives from a parent exon 2-3 encoded sequence, by at least one deletion and/or at least one substitution and/or at least one addition of amino acid, and has retained the capacity of at least one of the following features:
Preferably, said conservative variants have retained the feature described in iii. above.
Conservative variants notably comprise those which have an amino acid sequence that has an identity of at least 85% with the parent sequence, over the entire length of this parent sequence. Preferably, said percentage of identity is of at least 90%, still more preferably of at least 92%, most preferably of at least 95%, e.g., at least 96%, at least 97%, at least 98%, at least 99% or 100%.
Hinge Region (Located after the Sushi Domain, Encoded by a 3′ Part of Exon 2 and a 5′ Part of Exon 3, or by a 5′ Part of Exon 3):
The inventors demonstrate that the hinge region of IL-15Ralpha is more particularly involved in this increase in signal transduction efficiency, and in this increase in IL-15Rbeta/gamma-positive cell proliferation and activation.
Hence, according to a very advantageous embodiment of the present invention, said fragment of IL-15Ralpha extracellular region can, in addition to said IL-15Ralpha sushi domain, further comprise an IL-15Ralpha hinge region, or a fragment of IL-15Ralpha hinge region.
An IL-15Ralpha hinge region is defined as the amino acid sequence that begins at the first amino residue after the sushi domain (when considering the IL-15Ralpha sequence in the standard N-terminal to C-terminal orientation), and that ends at the last amino acid residue before the first potential site of glycosylation.
The positions of potential glycosylation sites are determined using the software NetOGlyc (http://www.cbs.dtu.dk/services/NetOGlyc-3.1/) for the identification of potential O-glycosylation sites, and the software NetNGlyc (http://www.cbs.dtu.dk/services/NetNGlyc/) for the identification of potential N-glycosylation sites.
In a human IL-15Ralpha, the amino acid sequence of the hinge region consists of the fourteen amino acids which are located after the sushi domain of this IL-15Ralpha, in a C-terminal position relative to said sushi domain, i.e., said IL-15Ralpha hinge region begins at the first amino acid after said (C4) cysteine residue, and ends at the fourteenth amino acid (counting in the standard “from N-terminal to C-terminal” orientation).
In the human IL-15Ralpha of SEQ ID NO: 3 (the extracellular region of which being the sequence of SEQ ID NO:40), the amino acid sequence of said human IL-15Ralpha hinge region is the sequence of SEQ ID NO: 20. It contains one amino acid encoded by exon 2 (amino acid i), and thirteen amino acids encoded by exon 3.
In the Mus musculus IL-15Ralpha of SEQ ID NO:73, the hinge region has the sequence of SEQ ID NO:76.
In the Pan troglodytes IL-15Ralpha of SEQ ID NO:79, the hinge region has the sequence of SEQ ID NO:82.
In the Rattus norvegicus IL-15Ralpha of SEQ ID NO:85, the hinge region has the sequence of SEQ ID NO:88.
Said at least one sushi-containing polypeptide may thus comprise the sushi domain of SEQ ID NO: 75 and the hinge region of SEQ ID NO: 76 (Mus musculus), the sushi domain of SEQ ID NO: 81 and the hinge region of SEQ ID NO: 82 (Pan troglodytes), or the sushi domain of SEQ ID NO: 87 and the hinge region of SEQ ID NO: 88 (Rattus norvegicus).
Advantageously, said at least one sushi-containing polypeptide preferably comprises the human sushi domain of SEQ ID NO: 14, and the human hinge region of SEQ ID NO: 20 (for example, SEQ ID NO: 16 or NO: 18, followed by the hinge region of SEQ ID NO: 20). Preferably, said at least one sushi-containing polypeptide comprises, or is, a polypeptide of SEQ ID NO: 30 (it+sushi+hinge), optionally deleted from its N-terminal i and/or t.
Said fragment of IL-15Ralpha extracellular region can alternatively comprise, in addition to the sushi domain, a fragment of hinge region. By fragment of a hinge region, it is herein meant any fragment thereof, down to only one amino acid of said hinge region. Preferably, a fragment of hinge region comprises at least two amino acids, more preferably at least three amino acids.
A fragment of IL-15Ralpha hinge region can therefore be a fragment of 1 (e.g., amino acid i), 2 (e.g., amino acids ir), 3 (e.g., amino acids ird), 4 (e.g., amino acids irdp), 5 (e.g., amino acids irdpa), 6 (e.g., amino acids irdpa), 7 (e.g., amino acids irdpal), 8 (e.g., amino acids irdpalv), 9 (e.g., amino acids irdpalvh), 10, 11, 12, 13 or 14 amino acids.
Advantageously, said at least one sushi-containing polypeptide preferably comprises the human sushi domain of SEQ ID NO: 14, and a fragment of the hinge region of SEQ ID NO: 20.
The amino acid sequence of said fragment of IL-15Ralpha hinge region comprises, or is, i, or ir, or ird.
The sushi-containing polypeptide of SEQ ID NO: 22, 24, and 26 comprises the sushi domain of SEQ ID NO: 14, and the “i” fragment of the hinge region of SEQ ID NO: 20.
The sushi-containing polypeptide of SEQ ID NO: 28 comprises the sushi domain of SEQ ID NO: 14, and the “ird” fragment of the hinge region of SEQ ID NO: 20.
Said amino acid sequence of a fragment of human IL-15Ralpha extracellular region may more particularly comprise, in addition to said sushi domain and hinge region amino acid sequences:
The region rich in glycosylation sites of IL-15Ralpha is a region which comprises several potential glycosylation sites. It is sometimes referred to as the “tail” region of IL-15Ralpha. It starts at the first amino acid residue after the hinge region (when considering the sequence in the standard “N-terminal to C-terminal” orientation), and ends at the last amino acid residue before the transmembranar region of IL-15Ralpha. It comprises several potential glycosylation sites.
The transmembranar domain is determined by the analysis of the amino-acid sequence of IL-15Ralpha with appropriate software such as: TopPred (http://biowed.pasteur.fr/seganal/interfaces/topred.html), TMpred (http://www.ch.embnet.org/software/TMPRED form.html).
The tail region of human IL-15Ralpha comprises several O-glycosylation sites, and one N-glycosylation site.
The human IL-15Ralpha tail region of SEQ ID NO: 32 is encoded by a 3′ part of exon 3, and by exon 4, exon 5, and a 5′ part of exon 6 of said human IL-15Ralpha.
Illustrative of the tail of non-human mammalian IL-15Ralpha extracellular region, are the amino acid sequences of SEQ ID NO: 77 (Mus musculus), of SEQ ID NO: 83 (Pan troglodytes), or of SEQ ID NO: 89 (Rattus norvegicus).
By fragment, or sub-fragment, of a region rich in glycosylation sites (or fragment or sub-fragment of tail region), it is herein meant any fragment, or sub-fragment, of said region, down to only one amino acid of said region. Preferably, said fragment, or sub-fragment, comprises at least two amino acids, more preferably at least three amino acids.
Said amino acid sequence of a fragment of IL-15Ralpha extracellular region may hence comprise:
A preferred amino acid sequence for the exon 3 encoded part of the region rich in glycosylation sites of human IL-15Ralpha is the amino acid sequence of SEQ ID NO: 34. A sushi-containing polypeptide of the invention advantageously is the polypeptide of SEQ ID NO: 36 (optionally deleted from the first C-terminal i and/or t amino acids).
As previously indicated, any fragment of exon 3 encoded part that the skilled person find appropriate can be used, e.g., any fragment of at least one amino acid, preferably of at least two amino acids, more preferably of at least three amino acids.
Extracellular Exons, Other than Exons 1, 2, 3:
The extracellular IL-15Ralpha exons, other than exons 1, 2, 3, code for a C-terminal fragment of the tail region.
Such parts, or fragments thereof, may further enhance the efficiency of the compounds of the invention.
Said amino acid sequence of a fragment of IL-15Ralpha extracellular region may hence further comprise a part of extracellular IL-15Ralpha which is encoded by exon 4, and/or exon 5 and/or exon 6, or any fragment of such a part.
Exon positions of the human IL-15Ralpha of SEQ ID NO: 3 are herein shown in the above table 1.
Illustrative of amino acid sequences of such sushi-containing polypeptides are the sequences of SEQ ID NO: 38, or the signal peptide deleted SEQ NO: 42, or the signal peptide deleted SEQ NO: 44.
Illustrative sushi-containing polypeptides are those which contain the sushi domain, the hinge region and the complete tail of IL-15Ralpha (e.g., the human IL-15Ralpha tail of SEQ ID NO: 32; the Pan troglodytes IL-15Ralpha tail of SEQ ID NO: 83; the Mus musculus IL-15Ralpha tail of SEQ ID NO: 77; the Rattus norvegicus IL-15Ralpha tail of SEQ ID NO: 89), and optionally a signal peptide.
IL-15 Biological Action:
At the organism or cellular level, a product of the invention is characterized in that it induces and/or stimulates IL-15 biological action. It stimulates those biological actions which are exerted by, inducible with, or stimulated by, IL-15, IL-15 mimetics, and/or IL-15 agonists.
The products of the invention (i.e., the sushi-containing polypeptides described herein, in isolated form, and more particularly the compounds of the invention) may thus be regarded as an agonist of IL-15 biological action.
One special and advantageous characterizing feature of a product of the invention is that it is capable of inducing and/or stimulating the IL-15Rbeta/gamma signaling pathway, and more particularly of stimulating IL15 biological action through the IL-15Rbeta/gamma signaling pathway.
At the molecular level, a product of the invention is thus more particularly characterized in that it increases the efficiency of the IL-15Rbeta/gamma signaling pathway. It sensitizes those cells which express the IL-15Rbeta/gamma complex to the action of IL-15. Still more particularly, it sensitizes those cells which express the IL-15Rbeta/gamma complex, but do not express IL-15Ralpha (IL-15Rβ/γ+ IL-15Rα− cells), to the action of IL-15.
Some of the products of the invention are IL-15Rbeta/gamma specific, in the sense that they do not enhance the efficiency of the IL-15Ralpha/beta/gamma signaling pathway. It is notably the case of the ILR fusion protein of the invention (amino acid sequence of SEQ ID NO: 62; and nucleic acid sequence of SEQ ID NO: 61).
Some other products of the invention are capable of enhancing the efficiency of both the IL-15Rbeta/gamma and the IL-15Ralpha/beta/gamma signaling pathways. It is notably the case of the RLI fusion protein of the invention (amino acid sequence of SEQ ID NO: 60; and nucleic acid sequence of SEQ ID NO: 59).
The invention also shows that the sushi domain of IL-15Rα is crucial for transpresentation. It thereby gives access to particularly useful and particularly needed medical applications in the field of cancer treatment and/or palliation and/or prevention, by vaccine administration, such as e.g. administration of a composition which comprises at least one compound containing at least one IL-15Ralpha sushi domain.
IL-15 is a cytokine which stimulates the proliferation and/or survival of lymphocytes (such as T cells, CD8+ T cells, NK cells, dendritic cells) and/or their activity against tumour cells.
IL-15 is involved in the cross-talk between accessory cells and lympoid cells.
It is essential in peripheral tissues for the development of NK cells, NKT cells, and CD8+ memory T cells.
It is the most powerful physiological factor able to induce the differentiation of CD34+ hematopoietic cells.
Said IL-15 biological action is a biological action exerted by, inducible by, or stimulated by IL-15, and/or IL-15 mimetics and/or IL-15 agonists.
The skilled person can choose any IL-15 biological response that he/she finds appropriate or convenient to assess or monitor.
Preferably, said IL-15 biological action is a biological action exerted by, inducible by, or stimulated by IL-15 and/or IL-15 mimetics and/or IL-15 agonists, on IL-15Rbeta/gamma+ IL-15Ralpha− cells.
A typical IL-15 biological response is the proliferation of, and/or the activation of, IL-15 sensitive cells.
Examples of IL-15 sensitive cells are T cells, CD8+ T cells, NK cells, dendritic cells, whose proliferation are induced and/or stimulated upon addition of IL-15 and/or IL-15 mimetics and/or IL-15 agonists, and/or whose activation is induced and/or stimulated upon addition of IL-15 and/or IL-15 mimetics and/or IL-15 agonists (e.g., induction of an anti-tumour activity).
Such cells can e.g., be collected from a mammalian organism.
Other examples of IL-15 sensitive cells comprise known cells lines, such as the CTL-L2 mouse cytotoxic T lymphoma cell line (ATCC accession number TIB-214), or TF1-beta cells.
TF1-beta cells are available by transfection of TF-1 cells with beta chains.
TF-1 cells are available from the American Type Culture Collection ATCC; P.O. Box 1549; Manassas, VA 20108; U.S.A.; cf. http://www.Idcpromochem.com/atcc/ under ATCC accession number CRL-2003. IL-2R beta recombinant retroviruses can then be used to infect TF-1 cells to generate TF-1β after selection in medium containing G418.
Preferably, said IL-15 sensitive cells are IL-15Rbeta/gamma+ IL-15Ralpha− cells. Examples of IL-15Rbeta/gamma+ IL-15Ralpha− cells include the human Mo-7 cell line, or resting NK and/or T cells.
Resting NK and/or T cells are available to the skilled. They can, e.g., be obtained by purification of a cell sample, such as a blood sample.
Resting NK and T cells can be isolated from the blood of healthy adult donors as follow: whole blood is centrifuged at high speed to obtain a buffy coat. This buffy coat is centrifuged on a density gradient (Histopaque, Sigma) to obtain peripheral blood lymphocytes. Resting NK cells are then isolated from peripheral blood lymphocytes using a NK cell negative isolation kit (Dynal, Biotech ASA, Oslo, Norway). Alternatively, resting T cells are isolated from peripheral blood lymphocytes using a T cell negative isolation kit (Dynal, Biotech ASA, Oslo, Norway).
Other examples of IL-15Rbeta/gamma+ IL-15Ralpha− cells include IL-15Ralpha− cells, which are transformed or transfected by IL-15Rbeta/gamma, preferably by a human IL-15Rbeta/gamma.
For example, the murine 32D cell line (ATCC CRL-11346) can be transfected by beta and gamma chains, preferably with human and gamma chains.
Beta chains (i.e., IL-15Rbeta chains, also referred to as IL-2Rbeta chains) are known by, and available to, the skilled person. Among beta chains, human beta chains are preferred.
Beta chain templates are available from RNA of HuT102 (ATCC TIB-162) by RT-PCR using the proofreading polymerase Pfu (Stratagène n° 600390) and 5′GAGAGACTGGATGGACCC 3′ as sense primer (SEQ ID NO: 70), and 5′ AAGAAACTAACTCTTAAAGAGGC3′ as anti-sense primer (SEQ ID NO: 71) according to human IL-2R beta sequence (NCBI accession number K03122). The PCR product is efficiently cloned using the Zero Blunt PCR Cloning Kit (In Vitrogen cat n° K2700-20) or the TOPO XL PCR cloning kit (In Vitrogen cat n° K4750-10). The cDNA for IL-2R beta gene is then subcloned into the multiple cloning site of the pLXRN retrovirus expression vector of the Pantropic Retroviral Expression System (BD Biosciences Clontech n° 631512) and transfected into GP2-293 cells, as described in the kit to generate recombinant retroviruses.
Gamma chains (i.e., IL-15Rgamma chains, also referred to as IL-2Rgamma chains) are known by, and available to, the skilled person. Among gamma chains, human gamma chains are preferred.
Gamma chain templates are available from RNA of TF1 (ATCC CRL 2003) or HuT 102 (ATCC TIB 162) by RT-PCR using the proof-reading polymerase Pfu and 5′ GAAGAGCAAG CGCCATGTTG 3′ (SEQ ID NO:100) as sense primer and 5′ TCAGGTTTCAGGCTTTAGGG 3′ as antisense primer (SEQ ID NO:101) according to human interleukin-2 receptor gamma sequence (NCBI Accession number D 11086). The PCR product is efficiently cloned using the Zero Blunt PCR Cloning Kit or the TOPO XL PCR cloning kit. The cDNA for IL-2Rγ gene is then subcloned into pcDNA 3.1/HYGRO (In Vitrogen) to generate a pcDNA IL-2Rγ/HYGRO plasmid.
IL-2R beta recombinant retroviruses can be used to infect 32D cells to generate 32Dβ after selection in medium containing G418. The pcDNA IL-2Rγ/HYGRO plasmid can then be transfected into 32Dβ cells by electroporation to generate 32Dβγ after selection in medium containing hygromycin.
The skilled person may alternatively choose to assess or monitor an IL-15 biological response that is more downstream in the signalling pathway, such as activation of a tyrosine kinase (e.g., Jak-1/Jak-3 Lck Syk), activation of a MAP kinase, or a nuclear translocation event (e.g., translocation of phosphorylated Stat-3 and/or Stat-5). Said IL15 biological response may then be an acellular response.
Additional Elements (Signal Peptide, Molecular Tag, Proteolytic Site, Etc.):
A compound of the invention may comprise a signal peptide. This signal peptide can be directly or indirectly linked to said at least one sushi-containing polypeptide or to said at least one IL-15Rbeta/gamma binding entity. Said signal peptide can be linked to said compound by covalence.
Signal peptides facilitate secretion of proteins from cells.
This signal peptide may, e.g., be the signal peptide of an IL-15Ralpha, such as a human IL-15Ralpha (such as the signal peptide of human IL-15Ralpha which is of sequence SEQ ID NO: 5) directly or indirectly linked to said fragment, or the signal peptide of another protein (such as the signal peptide of bovine preprolactine of SEQ ID NO: 58), directly or indirectly linked to said fragment. Exemplary signal peptides are:
Other signal peptides which are found appropriate by the skilled person may also be employed. Furthermore, certain nucleotides in the IL-15 leader sequence can be altered without altering the amino acid sequence. Additionally, amino acid changes that do not affect the ability of the sequence to act as a signal peptide can be made.
A sushi-containing polypeptide of the invention may be directly linked to the signal peptide of the IL-15Ralpha from which it derives. Such a sushi-containing polypeptide may nevertheless be:
A compound of the invention may further comprise at least one molecular tag and/or at least one proteolytic site.
For example, a molecular tag and/or a proteolytic site can be located between the signal peptide and the sushi domain, or between the signal peptide and the IL-15Rbeta/gamma binding entity. Said molecular tag and/or proteolytic site may be directly or indirectly linked to said at least one sushi-containing polypeptide, or to said IL-15Rbeta/gamma binding entity.
Examples of molecular tags notably comprise FLAG® tags.
Examples of proteolytic sites notably comprise Xa binding sites.
The FLAG® (a registered trademark) octapeptide (Hopp et al., Bio/Technology 6:1204, 1988) does not alter the biological activity of fusion proteins, is highly antigenic, and provides an epitope reversibly bound by a specific monoclonal antibody, enabling rapid detection and facile purification of the expressed fusion protein. The FLAG® sequence is also specifically cleaved by bovine mucosal enterokinase at the residue immediately following the AspLys pairing. Fusion proteins capped with this peptide may also be resistant to intracellular degradation in E. coli. A murine monoclonal antibody that binds the FLAG® sequence has been deposited with the ATCC under accession number HB 9259. Methods of using the antibody in purification of fusion proteins comprising the FLAG® sequence are described in U.S. Pat. No. 5,011,912.
Examples of sequences coding for a Flag epitope and a factor Xa binding site comprise those of SEQ ID NO: 53 and NO: 55 (amino acid sequences of SEQ ID NO: 54 and NO: 56, respectively).
Amino Acids:
In the context of the present invention, ‘amino acid residue’ means any amino acid residue known to those skilled in the art (see e.g.: Sewald et al., 2002 (42); IUPAC nomenclature under http://www.chem.gmul.ac.uk/iupac/AminoAcid/). This encompasses naturally occurring amino acids (including for instance, using the three-letter code, Ala, bAla, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val), as well as rare and/or synthetic amino acids and derivatives thereof (including for instance Aad, Abu, Acp, Ahe, Aib, Apm, Dbu, Des, Dpm, Hyl, MeLys, MeVal, Nva, HAO, NCap, Abu, Aib, MeXaa and the like (see e.g.: (Müller et al., 1993; Aurora et al., 1998; Obrecht et al., 1999; Maison et al., 2001; Formaggio et al., 2003; Nowick et al., 2003; (43-48). Said amino acid residue or derivative thereof can be any isomer thereof, especially any chiral isomer, e.g., the L- or D-isoform.
By amino acid derivative, we hereby mean any amino acid derivative as known in the art (see e.g.: Sewald et al., 2002 (42); IUPAC nomenclature under http://www.chem.gmul.ac.uk/iupac/AminoAcid/).
For instance, amino acid derivatives include residues derivable from natural amino acids bearing additional side chains, e.g. alkyl side chains, and/or heteroatom substitutions. Further examples of amino acid derivatives comprise amino acid bearing chemical modifications such the one found in mimetic peptides or peptidomimetics, which are compounds containing non-peptidic structural elements that are capable of mimicking or antagonizing the biological action(s) of a natural parent peptide. A peptidomimetic usually does no longer have classical peptide characteristics such as enzymatically scissille peptidic bonds.
Preferably, said amino acid belongs to the group of the non-essential amino acids. Preferred non-essential amino acids are glycine, alanine, proline, serine, cysteine, tyrosine, asparagine, glutamine, aspartic acid, glutamic acid, arginine, histidine. Appropriate amino acids may be accurately selected by selecting those amino acids which are in lower amounts in the patient into which the drug is to be administered. Dosage and administration regimen can be determined as a function of the patient's level in said amino acid. Preferred dosage and administration regimen are those which intend to increase the patient's amino acid level up to the normal standard level.
Linking Said at Least One Sushi-Containing Polypeptide to Said at Least One IL-15Rbeta/Gamma Binding Entity:
Said at least one sushi-containing polypeptide of the invention may be linked directly to said at least one IL-15Rbeta/gamma binding entity.
Alternatively, said at least one sushi-containing polypeptide of the invention, and said at least one IL-15Rbeta/gamma binding entity the proteins may be separated by a “linker” amino acid sequence of a length sufficient to ensure that the proteins form proper secondary and tertiary structures.
Preferably, said linker is a peptidic linker which comprises at least one, but less than 30 amino acids e.g., a peptidic linker of 2-30 amino acids, preferably of 10-30 amino acids, more preferably of 15-30 amino acids, still more preferably of 19-27 amino acids, most preferably of 20-26 amino acids.
Preferred linkers are those which allow the compound to adopt a proper conformation (i.e., a conformation allowing a proper signal transducing activity through the IL-15Rbeta/gamma signalling pathway). Examples of preferred linkers include flexible linkers.
The most suitable linker sequences (1) will adopt a flexible extended conformation, (2) will not exhibit a propensity for developing ordered secondary structure which could interact with the functional domains of fusion proteins, and (3) will have minimal hydrophobic or charged character which could promote interaction with the functional protein domains. Typical surface amino acids in flexible protein regions include Gly, Asn and Ser (i.e., G, N or S). Virtually any permutation of amino acid sequences containing Gly, Asn and Ser would be expected to satisfy the above criteria for a linker sequence. Other near neutral amino acids, such as Thr, Ala, Leu, Gln (i.e., T, A, L, Q) may also be used in the linker sequence. The length of the linker sequence may vary without significantly affecting the biological activity of the fusion protein.
Exemplary linker sequences are described in U.S. Pat. Nos. 5,073,627 and 5,108,910.
Illustrative flexible linkers which are more particularly suitable for the present invention include those coded by the sequences of SEQ ID NO: 49 or NO: 51 (amino acid sequences of SEQ ID NO: 50—also referred to as linker 20- and NO: 52—also referred to as linker 26-, respectively).
In a compound of the invention, the sequence of said at least one sushi-containing polypeptide can be in a N-terminal position relative to the sequence of said at least one IL-15Rbeta/gamma binding entity.
Alternatively, the sequence of said at least one sushi-containing polypeptide can be in a C-terminal position relative to the sequence of said at least one IL-15Rbeta/gamma binding entity.
A compound of the invention can be a fusion protein.
Fusion proteins are polypeptides that comprise two or more regions derived from different or heterologous, proteins or peptides. Fusion proteins are prepared using conventional techniques of enzyme cutting and ligation of fragments from desired sequences. PCR techniques employing synthetic oligonucleotides may be used to prepare and/or amplify the desired fragments. Overlapping synthetic oligonucleotide representing the desired sequences can also be used to prepare DNA constructs encoding fusion proteins. Fusion proteins can comprise several sequences, including a leader (or signal peptide) sequence, linker sequence, a leucine zipper sequence, or other oligomer-forming sequences, and sequences encoding highly antigenic moieties that provide a means for facile purification or rapid detection of a fusion protein.
Illustrative of the compounds of the invention are the fusion protein which comprise the sushi-containing polypeptide of SEQ ID NO: 30 (it+sushi+hinge), and the human wild-type IL-15 of SEQ ID NO: 48, optionally linked together via a linker.
Further illustrative of the compounds of the invention are the fusion protein which comprise:
Further Illustrative of the Compounds of the Invention are the Fusion Protein which Comprise:
The compounds of the invention can be produced by any means that the skilled person may find appropriate, such as e.g., chemical polypeptide synthesis, or polypeptide biosynthesis.
Chemical polypeptide synthesis is now routine (see e.g. Andersson et al., 2000, Biopolymers (Peptide Science) 55: 227-250), and many companies are specialized in such synthesis.
Preferably, the compounds of the present invention are synthesized by solid phase peptide synthesis (SPPS) techniques using standard FMOC protocols (See, e.g., Carpino et al., 1970, J. Am. Chem. Soc. 92(19):5748-5749; Carpino et al., 1972, J. Org. Chem. 37(22):3404-3409).
Alternatively, the skilled person may choose to produce the compounds biologically by in vitro or in vivo translation of a nucleic acid coding for such a compound.
Nucleic Acids, Vectors, Host Cells:
The present invention hence also relates to nucleic acids (DNA or RNA) coding for a product which is intended for stimulating the IL-15Rbeta/gamma signalling pathway, to thereby induce and/or stimulate the activation and/or proliferation of IL-15Rbeta/gamma-positive cells, such as NK and/or T cells.
More particularly, the nucleic acids of the invention code for an isolated sushi-containing polypeptide of the invention, as herein defined, or for a covalently linked compound of the invention, as herein defined (i.e., comprising at least one sushi-containing polypeptide directly or indirectly linked by covalence to at least one IL-15Rbeta/gamma binding entity). Said coding is in accordance with the universal genetic code, taking due account of its degeneracy.
The nucleic acids of the invention can optionally be contained within a vector, such as transfection vector, or an expression vector.
The nucleic acids of the invention may be operably linked to a suitable transcriptional or translational regulatory sequence such as transcriptional promoters or enhancers, an optional operator sequence to control transcription, a sequence encoding suitable mRNA ribosomal binding sites, and appropriate sequences that control transcription and translation initiation and termination. Examples of such vectors include pEF1/myc-His (In Vitrogen, V921-20), pcDNA3.1 (In Vitrogen, V800-20).
The nucleic acids of the invention may also be linked to a leader sequence that enables improved extracellular secretion of the translated polypeptide. Examples of such leader sequences include leader sequences from rat pre-prolactin (SEQ ID NO: 57) or from an IL-15Ralpha, such as the human IL-15Ralpha signal peptide CDS of SEQ ID NO: 4).
The sequence of these nucleic acids may also comprise a stop codon (TAG, TGA, TAA) at their 3′ terminal end.
The present invention relates to every nucleic acid encoding one of the described compounds of the invention. Table 4, which located before the claims section, indicates the respective SEQ ID NO: of these nucleic acids.
For example:
A nucleic acid of the invention can comprise a Kozak sequence at its 5′ end, e.g., a Kozak sequence from human wild-type IL-15R, such as gcc gcc; or a Kozak sequence from bovine preprolactine, such as gcc acc.
A nucleic acid of the invention can comprise a stop codon (e.g., tag, tga, or taa) at its 3′ end.
The present invention also relates to any vector, comprising a nucleic acid of the invention. Preferably, such a vector is a baculovirus vector.
Said vector can, e.g., be a transfection, or an expression vector.
The present invention also relates to any host cell, transformed or transfected by a nucleic acid of and/or by a vector of the invention.
As used herein, “transfected” or “transfection” means the introduction of one or more exogenous nucleic acids into a eukaryotic cell. Transfection includes introduction of naked nucleic acids such as plasmids by standard physical and chemical transfection techniques, including calcium phosphate precipitation, dextran sulfate precipitation, electroporation, liposome-mediated nucleic acid transfer, ballistic methods such as particle bombardment, etc. Transfection also includes introduction of nucleic acids into cells by biological methods, including viral transduction or infection (receptor-mediated and non-receptor-mediated). As used herein, “transformed” or “transformation” means the introduction of one or more exogenous nucleic acids into a prokaryotic cell. Transformation includes introduction of naked nucleic acids, as well as of a nucleic acid vector, such as a phage.
Suitable host cells include prokaryotes, yeast or higher eukaryotic cells under the control of appropriate promoters.
Prokaryotes include Gram positive and Gram negative organisms, for example Escherichia coli, Bacillus subtilis, Salmonella typhimurium, and various other species within the Bacillus, Pseudomonas, Streptomyces and Staphylococcus genera.
Examples of suitable host cells also include yeast such as Saccharomyces cerevisiae, and higher eukaryotic cells, such as established cell lines of mammalian or insect origin. Examples of suitable higher eukaryotic cells comprise mammalian cell lines, such as Chinese Hamster Ovary (CHO) cells, e.g. Chinese ovary hamster cell line CHO/dhfr− (CHO duk−) (ATCC n° CRL-9096), or such as epithelial cell lines, e.g. simian epithelial cell line COS-7 (ATCC n° CRL 1651), or human cell lines, e.g. 293 c18 human kidney cell line (ATCC n° CRL-10852) or FreeStyle 293-F human kidney cell line (In Vitrogen n° R790-07).
Said host cell may be a eukaryotic cell, a mammalian cell (human or non-human such as a CHO cell), a yeast cell, or a prokaryotic cell (such as E. coli).
Most preferably, said host cell is a mammalian cell, as the present invention that such cells are more efficient (independently from any problem of glycosylation).
Biological and Medical Applications:
The products of the invention notably comprise said sushi-containing polypeptides in isolated form as herein defined, and the covalently linked form thereof, which is herein referred to as the covalently linked compound of the invention (i.e., the compound which comprises at least one sushi-containing polypeptide directly or indirectly linked by covalence to at least one IL-15Rbeta/gamma binding entity).
The products of the invention also comprise the nucleic acids coding for such polypeptides and compounds, the vector comprising such nucleic acids, as well as the host cells transformed or transfected by such a nucleic acid or such a vector.
The products of the invention are useful to expand lymphocyte subsets, such as particular T/NK subsets. The present invention thus relates to the use of a product of the invention as an agent for expanding one or several lymphocyte populations, such as NK cells, NK-T cells, CD8+ memory cells, and to the adjuvants, compositions and kits intended for such a use, including the pharmaceutical compositions and drugs, which comprise at least one product of the invention.
Said at least one sushi-containing polypeptide and said at least one IL-15Rbeta/gamma binding entity can be used in a combined form, such as e.g., in the form of a covalently linked compound of the invention, or in separate forms.
The present invention thus relates to:
The present invention thus relates to such a preparation, which is an adjuvant, a composition or a kit, including a pharmaceutical composition and a drug.
The present application thus relates to the prevention and/or alleviation and/or treatment of a condition or disease in which an increase of IL-15 activity is desired, such as notably cancer or immunodeficiency. Such a prevention and/or alleviation and/or treatment may act by stimulating the proliferation and/or survival of lymphocytes (such as T cells, CD8+ T cells, NK cells, dendritic cells) and/or their activity against tumoral cells.
A prevention and/or alleviation and/or treatment method of the invention comprises the administration of a product of the invention to a patient in need thereof.
The present invention also relates to adjuvants, compositions, pharmaceutical compositions, drugs, and vaccines, which are intended for such a prevention and/or alleviation and/or treatment.
The pharmaceutical compositions, drugs and vaccines of the invention comprise at least one product of the invention, and optionally a pharmaceutically acceptable vehicle and/or carrier and/or diluent and/or adjuvant.
The present invention more particularly relates to an adjuvant. Such an adjuvant is notably adapted to the induction and/or stimulation of an immune response, which comprises an isolated IL-15Ralpha sushi domain, or a conservative variant thereof. Such an adjuvant may be an adjuvant for an anti-microbial (anti-viral, anti-bacterial, anti-fungal) vaccine, or for an anti-tumour vaccine.
The present invention also relates to:
The present application thus relates to a drug or vaccine comprising at least one sushi-containing polypeptide as herein defined, and optionally a pharmaceutically acceptable vehicle and/or carrier and/or diluent and/or adjuvant.
Such a drug or vaccine is intended for prevention and/or treatment and/or alleviation of a condition or disease in which an increase of IL-15 activity is desired, such as notably cancer or immunodeficiency. Such a drug or vaccine may act by stimulating the proliferation and/or survival of lymphocytes (such as T cells, CD8+ T cells, NK cells, dendritic cells) and/or their activity against tumoral cells.
The present invention more particularly relates to an anti-tumoral drug or vaccine which exerts its preventive and/or alleviating and/or therapeutic action through the stimulation of the proliferation of NK and CD8+ T cells expressing IL-15Rbeta/gamma but not IL-15Ralpha.
Such an antitumoral drug or vaccine is therefore intended for those patients, whose NK and/or CD8+ T cell populations are insufficiently active to exert an efficient antitumor surveillance or clearance.
Such an antitumoral drug or vaccine is more particularly intended for those patients who have an insufficient population or an insufficiently active population of NK and/or CD8+ T cells expressing IL-15Rbeta/gamma but not IL-15Ralpha.
An antitumoral drug or vaccine of the invention may comprise an isolated IL-15Ralpha sushi domain or a conservative variant thereof.
A preferred anti-tumoral drug or vaccine of the invention comprises:
Preferably, at least one IL-15Rbeta/gamma binding entity, such as IL-15, and said at least one sushi-containing polypeptide, such as an isolated II-15Ralpha sushi domain, or a conservative variant thereof, are linked in a fusion protein, thereby forming a covalently linked compound of the invention.
The present invention also relates to the prevention and/or alleviation and/or treatment of a disease or condition involving an immunodeficiency.
The present invention more particularly relates to the prevention and/or alleviation and/or treatment of a disease or condition involving a HIV-related immunodeficiency.
This prevention and/or alleviation and/or treatment comprise the administration of a product of the invention to a patient in need thereof.
The present invention relates to a drug and/or composition for such a prevention and/or alleviation and/or treatment.
The present invention thus relates to an adjuvant for immunotherapeutic composition, characterized in that it comprises at least one element among the following elements:
Advantageously, said adjuvant improves the CD8 memory response.
In the present application, «immunotherapy» encompasses therapy, palliation and/or prevention by induction and/or stimulation of an immune response. The term «immunotherapeutic composition» hence encompasses preventive vaccines, as well as palliative and/or therapeutic “vaccines”.
The term «adjuvant» is intended to define a substance which can be added to a composition to improve an immune response (innate immune response and/or adaptive immune response). In the present invention, it further encompasses a substance which can be added to a composition to improve the efficiency of this composition over time, i.e., the duration of the immune response (memory CD8+ T cells).
The compound of the invention may be used in a composition as an adjuvant compound, but can also act by itself as an active principle.
It is indeed, on and of its own, able to induce and/or stimulate the proliferation and activation of IL-15Rbeta/gamma-positive cells, and more particularly the differentiation of NK and/or T cells from naïve NK and/or T cells.
The term «active principle» is intended to define a substance which can elicit an immune response.
As an adjuvant for immunotherapeutic composition, a compound of the invention improves the intensity of the immune response (innate immune response; an adaptive immune response) and/or improves the duration of the immune response (it improves the T CD8 memory response).
As an active agent for an immunotherapeutic composition, a compound of the invention induces an immune response, which is of higher intensity and/or longer duration that that induced by other NK/T cell stimulators.
Hence, whether used as an adjuvant in association with another immune response induced, or used as an active principle which on and of its own induces an immune response, a compound of the invention improves the intensity and/or duration of the immune response. It advantageously:
The application also relates to an adjuvant composition, which comprises at least one element among the following elements:
The application also relates to a method of producing an adjuvant for an immunotherapeutic composition, characterized in that it comprises:
The present invention also relates to a composition, a pharmaceutical composition or a drug comprising at least one polypeptide containing the sushi domain of IL-15Ralpha, as herein defined, i.e., wherein the amino acid sequence of said at least one sushi-containing polypeptide:
Preferably, said percentage of identity is of at least 90%, still more preferably of at least 92%, most preferably of at least 95%, e.g., at least 96%, at least 97%, at least 98%, at least 99% or 100%.
The present invention more particularly relates to a composition, a pharmaceutical composition or a drug which comprises at least one polypeptide containing the sushi domain of IL-15Ralpha, as herein defined, wherein said at least one sushi-containing polypeptide comprises, or consists of, the part of extracellular IL-15Ralpha that is encoded by exons 2 and 3, or a fragment of such a part which has retained the sushi domain.
The present invention preferably relates to a composition, a pharmaceutical composition or a drug which comprises:
Preferably, said percentage of identity is of at least 90%, still more preferably of at least 92%, most preferably of at least 95%, e.g., at least 96%, at least 97%, at least 98%, at least 99% or 100%.
Such a composition, pharmaceutical composition, or drug may further comprise at least one IL-15Rbeta/gamma binding entity, such as IL-15, or an IL-15 fragment or variant as herein defined.
Said at least one IL-15Rbeta/gamma binding entity can be not linked to said at least one sushi-containing polypeptide by covalence, i.e., be placed in a free form in said composition, and/or can be linked by covalence to said to said at least one sushi-containing polypeptide. In the latter case, the composition, pharmaceutical composition, or drug of the invention in fact comprises a compound of the invention as herein defined.
Such a pharmaceutical composition or drug can be intended for agonizing an IL-15 biological action, and more particularly for inducing and/or stimulating the proliferation and/or activation of IL-15Rbeta/gamma-positive cells.
Such a pharmaceutical composition or drug can be intended for inducing and/or stimulating the proliferation and/or activation of a NK and/or T immune response.
Such a pharmaceutical composition or drug can be intended as a preventive and/or palliative and/or therapeutic vaccine composition.
Such a pharmaceutical composition or drug can be intended for the prevention and/or palliation and/or treatment of an infectious disease, and/or for the prevention and/or palliation and/or treatment of an immunodeficiency (such as a HIV-induced immunodeficiency), and/or for the prevention and/or palliation and/or treatment of a tumour development or presence (and may then further contain at least one tumour antigen), and/or for the prevention and/or palliation and/or treatment of X-SCID.
According to an advantageous embodiment of the present invention, said at least one sushi-containing polypeptide is covalently linked to a IL-15Rbeta/gamma binding entity. Most preferably, this IL-15Rbeta/gamma binding entity does not bind IL-2Ralpha.
According to a preferred embodiment of the present invention, said at least one sushi-containing polypeptide is covalently linked to a IL-15Rbeta/gamma binding entity, which is IL-15, or is an IL-15 fragment, mimetic, or agonist, which has an affinity for binding to IL-15Rbeta/gamma that is not significantly lower than the one of native IL-15 (i.e., a fragment, mimetic or agonist which is capable of competing with native IL-15 and/or IL-2 for binding to IL-15Rbeta/gamma).
The present invention thus more particularly relates to a pharmaceutical composition, intended for stimulating the IL-15Rbeta/gamma signalling pathway, to thereby induce and/or stimulate the activation and/or proliferation of IL-15Rbeta/gamma-positive cells, such as NK and/or T cells, characterized in that it comprises at least one element among the following elements:
Such a pharmaceutical composition may further comprise a pharmaceutically appropriate vehicle (carrier, diluent, excipient, additive, pH adjuster, emulsifier or dispersing agent, preservative, surfactant, gelling agent, as well as buffering and other stabilizing and solubilizing agent, etc.).
The present invention also relates to a drug, intended for stimulating the IL-15Rbeta/gamma signalling pathway, to thereby induce and/or stimulate the activation and/or proliferation of IL-15Rbeta/gamma-positive cells, such as NK and/or T cells, characterized in that it comprises at least one element among the following elements:
Said drug is preferably an immunotherapeutic composition,
Such a drug most preferably is a preventive and/or palliative and/or therapeutic vaccine composition.
Said drug may further comprise a physiologically appropriate vehicle (carrier, diluent, excipient, additive, pH adjuster, emulsifier or dispersing agent, preservative, surfactant, gelling agent, as well as buffering and other stabilizing and solubilizing agent, etc.).
Appropriate pharmaceutically acceptable vehicles and formulations include all known pharmaceutically acceptable vehicles and formulations, such as those described in “Remington: The Science and Practice of Pharmacy”, 20th edition, Mack Publishing Co.; and “Pharmaceutical Dosage Forms and Drug Delivery Systems”, Ansel, Popovich and Allen Jr., Lippincott Williams and Wilkins.
In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise, in addition to the one or more contrast agents, injectable fluids that include pharmaceutically and physiologically acceptable fluids, including water, physiological saline, balanced salt solutions, buffers, aqueous dextrose, glycerol, ethanol, sesame oil, combinations thereof, or the like as a vehicle. The medium also may contain conventional pharmaceutical adjunct materials such as, for example, pharmaceutically acceptable salts to adjust the osmotic pressure, buffers, preservatives and the like. The carrier and composition can be sterile, and the formulation suits the mode of administration.
For solid compositions (e.g., powder, pill, tablet, or capsule forms), conventional nontoxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, sodium saccharine, cellulose, magnesium carbonate, or magnesium stearate. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
The composition can be a liquid solution, suspension, emulsion, tablet, pill, capsule, sustained release formulation, or powder. The composition can be formulated with traditional binders and carriers, such as triglycerides.
A composition or drug of the invention is useful in inducing and/or stimulating an IL-15 biological action through the IL-15Rbeta/gamma signalling pathway. It is more particularly useful in inducing and/or stimulating an innate immune response (NK cells), and/or an adaptive immunity (T cells, and more particularly T CD8+ memory cells).
According to a very advantageous embodiment of the present invention, said drug can be intended for the prevention and/or palliation and/or treatment of a tumour development or presence.
Said tumour can, e.g., be a melanoma, a lymphoma, a carcinoma (e.g., cervical carcinoma), a breast cancer, an ovarian cancer, a pancreatic tumour.
Advantageously, said anti-tumour drug is an anti-tumour vaccine acting through transpresentation.
An anti-tumour drug of the invention can further comprise at least one tumour antigen. Said at least one tumour antigen can be in a soluble form, or be linked to a compound of the invention (by covalence or by another form of linkage).
Said at least one tumour antigen is advantageously provided in the form of dendritic cells loaded with such an antigen, e.g., genetically engineered dendritic cells which express said at least one tumour antigen.
Tumour antigens are antigens that are presented by MHC I molecules on the surface of tumour cells. Tumour antigens can also be on the surface of the tumour in the form of, for example, a mutated receptor, in which case they will be recognized by B cells.
Tumour antigens can sometimes be presented only by tumour cells and never by the normal ones. In this case, they are called tumour-specific antigens (TSA), or tumour-specific transplantation antigens (TSTA), or tumour rejection antigens (TRA), and typically result from a tumour specific mutation. TSA usually appear when an infecting virus has caused the cell to become immortal and to express virus antigen. TSA non induced by viruses are the idiotypes of BCR on B cell lymphomas or TCR on T cell lymphomas.
More common are antigens that are presented by tumour cells and normal cells, and they are called tumour-associated antigens (TAA). TAA are found on tumour cells and on ormal cells during fetal life (onco-fetal antigens), after birth in selected organs, or in many cells but at a much lower concentration than on tumour cells.
Oncogenes may be expressed in cancer-causing viruses. Most oncogenes are actually present in the host cell, where they function in regulated cell growth. When transduced by the virus and expressed under the control of viral promotor, the product of the host cell gene, i.e., the product of the proto-oncogene, contributes to the unregulated growth of the tumour cell. Since proteins encoded by proto-oncogenes are usually expressed by normal cells, their over-expression on tumour cells would qualify them as tumour-associated antigens.
Cytotoxic T lymphocytes that recognized these antigens may be able to destroy the tumour cells before they proliferate or metastasize. Tumour cells may however downregulate MHC Class I expression. They often lack co-stimulatory molecules like B7 or adhesion molecules that are necessary for them to interact with T CD8+ cells. Some tumour cells actively suppress the immune response by producing a suppressive cytokine, such as TGFbeta, that inhibits cellular immunity.
Examples of tumour antigens notably comprise:
A composition or drug of the invention can be intended for the prevention and/or palliation and/or treatment of an infectious disease (infection by a microorganism, such as virus, bacteria, yeast, fungus, etc.).
A composition or drug of the invention can be intended for the prevention and/or palliation and/or treatment of an immunodeficiency (e.g., an immunodeficiency induced as a side effect by a particular treatment, such as an anti-tumour treatment, or a pre-graft treatment; or induced by a virus, such as HIV).
A composition or drug of the invention can be intended for the prevention and/or palliation and/or treatment of SCID-X (X-linked severe combined immunodeficiency, which is linked to an IL-15Rgamma dysfunction).
The formulation of a pharmaceutical composition comprising at least one of the products of the invention is well within the skill of the art. The same holds true for the details of administering said composition. The physician treating the patient will have to take into account, among other parameters, the age, general condition and disease state.
The therapeutically useful compounds identified according to the method of the invention may be administered to a patient by any appropriate method for the particular compound, e.g., orally, intravenously, parenterally, transdermally, transmucosally, or by surgery or implantation (e.g., with the compound being in the form of a solid or semi-solid biologically compatible and resorbable matrix) at or near the site where the effect of the compound is desired. Therapeutic doses are determined to be appropriate by one skilled in the art, and are a function of the body weight.
The invention also relates to a method of treating by therapy and/or palliation and/or prevention a patient or non-human animal in need thereof with a compound.
The present invention also relates to a method of treating a patient in need thereof (treatment by therapy and/or palliation and/or prevention), by administration of a product, composition or drug of the invention.
The present invention also relates to a process for inducing and/or stimulating the proliferation and/or activation of IL-15Rbeta/gamma-positive cells, characterized in that it comprises:
Said contacting is performed under conditions enabling the proliferation and/or activation of said IL-15Rbeta/gamma-positive cells. Such conditions notably comprise the duration of time, and the environmental conditions (temperature, atmosphere, culture medium). Adjusting these conditions pertains to the competence of the person of ordinary skilled in the art.
The present invention also relates to an vitro process for inducing and/or stimulating the proliferation and/or activation of IL-15Rbeta/gamma-positive cells, characterized in that it comprises:
The present invention also relates to a process for producing activated NK and/or T cells, characterized in that it comprises:
The present invention also relates to an in vitro process for producing activated NK and/or T cells, characterized in that it comprises:
In the process for inducing and/or stimulating the proliferation and/or activation of IL-15Rbeta/gamma-positive cells, and in the process for producing activated NK and/or T cells, the contacted cells may be cell lines. They alternatively can be ex vivo cells collected from an organism (e.g., a human patient), and intended to be returned to this or another organism (e.g., the same patient) after in vitro treatment.
Hence, the present invention encompasses the ex vivo embodiment of said processes, and their implementation in the course of a treatment by therapy and/or palliation and/or prevention.
In the present application, the “stop” codon (TAG, TGA, or TAA) is usually not declared as being comprised within the CDS.
The term “comprising”, which is synonymous with “including” or “containing”, is open-ended, and does not exclude additional, unrecited element(s), ingredient(s) or method step(s), whereas the term “consisting of” is a closed term, which excludes any additional element, step, or ingredient which is not explicitly recited. The term “essentially consisting of” is a partially open term, which does not exclude additional, unrecited element(s), step(s), or ingredient(s), as long as these additional element(s), step(s) or ingredient(s) do not materially affect the basic and novel properties of the invention.
The term “comprising” (or “comprise(s)”) hence includes the term “consisting of” (“consist(s) of”), as well as the term “essentially consisting of” (“essentially consist(s) of”). Accordingly, the term “comprising” (or “comprise(s)”) is, in the present application, meant as more particularly encompassing the term “consisting of” (“consist(s) of”), and the term “essentially consisting of” (“essentially consist(s) of”).
The term “significantly” is herein used in its usual meaning in the field of statistics (e.g., t test, z test, chi squared value, or F ratio, etc.), i.e., for comparing a value to another one, and determining whether these values differ from each other. The term “significantly” hence encompasses the fact that the skilled person may take into account the standard deviation (if any), which measures the amount of spread of data in a frequency distribution. The desired p value is usually set at an alpha level of 5%, or at the more stringent alpha level of 1%.
Each of the relevant disclosures of all references cited herein are specifically incorporated by reference. The following examples are offered by way of illustration, and not by way of limitation.
Cell Culture and Cytokines—
Recombinant human IL-15 (rIL-15) was from Peprotech Inc (Rocky Hill, NJ). The Mo-7 myeloid leukemia cell line (human cell line expressing IL-15Rβ/γ but not IL-15Rα), and the TF-1 erythroleukemia human cell line (cell line expressing IL-15Rα and IL-15Rγ, but not IL-15Rβ, ATCC CRL-2003) were cultured in RPMI 1640 medium containing 10% heat inactivated fetal calf serum (FCS), 2 mM glutamine, and 1 ng/ml GM-CSF (R&D Systems; Abington, UK). TF1-β cells (22) were cultured in the same medium supplemented with 250 μg/ml geneticin. The Kit 225 human T lymphoma cell line (IL-2-dependent cell line) was cultured in RPMI 1640 medium containing 6% FCS, 2 mM glutamine, 10 ng/ml rIL-2 (Chiron; Emeryville, CA).
The mouse 32Dβ cell line that expresses endogenous mouse IL-15Rγ chain and transfected human IL-15Rβ chain (32D cell line available from ATCC CRL-11346) was cultured in RPMI, 10% FCS, 0.4 ng/ml m-IL-3, 10 μg/ml b-mercaptoethanol, 250 μg/ml geneticine.
sIL-15Rα-IL2, sIL-15Rα-Sushi-IL-2 and sIL-15Rα-Sushi—
sIL-15Rα-IL-2 was expressed in CHO cells and prepared as described (23). A similar construction was made in which the sushi domain of IL-15Rα (amino acids 1-66 of mature coding sequence) was linked to a molecule of human IL-2 (sIL-15Rα-sushi-IL-2).
The sushi-domain of IL15Rα was amplified by PCR. PCR products were purified, digested with BamHI and HindIII (Fermentas, Vilnius, Lithuania) and ligated into pQE30 expression vector. Expression was done in E. coli SG13009 cells under IPTG induction. After cell lysis, inclusions bodies were washed, solubilised in 6 mM guanidine HCl, 20 mM sodium phosphate, pH 7.4, 20 mM imidazol, 150 mM sodium chloride and 1 mM DTT. The IL-15Rα-sushi was trapped on a Ni-NTA agarose column (Qiagen) equilibrated with the solubilisation buffer plus 1 mM reduced glutathione and 0.2 mM oxidized glutathione. It was refolded via a gradient from 6 to 0 M guanidine HCl in column buffer (24) and eluted with 250 mM imidazol.
RLI and ILR Fusion Proteins—
The constructions of the fusion proteins are shown on
These constructions were inserted between the BamHI and the HindIII site of pFastBac 1 (InVitrogen) expression vector to generate two expression vectors which were recombined in the baculovirus DNA using the Bac to Bac expression system (InVitrogen). The recombinant baculoviruses were used to infect SF9 cells (ATCC CRL-1711), and fusion proteins were expressed in the SF 900 II medium (Gibco™ Invitrogen Corp.) and harvested 4 days post infection. The concentrations of the fusion proteins were measured by ELISA with the anti-IL-15 mAb 247 (R & D Systems) as capture antibody, and the anti-Flag M2-peroxydase conjugate (Sigma; St Louis, MO) as revealing antibody.
Surface Plasmon Resonance (SPR) Studies—
These experiments were performed with a BIACore 2000 biosensor (BIACore, Uppsala, Sweden). rIL-15 was covalently linked to CM5 sensor chips, and the binding of increasing concentrations of sIL-15Rα-IL-2, sIL-15Rα-sushi-IL-2 or sIL-15Rα-sushi was monitored. Analysis of sensograms was performed using BIAlogue kinetics evaluation software.
Proliferation Assays—
The proliferative responses of Mo-7, TF-1β and Kit 225 cells to rIL-15, rIL-2, RLI or ILR were measured by [3H]-thymidine incorporation as described (19) after 4 h in cytokine-deprived medium, 48 h culture and 16 h with [3H]-thymidine.
Apoptosis—
The annexin V assay was performed using a FACScan flow-cytometer and the Annexin V-FITC Apoptosis detection kit (BD Biosciences Pharmingen, France). After cytokine starvation, cells were seeded in multiwell plates at 5.105 cells/well in 1 ml and cultured in medium supplemented with the various reactants (rIL-15, sIL-15Rα-sushi and RLI fusion protein. Data were acquired and analyzed with the use of the CellQuest software.
Binding Assays and Internalization—
Labeling with [125I]-iodine of human rIL-15, sIL-15Rα-sushi and RLI fusion protein, and subsequent binding experiments were performed as described previously (19). For internalization, cells were equilibrated at 4° C. with labeled sIL-15Rα-sushi or RLI, and the temperature switched to 37° C. At different time intervals, two samples were washed and centrifuged. One of the cell pellets was treated with glycine-HCl buffer 0.2 M, pH 2.5, whereas the other was treated with PBS pH 7.4 at 4° C. for 5 min. After centrifugation, total ligand binding was determined from the pellet of the cells treated with PBS, whereas the membrane bound and internalized fractions were determined respectively from the supernatant and pellet of cells treated with acid pH.
sIL-15Rα-Sushi+:
The Flag-Factor Xa tagged sIL-15Rα-Sushi+ was expressed in insect SF9 cells (ATCC CRL-1711) medium, SF 900 II (In Vitrogen, Cergy-Pontoise, France) as described for the fusion proteins RLI and ILR. The supernatants were concentrated by precipitation with ammonium sulfate at 90% saturation and loaded onto an anti-Flag agarose immunoaffinity column (Sigma-Aldrich, Saint-Quentin Fallavier, France). The purity of the sIL-15Rα-Sushi+ was 100% with an apparent molecular mass of 12 kDa, as assessed by SDS-PAGE after iodination with chloramine-T method as described previously (Lehours et al. Eur. Cytokine Netw. 11 (2000), 207-5). Its concentration was determined by Bicinchoninic Acid (BCA) based protein assay (Pierce, Perbio Science, Brebières, France).
IL-15Rα Binding to IL-15 is Mainly Due to the Sushi Domain—
A previous study (25) has shown that removal of the “sushi” domain encoded by exon 2 of IL-15R resulted in a complete abrogation of the IL-15 binding to membrane anchored IL-15Rα, suggesting that the sushi domain was indispensable for binding. In order to directly measure the contribution of the sushi domain in IL-15 binding, soluble forms of IL-15Rα containing the entire extracellular domain or only the N-terminal sushi domain were prepared and assayed for IL-15 binding in a competition assay and by using the surface plasmon resonance (SPR) technology.
As shown in
A soluble sushi domain was also produced in E. coli. This sIL-15Rα-sushi also bound IL-15 with a lower affinity (kon=2.5 105 M−1 s−1; koff=3.8 10−4 s−1; Kd=1.5 nM) (
These results indicates that the sushi domain is responsible for a major part of the binding affinity of IL-15, but that it does not fully reconstitute the high-affinity binding displayed by the full length extracellular domain.
As shown in
Results of the analysis of sensorgrams giving the affinity constants for IL-15 (KD), calculated for the various soluble IL-15Rα proteins, and the statistical test constant (Chi 2), are shown in table 3 below:
Soluble IL-15Rα Proteins Inhibit IL-15 Binding to Membrane-Anchored IL-15Rα—
The three soluble forms of IL-15Rα were tested for their ability to compete out the binding of radio-iodinated IL-15 to IL-15Rα expressed by the human cell line TF-1 which also expresses the IL-15Rγ chain, but not the IL-15Rβ chain (
sIL-15Rα-Sushi Increases IL-15 Driven Cell Proliferation Through the IL-15Rβ/γ Complex—
Since the soluble sushi domain was easily produced in E. coli in high yields, it was selected for all further studies. In a first instance, it was tested on cell lines that only express the IL-15Rβ/γ complex (human Mo-7 cell line, and mouse 32Dβ cell line that express endogenous mouse IL-15Rγ chain and transfected human IL-15Rβ chain). As expected, the Mo-7 cell line proliferated in response to nanomolar concentrations of rIL-15 or rIL-2 (
RLI and ILR Fusion Proteins are Potent Inducers of Cell Proliferation Through the IL-15Rβ/γ Complex—
In order to evaluate whether the synergistic effect of sushi on IL-15 bio-activity could be transferred on a single molecule, molecular constructs encoding fusion proteins linking IL-15 and the sushi domain were elaborated. For the two constructions, a flexible linker was introduced between the C terminus of IL-15 and the N terminus of the sushi domain (ILR) or vice-versa (RLI) (
As shown in
sIL-15Rα-Sushi Increases IL-15 Induced Prevention of Apoptosis, and RLI Efficiently Prevents Cellular Apoptosis—
Following cytokine withdrawal, the fraction of apoptotic Mo-7 cells raised from 10% to 80% in 48 hours (
sIL-15Rα-Sushi Increases IL-15 Binding to Mo-7 Cells and the RLI Fusion Protein Binds to and is Internalized by Mo-7 Cells—
As expected, Mo-7 cells bound IL-15 with intermediate affinity (Kd=13.5 nM), with a maximal binding capacity of 800 sites/cell
sIL-15Rα-Sushi does not Affect IL-15 Driven Cell Proliferation Nor Inhibition of Apoptosis Through the High Affinity IL-15Rα/β/γ Complex—
The human lymphoma cell line Kit 225 expresses endogenous IL-15Rα, β and γ chains, and the human TF-1β cell line expresses endogenous IL-15Rα and γ chains plus transfected human IL-15Rβ chain. Consequently, these cell lines proliferate in response to low, picomolar concentrations of IL-15 as shown in
The effects of sIL-15Rα-sushi and RLI were further analyzed on TF-1β cell apoptosis induced by cytokine deprivation. Histograms are shown in
IL-15, sIL-15Rα-Sushi and RLI Binding to TF1β Cells—
As far as IL-15Rα-sushi did not affect IL-15 proliferation of TF-1β, we examined its effect on IL-15 binding that was analyzed on a wide concentration range (
In order to more specifically test the effect of sIL-15Rα on the high affinity component, its effect was analyzed at low concentrations of radiolabeled IL-15. As shown in
The binding of radiolabeled sIL-15Rα-sushi to TF-1β cells (
Deletion of exon 2 of human IL-15Rα was formerly shown to completely abrogate IL-15 binding, indicating the dispensable role of the sushi domain in cytokine recognition (25). The present invention shows that removal of the C-terminal tail (exons 3 to 5) of the extracellular part of IL-15Rα (in the context of the sIL-15Rα-IL-2 fusion protein) results in a 10 fold decrease of its binding affinity for IL-15, as seen by SPR, and a 3.5 fold decrease of its affinity as seen in a competition assay.
In terms of thermodynamics, the 10 fold decrease in affinity was calculated to correspond to a 10% loss of the free energy of interaction of IL-15 with IL-15Rα. Thus the N-terminal structural domain encoded by exon 2 (sushi domain) bears most (90%) but not all of the IL-15 binding capacity. Recent data from our laboratory indicate that domain encoded by exon 3 also contributes to IL-15 binding.
The sIL-15Rα-sushi produced in E. coli had an affinity that was 3 to 4 fold lower than that of sIL-15Rα-sushi-IL-2 produced in CHO cells. This difference cannot be explained by differences in the glycosylation status of the two proteins, as far as the sushi domain does not contain any potential sites for N- or O-linked glycosylations (2). It is therefore likely due to differences in the structural foldings of the two proteins.
While competing with IL-15 binding to membrane IL-15Rα, sIL-15Rα-sushi was found to exert agonist effects by enhancing IL-15 action through the IL-15β/γ complex. Studies on cells expressing either only intermediate affinity IL-15 receptors (Mo-7, 32Dβ) or both high and intermediate affinity IL-15 receptors (TF-1β, Kit 225) showed that the agonist action of sIL-15Rα-sushi was specifically directed to the IL-15Rβ/γ complex: (i) it had no effect in the absence of IL-15, (ii) it bound to TF-1β cells in the presence of IL-15 with a single affinity class of binding sites, the density of which was comparable to that of intermediate IL-15 binding sites, (iii) on Mo-7 cells and TF-1β cells, it increased the affinity of IL-15 for the IL-15Rβ/γ complex whereas it did not affect the binding of IL-15 to the high affinity complex on TF-1β cells, (iv) it enhanced the efficiency of IL-15 biological action (proliferation, prevention from apoptosis) through IL-15Rβ/γ on Mo-7 cells, but had no effect on the same biological effects mediated through the high affinity receptor on TF-1β cells.
The functionality of this agonist action was further supported by the fact that sIL-15Rα-sushi, once bound in conjunction with IL-15 to IL-15Rβ/γ on Mo-7 cells, was efficiently cell internalized. Its potency was strengthened in the context of the ILR and RLI fusion proteins: (i) RLI bound to IL-15Rβ/γ with an affinity almost 20 fold better than IL-15 itself. (ii) binding of RLI was followed by a rapid internalization of the fusion protein. (iii) the RLI or ILR fusion proteins were much more potent than IL-15 in the functional assays. The dose response curves of the two fusion proteins on Mo-7 cells were comparable to those of IL-15 through the high affinity receptor on Kit 225 or TF-1β cells, indicating that these fusion proteins almost fully reconstituted the high affinity response on cells that only express the intermediate affinity receptor.
The results therefore indicate that sIL-15Rα-sushi and IL-15 make a complex that cooperatively increases their binding affinities to the IL-15Rβ/γ receptor. In contrast, sIL-15Rα-sushi is not able to affect IL-15 binding and bioactivity once this latter is already associated with the membrane high affinity receptor complex. Whether sIL-15Rα-sushi can still bind to IL-15 already engaged in this high affinity complex cannot however be excluded and could be tested with the availability of cells expressing mainly high affinity receptor i.e., cells expressing similar levels of the three receptor subunits.
Our laboratory has formerly shown that sIL-15Rα expressed in COS cells or naturally produced by IL-15Rα positive cells, behave as powerful antagonists by binding IL-15 with high affinity (Kd=166 pM) and inhibiting IL-15 induced proliferation of Kit 225 cells at low (IC50 between 3 and 10 pM) concentrations (19). These results are in contrast with the present invention showing that sIL-15Rα-sushi has no effect on the proliferation of Kit 225 cells or of TF-1β cells, and is agonist on Mo-7 cells.
Another contrasting result is a recent report showing that a mixture of rIL-15 with a recombinant human sIL-15Rα(lacking exon 3)-Fc homodimeric chimera could induce an anti-apoptotic effect on Mo-7 cells, whereas rIL-15 alone at the same dose was without effect (26).
In an attempt to explain these differences of action, a model is proposed in
The functional differences between sIL-15Rα and sIL-15Rα-sushi indicate that the C terminal tail of sIL-15Rα plays a crucial role for competing with membrane IL-15Rα and hence for the antagonist action of sIL-15Rα. This tail would either impede soluble IL-15Rα association with IL-15Rβ/γ, or allow such an association, but result in an inappropriate conformation of IL-15Rβ/γ for functioning. A similar mechanism has been proposed in the case of a soluble common γ chain (27). The inhibitory activity of this soluble γ chain (corresponding to the entire extracellular part of the γ chain) was abolished by removal of its C-terminal part or by mutations of the WSXWS motif, two regions not involved in cytokine binding.
The agonist effects of sushi are reminiscent of the agonist effects described for soluble receptors within the extended IL-6 family of cytokines (namely sIL-6R, sIL-11R, sCNTFR and the IL-12p40 subunit) (28). However, such an agonist action in the case of IL-15R could not be anticipated as far as all soluble receptors so far described within the γc family, (sIL-2Rα, sIL-2Rβ, sIL-4R), and sIL-15Rα itself, behave as cytokine antagonists (19,29), The present results therefore identify the soluble sushi domain of IL-15Rα as an unexpected and efficient agonist within this family.
The concept of cytokine transsignaling has first been used in the case of IL-6, where soluble IL-6R was shown to enhance the sensitivity of IL-6 responsive cells to the action of IL-6 and to render cells that express gp130 but not membrane IL-6R responsive to IL-6 (30). This concept has been extended to other members of the gp130 cytokine family (IL-11R, CNTFR, CLC) (31-34). In the case of IL-15, a mechanism of cytokine transpresentation has been shown (12), in which IL-15 produced by monocytes/dendritic cells is associated to membrane IL-15Rα expressed by the same cells and can stimulate the proliferation of IL-15Rβ/γ+ IL-15Rα− bystander cells. Recent reports have suggested that transpresentation is a dominant mechanism in vivo, that necessitates expression of IL-15 and IL-15Rα by the same cells (13,14,35,36). It has some similarity with the transsignaling concept, in that transpresented IL-15/IL-15Rα complex can sensitize IL-15Rβ/γ+ IL-15Rα− cells to physiological concentrations of IL-15. In this respect, membrane IL-15Rα acts as an agonist of IL-15 action by increasing its avidity for the IL-15Rβ/γ complex and the efficiency of signaling (12). Our data show that sIL-15Rα-sushi behaves similarly and sensitizes IL-15Rβ/γ+ IL-15Rα− cells to the action of IL-15. This suggests that the sushi domain of membrane IL-15Rα is crucial for transpresentation. We have shown that sIL-15Rα produced by IL-15Rα expressing cells and that encompasses the entire extracellular part of IL-15Rα, is inhibitory of IL-15 action (19). It likely constitutes a negative feed-back mechanism that limits the biological effects of IL-15. In contrast, the sIL-15Rα-sushi described in this study displays an agonist effect. If such soluble sushi is generated by IL-15Rα expressing cells, it could participate in the IL-15 transpresentation mechanism. The existence of such naturally produced soluble sushi domains has not yet been described, but is supported by the facts that (i) different isoforms of the membrane IL-15Rα have been described, including some that lack the tail (encoded by exons 3 to 5) linking the sushi domain to the transmembrane domain (3,25,37), and (ii) generation of soluble counterparts for some of them by shedding has been demonstrated (19). Thus, sIL-15Rα and sIL-15Rα-sushi could have opposing regulatory effects, and as such both participate in the tuning of the magnitude and duration of IL-15 biological action.
The present invention also shows that using a flexible linker to produce a fusion protein such as ILR or RLI is a valid approach in the case of IL-15. A molecular model of IL-15 with the sushi domain was generated (
Rattus norvegicus IL-15Ralpha cDNA (765 bp)
Rattus norvegicus IL-15Ralpha protein (254 aa)
Rattus norvegicus IL-15Ralpha extracellular region
Rattus norvegicus IL-15Ralpha sushi domain (24..84 of SEQ ID NO: 85)
Rattus norvegicus IL-15Ralpha hinge region (85..96 of SEQ ID NO: 85)
Rattus norvegicus IL-15Ralpha tail region (97..182 of SEQ ID NO: 85)
| Number | Date | Country | Kind |
|---|---|---|---|
| 05292210 | Oct 2005 | EP | regional |
The present application is a continuation of U.S. patent application Ser. No. 12/090,930 filed Aug. 6, 2008, which has issued as U.S. Pat. No. 10,358,477, which claims the benefit of International Application No. PCT/IB2006/003917, filed Oct. 6, 2006, which claims the benefit of foreign Application No. EP 05 292 210.1, filed on Oct. 20, 2005, which are incorporated herein by reference in their entireties.
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| Number | Date | Country | |
|---|---|---|---|
| 20200109184 A1 | Apr 2020 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 12090930 | US | |
| Child | 16440779 | US |
