Patent Application
20170157228
The present invention pertains to the field of anti-cancer vaccines. More particularly, the invention relates to an optimized chimeric polypeptide for use in HLA-B7 cancer patients, which comprises four optimized peptides derived from cryptic tumor epitopes to enhance their immunogenicity.
Antitumor vaccines currently in development take many forms, including free peptides, recombinant proteins, dendritic cells loaded with peptides or tumor lysates, and DNA. Although peptide-based vaccines are very attractive over other forms in terms of feasibility, many studies with vaccines targeting dominant tumor peptides were found to elicit only weak immunological and clinical responses, with strong inter-patient variability. This was the case of several peptide-vaccines derived from gp100 tested in several clinical studies, the MUC1 derived BLP25 peptide tested in a randomized phase II trial and the HER-2/neu derived E75 peptide tested in a very large number of phase I and phase II clinical studies (Butts et al, 2005; Peoples et al, 2008; Rosenberg et al, 2004).
Optimized cryptic peptides induce antitumor immunity more efficiently than dominant peptides in transgenic mice model (Gross et al, 2004) and two vaccines based on this technology are currently in clinical development:
Approaches eliciting CTL responses to multiple antigens using polypeptide-based vaccine have several advantages. In particular, expression of at least one target antigen should be sufficient to trigger killing of tumor cells by vaccine-induced CTLs, and tumor cells are unlikely to lose all the target antigens simultaneously, especially when these antigens are essential for cell survival and tumor growth. This approach can elicit strong immune responses (Oukka et al, 1996) and increase the proportion of patients likely to benefit from the vaccine. Moreover, broad-spectrum cancer vaccines should target universal tumor antigens, such as TERT, HER-2/neu, MUC-1, CEA, EphA2 and MAGE-A, which are over-expressed by a wide variety of tumors (Minev et al, 2000; Ofuji et al, 1998; Ogata et al, 1992; Reese & Slamon, 1997; Slamon et al, 1987; Van den Eynde & van der Bruggen, 1997; Vonderheide et al, 1999). Most of these antigens are involved in tumor cell survival and tumorigenicity, and their down-regulation to escape the immune response may therefore have deleterious effect on tumor growth.
To increase the number of patients who can benefit from such products, the inventors have developed a polypeptide-based vaccine, named Vbx-016, designated to HLA-B7 expressing patients, which targets four widely expressed tumor antigens: TERT, HER-2/neu, MAGE and CEA. The four optimized cryptic peptides (Table 1) that compose the Vbx-016, were already described (WO2008/010098, WO2010/143010). Each of the four peptides was shown to elicit an antitumor response in vivo and in vitro (WO2008/010098, WO2010/143010), both against the optimized peptide and against the native cognate peptide naturally expressed by tumour cells (table 1). Interestingly, CTLs elicited by MAGE-A273V6L9 targeted six MAGE-A antigens (-A1, -A2, -A3, -A4, -A6, and -A12). Indeed, specific CTLs induced using the MAGE-A273V6L9 are able to recognize cells loaded with MAGE-A273A6 (included in MAGE-A1 and MAGE-A4), MAGE-A273I6 (included in MAGE-A2 and MAGE-A6) and MAGE-A273V6 (included in MAGE-A3 and MAGE-A12).
Classically, polypeptide-based vaccines are emulsified with an adjuvant such as Montanide ISA51VG (Seppic, Castres, France) before subcutaneous injection. After injection, the polypeptide is internalized into professional Antigen Presenting Cells (APC), especially Langerhans cells present locally in the skin. The polypeptide is then processed by the proteasome in the Golgi apparatus and the epitopes are presented at the cell surface in association with HLA molecules. To ensure the efficient presentation of each epitope of the polypeptide, it is mandatory to test if each junction is correctly processed by the proteasome. Moreover, the inventors have previously described, with Vx006 three-epitopes polypeptide, that the order of the epitopes in the sequence of a polyepitopic vaccine is crucial for each epitope processing and finally for obtaining an immune response against all the corresponding epitopes (WO2007/073768).
To avoid testing the 24 putative arrangements, the optimal organization of the four optimized peptides in the polypeptide was then determined in two steps: (i) test of each junctional sequences; and (ii) test of the corresponding complete polypeptide.
Each potential junction was thus tested. Twelve possible dipeptides presented in table 2 were then tested in vivo in HLA-B*0702 transgenic mice and in vitro in healthy donor PBMCs culture for:
First of all, each dipeptide sequence was submitted to the two main in silico proteasome cleavage prediction softwares, MAPPP (developed by Jörg Hakenberg and Hans-Joachim Mollenkopf at the Max-Planck-Institute for infection Biology, available on the world wide web) and PAProC (Prediction Algorithm for Proteasomal Cleavages, also available on the world wide web) which predict the probability of processing of each epitope.
According to PAProC, none of the dipeptide should be processed correctly by the proteasome (predicted cleavage sites are represented by dashes, table 3), except the 7T5HN3M that could produce both epitopes (cleavage site with a double dash).
According to MAPPP prediction model, many combinations should allow the processing of the four epitopes (data not shown). The predicted best sequence that should ensure the efficient processing of each epitope by the proteasome is CEA188L9/MAGE273L9/TERT444A1/HER-2/neu246A1.
Dipeptides were then tested in vivo in HLA-B*0702 transgenic mice. As described in example 1, combinations 7C1HN3M, 7C1T5M, 7T5HN3M, 7M1HN3M and 7T5M1M gave better results than the corresponding inverted sequences, in terms of number of responding mice. 7C1M1M and 7M1C1M gave the same results.
Based on these in vivo experimental data, the following theoretical optimal polypeptide was then designed: CEA188L9/TERT444A1/MAGE273L9/HER-2/neu246A1.
In order to assess whether the epitopes are efficiently processed in the quadripeptide, the corresponding polypeptide SPRLQLSNLAPRRLVQLLGPRALVETLAPKHSDCLA (SEQ ID No: 23) was then tested in HLA-B*0702 transgenic mice for its capacity to induce specific CTLs recognizing the four optimized epitopes and the four cognate native peptides which are naturally present at the surface of tumor cells. As described in example 2, after two vaccinations with the polypeptide, all mice responded to at least one native peptide and a large majority of vaccinated mice responded to two or more cognate native peptides confirming that the polypeptide is efficiently processed by the proteasome. Importantly, all the native peptides were recognized at least once in one vaccinated mouse.
Interestingly, this sequence is different from the sequence selected by the proteasome MAPPP cleavage prediction model, since the 7M1T5M was predicted to not be processed correctly, contrary to what happens in vivo.
In order to confirm the results obtained in HLA-B*0702 transgenic mice in vitro in humans, each junction of the defined polypeptide (CEA188L9/TERT444A1, TERT444A1/MAGE273L9 and MAGE273L9/HER-2/neu246A1) was tested independently in vitro in a PBMC culture from a healthy human donor. Results described in example 3 show that each dipeptide was efficiently processed in vitro in humans and that specific CTLs induced were able to recognize cells loaded either with the optimized or with the cognate native peptide.
Finally, the polypeptide SPRLQLSNLAPRRLVQLLGPRALVETLAPKHSDCLA (SEQ ID No: 23) was tested in a PBMC culture from one HLA-B*0702 healthy donor (example 4), confirming the capacity of the polypeptide to generate a polyspecific CTLs immune response. Importantly, several native peptides were recognized. These results confirm that the polypeptide is processed efficiently by the proteasome and that the induced immune response is polyspecific.
A first aspect of the invention is hence a polypeptide which comprises the sequence SPRLQLSNLXXXAPRRLVQLLXXXGPRALVETLXXXAPKHSDCLA (Seq ID No: 24). In this sequence, the CEA188L9, TERT444A1, MAGE273L9 and HER-2/neu246A1 epitopes are separated by spacers XXX, in which each X is (independently from each other) any amino acid or none. The polypeptide is hence at least 36-aminoacids long; its length can be increased by the addition of spacers between the epitopes, and/or by the addition of signals, at its N-terminal and/or C-terminal extremities, which favor its processing. In particular, the polypeptide according to the invention can further comprise an endoplasmic reticulum-translocating signal sequence at its N-terminal extremity. Several endoplasmic reticulum-translocating signal sequences have been described in the scientific literature and can be used in the context of the invention. For example, the Ig kappa-chain signal sequence (Ishioka et al, 1999), and the E3/19-kD protein signal sequence (Anderson et al, 1991) can be added at the N-terminal extremity of the peptides according to the invention. Alternatively or in addition, the polypeptide according to the invention can further comprise ubiquitin at its C-terminal extremity, since ubiquitination of proteins results in increased proteolysis.
In a preferred embodiment of the polypeptide according to the invention, the four epitopes are directly bound to each other without the use of any spacer (X=none for each position). Hence, the polypeptide comprises the sequence SPRLQLSNLAPRRLVQLLGPRALVETLAPKHSDCLA (Seq ID No: 23). In the absence of ubiquitin and ER-translocating signal, the polypeptide hence consists of the polypeptide illustrated in the examples below (SPRLQLSNLAPRRLVQLLGPRALVETLAPKHSDCLA, Seq ID No: 23).
In the polypeptides according to the invention, the amino acids can be either L- or D-amino acids.
A polypeptide according to the invention induces a specific CD8+ T cells response against at least one and preferably at least two peptides selected amongst CEA188, TERT444, MAGE273 and HER-2/neu246 cognate native peptides, in a majority of HLA-B*0702 transgenic mice vaccinated with said polypeptide.
A polypeptide according to the invention also induces a specific CD8+ T cells response against at least one and preferably at least two peptides selected amongst CEA188, TERT444, MAGE273 and HER-2/neu246 native peptides in an in vitro assay with human PBMC from healthy HLA-B*0702 donors
In order to control that the polypeptide of SEQ ID No: 23 is correctly processed and has a good immunogenicity, the inventors have also demonstrated that:
In a more preferred embodiment, the polypeptide according to the invention exhibits all the above properties, which can easily be tested by the skilled artisan, using the protocols and assays described in the experimental part below.
Another aspect of the invention is an isolated dendritic cell loaded with a polypeptide as above-described. In the present context “isolated” means that said dendritic cell is outside the body of the patient. The cell is preferably loaded ex vivo. For example, the dendritic cell can be loaded with the polypeptide by the technique described by Vonderheide et al. (Vonderheide et al, 2004).
The invention also pertains to a complex comprising a peptide delivery vector and a polypeptide as described above. Examples of peptide delivery vectors that can be used according to the invention are cell-penetrating peptides such as those described, for example, in the patent applications published as WO2013/150338, EP1795539 and WO2014/053629, bacterial toxins such as the adenylate cyclase of B. pertussis (Fayolle et al, 1999), the diphtheria toxin (Fayolle et al, 1999), the anthrax toxin (Doling et al, 1999), the B subunit of shiga toxin (Haicheur et al, 2000) and other vectors such as the bee venom PLA2 (Babon et al, 2005), liposomes, virosomes (Bungener et al, 2002) and the like.
The invention also concerns a pharmaceutical composition comprising a polypeptide and/or an engineered dendritic cell and/or a complex as described above, as well as a pharmaceutically acceptable carrier. In particular, polypeptides, dendritic cells and complexes according to the invention can be used for the preparation of an immunogenic composition for anti-cancer immunotherapy. These compositions are particularly useful for immunoherapy of tumors which express at least one antigen selected in the group consisting of the MAGE-A family, the HER family, CEA and TERT, especially for treating HLA-B*0702 individuals.
The present invention can be used to treat (or prevent relapse of) virtually any type of cancers, such as adrenal cortical cancer, colorectal cancer, biliary tract carcinoma, bladder cancer, bone cancers, brain and central nervous system cancers, breast cancer, cervical cancer, endometrial cancers, oesophagus cancer, gastric cancer, gastrointestinal carcinoid tumors, Hodgkin's disease, non-Hodgkin's lymphoma, Kaposi's sarcoma, kidney cancer, Head and Neck cancer, liver cancers, lung cancers mesothelioma, ovarian cancer, pancreatic cancer, penile cancer, pituitary cancer, prostate cancer, retinoblastoma, rhabdomyosarcoma, skin cancer (e.g. melanoma, non-melanoma skin cancer), testicular cancers, thymus cancer, thyroid cancers, vaginal cancer, vulvar cancer, and uterine cancer.
Cancer vaccination or treatment methods, comprising a step of emulsifying the polypeptide with an adjuvant and administering a polypeptide according to the invention in vivo to a patient in need thereof, are also part of the invention, as well as vaccination or treatment methods comprising a step of administering engineered dendritic cells or complexes as described above to an individual.
Another aspect of the present invention is a kit of parts comprising at least one dose of polypeptide (or complexes) as described above and at least one dose of adjuvant. Immunological adjuvants are substances which are added to vaccine formulations to increase their efficacy. Adjuvants can increase the magnitude and duration of the immune response induced by vaccination. Preferred examples of adjuvants which can be used in the kits according to the invention are those derived from the Incomplete Freund's adjuvant (IFA). Vaccine formulations with these adjuvants are water-in-oil (W/O) emulsions. Non-limitative examples of IFA-type detoxified adjuvants which can be used to for emulsions with the peptide according to the present invention include the mineral oil-based Montanide® ISA 51 and the squalene-based Montanide® ISA 720 (SEPPIC, France).
Another kit of parts according to the present invention comprises at least two doses of polypeptide or complexes as described above. The peptide can be already formulated with the adjuvant or not.
Since cancer vaccination necessitates several stimulations to be fully efficient, a kit of parts according to the present invention can comprise 3 to 50, preferably 6 to 20 doses of polypeptide as above-described.
According to a preferred embodiment of the kits described above, each dose of polypeptide comprises between 0.5 and 10 mg of polypeptide.
The invention is further illustrated by the following examples.
The examples have been performed using the following materials and methods:
Transgenic Mice. The HLA-B7 H-2 class-I knockout mice were previously described (Rohrlich et al, 2003) and kindly provided by F. Lemonnier (Institut Pasteur, Paris, France).
Cells. HLA-B*0702 transfected human T2-B7 cells were previously described (Rohrlich et al, 2003). Cells were grown in penicillin streptomycin FCS 20% supplemented RPMI1640 culture medium.
Peptides and Plasmids. Peptides were synthesized either by Millegen (Labège, France) or Eurogentec (Seraing, Belgique).
CTL Induction in vivo in HLA-B*0702 Transgenic Mice. HLA-B*0702 transgenic mice were vaccinated subcutaneously at the base of the tail with 200 μg of optimized dipeptides or 400 μg of Vbx-016 in association with the HV core T13L helper (150 μg) helper peptide and emulsified in Incomplete Freund Adjuvant (IFA) or Montanide ISA51VG (Seppic, Castres, France) twice at two weeks interval.
Seven days after the last vaccination, spleens were removed and T cells were isolated by Ficoll centrifugation and tested ex vivo for the recognition of 10 μM of either the native or optimized peptides. Positive control was Concanavalin A and negative control was medium alone. All conditions were tested in quadriplicates. IFNγ producing T cells was quantified by ELISpot using the Diaclone Kit Murine IFNγ ELISpot.
An immune response was considered positive when there was 1) more than 10 spots difference/106 cells between the negative control and the tested peptide and 2) a statistically significant difference between these two groups with T Test (p<0.05).
Generation of CTL from human PBMC. PBMC were collected by leukapheresis from healthy HLA-B*0702 volunteers. Dendritic cells (DC) were produced from adherent cells cultured for seven days with 500 IU/ml GM-CSF and 500 IU/ml IL-4, in complete synthetic medium (AIMV). On day 6, DCs were pulsed with 10 μM of polypeptides overnight. On day 7, CD8+ cells were purified by negative selection with CD8 Dynabeads Untouched Human CD8. CD8+ cells (2×105)+CD8− cells (6×104) were stimulated with 3×104 peptide-pulsed DC in AIMV medium supplemented with 1000 IU/ml IL-6 and 5 IU/ml IL-12, 1 μg/ml anti-CD40 and 500 IU/ml IFNγ in round-bottomed 96-well plates.
From day 7, cultures were restimulated weekly with peptide-loaded DC in the presence of 20 IU/ml IL-2 and 10 ng/ml IL-7, 1 μg/ml anti-CD40 and and 500 IU/ml IFNγ.
After the third restimulation, CD8 cells were maintained in AIMV supplemented with 20 IU/ml IL-2 during 7 days. Cultures were starved during one night with AIMV and then were tested in an IFNγ ELISpot assay.
IFNγ ELISpot Assay. For one culture of 96 wells, four pools of 24 wells were collected, CD8 cells were counted and 50 000 CD8 per well were dispatched on the ELISpot plate with 25 000 T2B7 loaded eiher with 10 μM of each native monopeptide or with 10 μM of modified monopeptides composing the polypeptide. Eight replicates of each condition were performed. Positive control was Phytohaemagglutinin A and negative control was T2B7 loaded with an irrelevant peptide not able to bind HLA-B7 molecules.
Each dipeptide was used to vaccinate HLA-B*0702 transgenic mice twice at 2 weeks interval and tested for its capacity to induce an immune response against both optimized peptides and their cognate native counterparts. Dipeptides are described in table 2. In each experiment, the best combination is highlighted in grey. 7C1HN3M, 7C1T5M, 7T5HN3M, 7M1HN3M and 7T5M1M gave better results than the inverted sequence, in terms of number of responding mice. 7C1M1M and 7M1C1M gave the same results.
To evaluate if the Vbx-016 (SEQ ID No: 23) determined in the dipeptidic experiments is optimum, HLA-B*0702 transgenic mice were vaccinated subcutaneously at the base of the tail with 400 μg of Vbx-016 and 150 μg of the HBV core T13L helper peptide emulsified in Incomplete Freund Adjuvant (IFA) or Montanide ISA51VG (Seppic, Castres, France) twice at two weeks interval.
After two vaccinations, all mice respond to at least one native peptide, and 13/14 vaccinated mice responded to two or more cognate native peptides. Importantly, each native peptide was recognized at least once in one vaccinated mouse.
To evaluate if the junction present in the polypeptide CEA188L9/TERT444A1/MAGE273L9/HER-2/neu246A1 validated in transgenic mice are processed efficiently in humans, human PBMC were stimulated with each dipeptide (CEA188L9/TERT444A1, TERT444A1/MAGE273L9 and MAGE273L9/HER-2/neu246A1) according to the protocol described in the methods. Recognition of the cognate native peptides was evaluated by measuring specific IFNγ producing cells from the CD8+ stimulated by the dipeptide, divided in 4 pools for the test. T test was performed when the mean number of spots obtained for the peptide of interest was superior to the mean number of spots obtained with the irrelevant peptide; when t test value was less than 0.05, the result was considered to be significantly positive and is highlighted in grey in the following table.
In each donor, CTLs were able to recognize both optimized and cognate native peptides (and the four natives for the MAGE-A273L9 shared peptide), confirming that each junction is well processed by the proteasome.
Vbx-016 was finally used to stimulate human PBMC from a healthy donor.
t test was performed when the mean number of spots obtained for the peptide of interest was superior to the mean number of spots obtained with the irrelevant peptide; when t test value was less than 0.05, the result was considered to be significantly positive and is highlighted in grey in the following table. A polyspecific response was induced and several native peptides were recognized by the induced CTLs, confirming that
| Number | Date | Country | Kind |
|---|---|---|---|
| 14306187.7 | Jul 2014 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/IB2015/055438 | 7/17/2015 | WO | 00 |
